NCBI Conserved Domain Search

PDZ domain of PDZ-LIM family proteins, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of PDZ-LIM family proteins including PDLIM1-7, and related domains. PDZ-LIM family proteins (also known as Zasp PDZ domain proteins) are involved in the rearrangement of the actin cytoskeleton; they mediate association with the cytoskeleton through alpha-actinin as well as with other proteins involved in signal transduction pathways. Members of this family include PDLIM1 (also known as C-terminal LIM domain protein 1, elfin, LIM domain protein CLP-36), PDLIM2 (also known as PDZ-LIM protein mystique), PDLIM3 (also known as actinin-associated LIM protein, alpha-actinin-2-associated LIM protein, ALP), PDLIM4 (also known as LIM protein RIL, Reversion-induced LIM protein), PDLIM5 (also known as enigma homolog, ENH, enigma-like PDZ and LIM domains protein), PDLIM6 (also known as LIM domain-binding protein 3, ZASP, Cypher, Oracle), and PDLIM7 (also known as PDZ and LIM domain protein 7, LIM mineralization protein, LMP; protein enigma). PDLIM1 has been shown to negatively regulate NF-kappaB-mediated signaling in the cytoplasm. PDLIM7 negatively regulates p53 through binding murine double minute 2 (MDM2). The PDZ domains of PDZ-LIM family proteins PDLIM1, 2, 3, 5, 6, 7 have been shown to bind actin. Other PDZ-LIM family PDZ domain binding partners include thyroid receptor interacting protein-6 (PDLIM4-PDZ), the LIM domain of PDLIM4 (PDLIM4-PDZ), tropomyosin (PDLIM7-PDZ), myotilin and calsarcin 1 (PDLIM6-PDZ), and proteins from the myotilin and FATZ (calsarcin/myozenin) families (PDLIM1, 3, 4, 6 PDZ domains). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDLIM-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467235 [Multi-domain] Cd Length: 79 Bit Score: 170.40 E-value: 5.10e-51

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 122056614   4 SVTLTGPGPWGFRLQGGKDFNMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQK 82
Cdd:cd06753    1 SVTLSGPAPWGFRLQGGKDFNQPLTISRVTPGGKAAQANLRPGDVILAINGESTEGMTHLEAQNKIKAATGSLSLTLER 79

The first LIM domain of ZASP/Cypher family; The first LIM domain of ZASP/Cypher family: ZASP was identified in human heart and skeletal muscle and Cypher is a mice ortholog of ZASP. ZASP/Cyppher contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188838 [Multi-domain] Cd Length: 52 Bit Score: 128.94 E-value: 4.09e-36

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 441 CGHCNNVIRGPFLVAMGRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERCY 492
Cdd:cd09454    1 CGHCNNIIRGPFLVALGRSWHPEEFTCHYCHTSLADVSFVEEQNNVYCENCY 52

The third LIM domain of Enigma-like family; The third LIM domain of Enigma-like family: The Enigma LIM domain family is comprised of three members: Enigma, ENH, and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. Enigma was initially characterized in humans and is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. The second member, ENH protein, was first identified in rat brain. It has been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188749 [Multi-domain] Cd Length: 54 Bit Score: 122.54 E-value: 8.87e-34

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                 ....*....|....*....|....*....|....*....|....*....|....
gi 122056614 559 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKKHA 612
Cdd:cd09363    1 CHGCDFPIEAGDRFLEALGHTWHDTCFVCAVCHVNLEGQTFYSKKDKPLCKNHA 54

The third LIM domain of ZASP/Cypher family; The third LIM domain of ZASP/Cypher family: ZASP was identified in human heart and skeletal muscle and Cypher is a mice ortholog of ZASP. ZASP/Cyppher contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188844 Cd Length: 55 Bit Score: 121.68 E-value: 1.89e-33

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 122056614 559 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKKHAH 613
Cdd:cd09460    1 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKHAH 55

The third LIM domain of the Enigma Homolog (ENH) family; The third LIM domain of the Enigma Homolog (ENH) family: ENH was initially identified in rat brain. Same as enigma, it contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ENH is implicated in signal transduction processes involving protein kinases. It has also been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ENH is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188843 [Multi-domain] Cd Length: 55 Bit Score: 120.84 E-value: 3.32e-33

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 122056614 559 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKKHAH 613
Cdd:cd09459    1 CHGCEFPIEAGDRFLEALGHTWHDTCFVCSVCCESLEGQTFFSKKDKPLCKKHAH 55

The second LIM domain of Enigma-like family; The second LIM domain of Enigma-like family: The Enigma LIM domain family is comprised of three members: Enigma, ENH, and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. Enigma was initially characterized in humans and is expressed in multiple tissues, such as skeletal muscle, heart, bone and brain. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. The second member, ENH protein, was first identified in rat brain. It has been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188748 [Multi-domain] Cd Length: 52 Bit Score: 115.65 E-value: 2.24e-31

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 500 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 551
Cdd:cd09362    1 CARCHKKILGEVMHALKQTWHVSCFVCAACKQPIGNSLFHMEDGEPYCEKDY 52

Domain of unknown function (DUF4749); This presumed domain is functionally uncharacterized. This domain family is found in eukaryotes, and is typically between 121 and 170 amino acids in length. It is usually found in association with pfam00595 (PDZ) and pfam00412 (LIM), and often contains the conserved Zasp-like motif (IPR006643).

Pssm-ID: 464948 [Multi-domain] Cd Length: 98 Bit Score: 115.60 E-value: 8.07e-31

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  148 TIIHAQYNTPISMYSQDAIMDAIAGQAQ-----AQGSDFSGSLPIKDLAVDSASPVYQAVIKSQNKPEDEAdewarrssn 222
Cdd:pfam15936   1 KVVHAQYNSPIGLYSSENIQDALSGQLSglagsSEGGKPPPSRPPKKPVVDADSEVYKMLQENQEPKEPPR--------- 71

                          90       100
                  ....*....|....*....|....*...
gi 122056614  223 lQSRSFRILAQMTGTEFMQDPDEEALRR 250
Cdd:pfam15936  72 -QSGSFRVLQEILETEYLQPPEEELNRP 98

The first LIM domain of Enigma-like family; The first LIM domain of Enigma-like family: The Enigma LIM domain family is comprised of three members: Enigma, ENH, and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. Enigma was initially characterized in humans and is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. The second member, ENH protein, was first identified in rat brain. It has been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188747 [Multi-domain] Cd Length: 52 Bit Score: 111.68 E-value: 5.88e-30

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                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 441 CGHCNNVIRGPFLVAMGRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERCY 492
Cdd:cd09361    1 CAHCNQVIRGPFLVALGRSWHPEEFTCSHCHCSLAEIGFVEEKGSLYCELCY 52

PDZ domain of Drosophila melanogaster PDZ and LIM domain protein Zasp52 (also known as Zasp), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Drosophila melanogaster Zasp52 and related domains. Drosophila melanogaster Zasp52 (also known as Z band alternatively spliced PDZ-motif protein or Zasp) colocalizes with integrins at myotendinous junctions and with alpha-actinin at Z-disks and is required for muscle attachment as well as Z-disk assembly and maintenance. The Zasp52 actin-binding site includes the extended PDZ domain and the ZM region. The Zasp52-PDZ domain is required for myofibril assembly. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Zasp52-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467281 [Multi-domain] Cd Length: 82 Bit Score: 110.70 E-value: 3.39e-29

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gi 122056614  12 PWGFRLQGGKDFNMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQK 82
Cdd:cd23068   12 PWGFRLQGGADFGQPLSIQKVNPGSPADKAGLRRGDVILRINGTDTSNLTHKQAQDLIKRAGNDLQLTVQR 82

The third LIM domain of Enigma; The third LIM domain of Enigma: Enigma was initially characterized in humans as a protein containing three LIM domains at the C-terminus and a PDZ domain at N-terminus. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes such as mitogenic activity, insulin related actin organization, and glucose metabolism. Enigma is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188842 Cd Length: 55 Bit Score: 103.97 E-value: 4.25e-27

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                 ....*....|....*....|....*....|....*....|....*....|....
gi 122056614 559 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKKHA 612
Cdd:cd09458    1 CHGCDFKIDAGDRFLEALGFSWHDTCFVCAICQINLEGKTFYSKKDKPLCKSHA 54

The first LIM domain of the Enigma Homolog (ENH) family; The first LIM domain of the Enigma Homolog (ENH) family: ENH was initially identified in rat brain. Same as enigma, it contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ENH is implicated in signal transduction processes involving protein kinases. It has also been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ENH is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188837 [Multi-domain] Cd Length: 52 Bit Score: 97.01 E-value: 1.06e-24

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                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 441 CGHCNNVIRGPFLVAMGRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERCY 492
Cdd:cd09453    1 CATCNQVIRGPFLVALGKSWHPEEFNCAHCKSSMAYIGFVEEKGALYCEICY 52

The second LIM domain of Enigma; The second LIM domain of Enigma: Enigma was initially characterized in humans as a protein containing three LIM domains at the C-terminus and a PDZ domain at N-terminus. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. Enigma is expressed in multiple tissues, such as skeletal muscle, heart, bone and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188840 [Multi-domain] Cd Length: 52 Bit Score: 95.83 E-value: 2.79e-24

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                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 500 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 551
Cdd:cd09456    1 CAKCKKKITGEIMHALKMTWHVHCFTCAACKTPIRNRAFYMEEGAPYCERDY 52

The second LIM domain of the Enigma Homolog (ENH) family; The second LIM domain of the Enigma Homolog (ENH) family: ENH was initially identified in rat brain. Same as enigma, it contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ENH is implicated in signal transduction processes involving protein kinases. It has also been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ENH is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188841 [Multi-domain] Cd Length: 52 Bit Score: 93.94 E-value: 1.27e-23

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                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 500 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 551
Cdd:cd09457    1 CGRCQRKILGEVINALKQTWHVSCFVCVACHNPIRNNVFHLEDGEPYCETDY 52

PDZ domain of synaptopodin 2 (SYNPO2), synaptopodin 2-like protein (SYNPO2L), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of SYNPO2, SYNPO2L, and related domains. SYNPO2 (also known as genethonin-2, myopodin) is a cytoskeleton adaptor protein. It participates in chaperone-assisted selective autophagy (CASA), a mechanism for the disposal of misfolded and damaged proteins and provides a link between the CASA chaperone complex and a membrane-tethering and fusion machinery that generates autophagosome membranes. The SYNPO2 PPxY motif binds CASA cochaperone BCL2-associated athanogene 3 (BAG3) and the SYNPO2 PDZ domain binds vacuolar protein sorting 18 homolog (VPS18). There are three isoforms of SYNPO2, which possess an amino-terminal PDZ domain (SYNPO2a, b, c); the short isoform SYNPO2d, lacks the PDZ domain. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This SYNPO2-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467264 [Multi-domain] Cd Length: 78 Bit Score: 86.98 E-value: 6.86e-21

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                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 122056614   5 VTLTGPGPWGFRLQGGKDFNMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQ 81
Cdd:cd10820    2 VTLTGGAPWGFRLQGGSEQKKPLQVAKIRKKSKAALAGLCEGDELLSINGKPCADLSHSEAMDLIDSSGDTLQLLIK 78

The third LIM domain of an Enigma subfamily with unknown function; The third LIM domain of an Enigma subfamily with unknown function: The Enigma LIM domain family is comprised of three characterized members: Enigma, ENH, and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. They serve as adaptor proteins, where the PDZ domain tethers the protein to the cytoskeleton and the LIM domains, recruit signaling proteins to implement corresponding functions. The members of the enigma family have been implicated in regulating or organizing cytoskeletal structure, as well as involving multiple signaling pathways. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188845 Cd Length: 54 Bit Score: 86.07 E-value: 7.94e-21

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                 ....*....|....*....|....*....|....*....|....*....|....
gi 122056614 559 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKKHA 612
Cdd:cd09461    1 CVSCGFPIEAGDRWVEALNNNYHSQCFNCTRCNVNLEGQSFYAKGGRPFCKLHA 54

The first LIM domain of an Enigma subfamily with unknown function; The first LIM domain of an Enigma subfamily with unknown function: The Enigma LIM domain family is comprised of three characterized members: Enigma, ENH and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. They serve as adaptor proteins, where the PDZ domain tethers the protein to the cytoskeleton and the LIM domains, recruit signaling proteins to implement corresponding functions. The members of the Enigma family have been implicated in regulating or organizing cytoskeletal structure, as well as involving multiple signaling pathways. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188839 Cd Length: 54 Bit Score: 79.81 E-value: 1.00e-18

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                 ....*....|....*....|....*....|....*....|....*....|....
gi 122056614 441 CGHCNNVIRGPFLVAMGRSWHPEEFTCA--YCKTSLADVCFVEEQNNVYCERCY 492
Cdd:cd09455    1 CESCNQQIRGPFITALGKIWCPDHFICAnaSCRRPLQDIGFVEEKGQLYCEYCF 54

LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid).

Pssm-ID: 259829 [Multi-domain] Cd Length: 53 Bit Score: 80.05 E-value: 1.03e-18

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gi 122056614 500 CAKCNTKIMG-EVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 551
Cdd:cd08368    1 CAGCGKPIEGrELLRALGKKWHPECFKCAECGKPLGGDSFYEKDGKPYCEKCY 53

Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.

Pssm-ID: 214570 [Multi-domain] Cd Length: 85 Bit Score: 80.12 E-value: 2.25e-18

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                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614     1 MSYSVTLT-GPGPWGFRLQGGKDFNMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLT 79
Cdd:smart00228   1 EPRLVELEkGGGGLGFSLVGGKDEGGGVVVSSVVPGSPAAKAGLRVGDVILEVNGTSVEGLTHLEAVDLLKKAGGKVTLT 80


                   ..
gi 122056614    80 LQ 81
Cdd:smart00228  81 VL 82

The first LIM domain of the paxillin like protein family; The first LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 259830 [Multi-domain] Cd Length: 53 Bit Score: 75.89 E-value: 2.88e-17

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 500 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 551
Cdd:cd09336    1 CAACNKPIVGQVVTALGKTWHPEHFVCVHCQTELGTSNFFERDGKPYCEKDY 52

Zinc-binding domain present in Lin-11, Isl-1, Mec-3; Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.

Pssm-ID: 214528 [Multi-domain] Cd Length: 54 Bit Score: 75.88 E-value: 3.08e-17

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 122056614   558 KCHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKKH 611
Cdd:smart00132   1 KCAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 54

The first LIM domain of Enigma; The first LIM domain of Enigma: Enigma was initially characterized in humans as a protein containing three LIM domains at the C-terminus and a PDZ domain at N-terminus. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes such as mitogenic activity, insulin related actin organization, and glucose metabolism. Enigma is expressed in multiple tissues, such as skeletal muscle, heart, bone and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188836 [Multi-domain] Cd Length: 52 Bit Score: 75.22 E-value: 4.43e-17

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 441 CGHCNNVIRGPFLVAMGRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERCY 492
Cdd:cd09452    1 CAQCNKIIRGRYLVALGRSYHPEEFTCSQCKKVLDEGGFFEEKGSIFCPKCY 52

canonical PDZ domain; Canonical PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain. PDZ domains usually bind to short specific peptide sequences located at the C-terminal end of their partner proteins known as PDZ binding motifs. These domains can also interact with internal peptide motifs and certain lipids, and can take part in a head-to-tail oligomerization with other PDZ domains. The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467153 [Multi-domain] Cd Length: 81 Bit Score: 76.04 E-value: 5.52e-17

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614   5 VTLTGP--GPWGFRLQGGKDFNMPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQ 81
Cdd:cd00136    2 VTLEKDpgGGLGFSIRGGKDGGGGIFVSRVEPGGPAARDgRLRVGDRILEVNGVSLEGLTHEEAVELLKSAGGEVTLTVR 81

The second LIM domain of the paxillin like protein family; The second LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188723 [Multi-domain] Cd Length: 52 Bit Score: 73.96 E-value: 1.31e-16

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 500 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 551
Cdd:cd09337    1 CAYCNGPILDKCVTALDKTWHPEHFFCAQCGKPFGDEGFHEKDGKPYCREDY 52

PDZ domain of shroom2, shroom3, shroom4, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of shroom2, shroom3, shroom4, and related domains. Shroom family proteins shroom2 (also known as apical-like protein; protein APXL), shroom3 (also known as shroom-related protein), and shroom4 (also known as second homolog of apical protein) are essential regulators of cell morphology during animal development; they regulate cell architecture by directing the subcellular distribution and activation of Rho kinase (ROCK), which results in the localized activation of non-muscle myosin. The interaction between shroom and ROCK is mediated by the shroom domain 2 (SD2). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This shroom2,3,4-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467232 [Multi-domain] Cd Length: 82 Bit Score: 72.37 E-value: 1.15e-15

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614   4 SVTLTGPGPWGFRLQGGKDFNMPLTISRITPGSKAA-QSQLSQGDLVVAIDGVNTDTMtHLEAQNKIKSASYNLSLTLQK 82
Cdd:cd06750    4 EVQLQGGAPWGFTLKGGLEHGEPLVISKIEEGGKAAsVGKLQVGDEVVNINGVPLSGS-RQEAIQLVKGSHKTLKLVVRR 82

PDZ domain; PDZ domains are found in diverse signaling proteins.

Pssm-ID: 395476 [Multi-domain] Cd Length: 81 Bit Score: 71.54 E-value: 1.69e-15

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 122056614    9 GPGPWGFRLQGGKDF-NMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQ 81
Cdd:pfam00595   8 GRGGLGFSLKGGSDQgDPGIFVSEVLPGGAAEAGGLKVGDRILSINGQDVENMTHEEAVLALKGSGGKVTLTIL 81

Zinc-binding domain present in Lin-11, Isl-1, Mec-3; Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.

Pssm-ID: 214528 [Multi-domain] Cd Length: 54 Bit Score: 70.49 E-value: 2.25e-15

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 122056614   500 CAKCNTKIMG--EVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKD 550
Cdd:smart00132   2 CAGCGKPIYGteRVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 54

LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid).

Pssm-ID: 259829 [Multi-domain] Cd Length: 53 Bit Score: 70.04 E-value: 2.85e-15

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 122056614 559 CHGCDFPVEaGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKKHA 612
Cdd:cd08368    1 CAGCGKPIE-GRELLRALGKKWHPECFKCAECGKPLGGDSFYEKDGKPYCEKCY 53

LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid).

Pssm-ID: 259829 [Multi-domain] Cd Length: 53 Bit Score: 70.04 E-value: 3.36e-15

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 122056614 441 CGHCNNVIRGPFLV-AMGRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERCY 492
Cdd:cd08368    1 CAGCGKPIEGRELLrALGKKWHPECFKCAECGKPLGGDSFYEKDGKPYCEKCY 53

LIM domain; This family represents two copies of the LIM structural domain.

Pssm-ID: 395333 [Multi-domain] Cd Length: 57 Bit Score: 69.28 E-value: 6.80e-15

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 122056614  500 CAKCNTKIMG-EVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDYINLF 555
Cdd:pfam00412   1 CAGCNRPIYDrELVRALGKVWHPECFRCAVCGKPLTTGDFYEKDGKLYCKHDYYKLF 57

The first LIM domain of Leupaxin; The first LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188790 [Multi-domain] Cd Length: 55 Bit Score: 66.82 E-value: 4.28e-14

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 500 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 551
Cdd:cd09406    3 CASCQKPIAGQVVTALGQTWHPEHFVCCQCGKELGSRPFFERNGQAYCEEDY 54

The first LIM domain of the paxillin like protein family; The first LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 259830 [Multi-domain] Cd Length: 53 Bit Score: 66.26 E-value: 7.56e-14

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 441 CGHCNNVIRGPFLVAMGRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERCY 492
Cdd:cd09336    1 CAACNKPIVGQVVTALGKTWHPEHFVCVHCQTELGTSNFFERDGKPYCEKDY 52

The third LIM domain of the paxillin like protein family; The third LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188724 [Multi-domain] Cd Length: 53 Bit Score: 65.43 E-value: 1.14e-13

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 500 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 551
Cdd:cd09338    1 CGGCNKPILENYISALNTQWHPECFVCRECHKPFINGSFFEHEGLPYCETHY 52

PDZ domain 5 of membrane-associated guanylate kinase inverted 1 (MAGI-1), MAGI-2, and MAGI-3, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 5 of MAGI1, 2, 3 (MAGI is also known as Membrane-associated guanylate kinase, WW and PDZ domain-containing protein) and related domains. MAGI proteins have been implicated in the control of cell migration and invasion through altering the activity of phosphatase and tensin homolog (PTEN) and modulating Akt signaling. Four MAGI proteins have been identified (MAGI1-3 and MAGIX). MAGI1-3 have 6 PDZ domains and bind to the C-terminus of PTEN via their PDZ2 domain. MAGIX has a single PDZ domain that is related to MAGI1-3 PDZ domain 5, and belongs to this MAGI1,2,3-like family. Other binding partners for MAGI1 include JAM4, C-terminal tail of high risk HPV-18 E6, megalin, TRAF6, Kir4.1 (basolateral K+ channel subunit), and cadherin 23; for MAGI2, include DASM1, dendrin, axin, beta- and delta-catenin, neuroligin, hyperpolarization-activated cation channels, beta1-adrenergic receptors, NMDA receptor, and TARPs; and for MAGI3 includes LPA2. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MAGI family PDZ5 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467217 [Multi-domain] Cd Length: 84 Bit Score: 66.06 E-value: 1.69e-13

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614   3 YSVTLT-GPGPWGFRLQGGKDF-NMPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLT 79
Cdd:cd06735    2 YSVELErGPKGFGFSIRGGREYnNMPLYVLRLAEDGPAQRDgRLRVGDQILEINGESTQGMTHAQAIELIRSGGSVVRLL 81


                 ...
gi 122056614  80 LQK 82
Cdd:cd06735   82 LRR 84

PDZ domain of tyrosine-protein phosphatase non-receptor type 3 (PTPN3), tyrosine-protein phosphatase non-receptor type 4 (PTNP4), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of PTPN3, PTPN4 and related domains. PTPN3 (also known as protein-tyrosine phosphatase H1, PTP-H1) has a tumor-suppressive or a tumor-promoting role in many cancers. It serves as a specific phosphatase for the MAP kinase p38gamma; the two interact via their PDZ domains and cooperate to promote Ras-induced oncogenesis. Interaction partners of the PTPN3 PDZ domain include p38gamma and human papillomavirus E6 oncoprotein. PTPN4 (also known as protein-tyrosine phosphatase MEG1) plays a role in immunity, learning, synaptic plasticity or cell homeostasis. p38gamma is also an interaction partner of the PTPN4 PDZ domain: PTPN4 regulates neuronal cell homeostasis by protecting neurons against apoptosis; binding of the C terminus of p38gamma to the PDZ domain of PTPN4, antagonizes the catalytic autoinhibition of PTPN4, leading to cell apoptosis. Other interaction partners of the PTPN4 PDZ domain include glutamate receptor subunit GluN2A, and RABV strain G protein, among others. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PTPN3-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467190 [Multi-domain] Cd Length: 90 Bit Score: 65.80 E-value: 2.58e-13

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 122056614  11 GPWGFRLQGGKDFNMPLTISRITPGSKAAQSQ--LSQGDLVVAIDGVNTDTMTHLEAQNKIKSA 72
Cdd:cd06706   14 GRFGFNVKGGVDQKMPVIVSRVAPGTPADLCIprLNEGDQVLLINGRDISEHTHDQVVMFIKAS 77

LIM domain; This family represents two copies of the LIM structural domain.

Pssm-ID: 395333 [Multi-domain] Cd Length: 57 Bit Score: 63.51 E-value: 6.95e-13

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 122056614  559 CHGCDFPVEAGDKFIeALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKKH 611
Cdd:pfam00412   1 CAGCNRPIYDRELVR-ALGKVWHPECFRCAVCGKPLTTGDFYEKDGKLYCKHD 52

Zinc-binding domain present in Lin-11, Isl-1, Mec-3; Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.

Pssm-ID: 214528 [Multi-domain] Cd Length: 54 Bit Score: 62.79 E-value: 1.26e-12

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 122056614   441 CGHCNNVIRG--PFLVAMGRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERC 491
Cdd:smart00132   2 CAGCGKPIYGteRVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 54

The first LIM domain of paxillin; The first LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight cons erved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188789 [Multi-domain] Cd Length: 54 Bit Score: 62.72 E-value: 1.43e-12

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 122056614 499 LCAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 551
Cdd:cd09405    1 VCGACKKPIAGQVVTAMGKTWHPEHFVCTHCQEEIGSRNFFERDGQPYCEKDY 53

LIM domain; This family represents two copies of the LIM structural domain.

Pssm-ID: 395333 [Multi-domain] Cd Length: 57 Bit Score: 61.19 E-value: 4.19e-12

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 122056614  441 CGHCNNVIRGPFLV-AMGRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERCYEQFF 496
Cdd:pfam00412   1 CAGCNRPIYDRELVrALGKVWHPECFRCAVCGKPLTTGDFYEKDGKLYCKHDYYKLF 57

The fourth LIM domain of the Paxillin-like protein family; The fourth LIM domain of the Paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188725 [Multi-domain] Cd Length: 52 Bit Score: 60.05 E-value: 9.60e-12

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 441 CGHCNNVIRGPFLVAMGRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERCY 492
Cdd:cd09339    1 CAGCGKPITGRCITAMGRKFHPEHFVCAFCLKQLSKGTFKEQDDKPYCHPCF 52

The third LIM domain of the paxillin like protein family; The third LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188724 [Multi-domain] Cd Length: 53 Bit Score: 60.04 E-value: 9.68e-12

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 122056614 559 CHGCDFPVEagDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKKHAH 613
Cdd:cd09338    1 CGGCNKPIL--ENYISALNTQWHPECFVCRECHKPFINGSFFEHEGLPYCETHYH 53

The first LIM domain of protein PINCH; The first LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188717 Cd Length: 59 Bit Score: 60.04 E-value: 1.22e-11

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 122056614 488 CERCYEQFfAPlcakcNTKIM---GEVmhalrqtWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDYINLFS 556
Cdd:cd09331    1 CERCREGF-EP-----DEKIVnsnGEL-------YHEQCFVCAQCFQPFPDGLFYEFEGRKYCEHDFQVLFA 59

The second LIM domain of protein PINCH; The second LIM domain of protein PINCH: PINCH plays a pivotal role in the assembly of focal adhesions (FAs), regulating diverse functions in cell adhesion, growth, and differentiation through LIM-mediated protein-protein interactions. PINCH comprises an array of five LIM domains that interact with integrin-linked kinase (ILK), Nck2 (also called Nckbeta or Grb4) and other interaction partners. These interactions are essential for triggering the FA assembly and for relaying diverse mechanical and biochemical signals between Cell-extracellular matrix and the actin cytoskeleton. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188718 [Multi-domain] Cd Length: 52 Bit Score: 59.27 E-value: 1.83e-11

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 122056614 441 CGHCNNVIRGPFLVAMGRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERC 491
Cdd:cd09332    1 CGKCGEFVIGRVIKAMNNNWHPDCFRCEICNKELADIGFVKNAGRALCHPC 51

PDZ domain 7 of PDZ domain containing 2 (PDZD2), PDZ domain 4 of human pro-interleukin-16 (isoform 1, 1332 AA), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 7 of PDZD2, also known as KIAA0300, PIN-1, PAPIN, activated in prostate cancer (AIPC) and PDZ domain-containing protein 3 (PDZK3). PDZD2 has seven PDZ domains. PDZD2 is expressed at exceptionally high levels in the pancreas and certain cancer tissues, such as prostate cancer. It promotes the proliferation of insulinoma cells and is upregulated during prostate tumorigenesis. In osteosarcoma (OS), the microRNA miR-363 acts as a tumor suppressor by inhibiting PDZD2. This family include the PDZ domain of the secreted mature form of human interleukin-16 (IL-16); this is the fourth PDZ domain (PDZ4) of human pro-interleukin-16 (isoform 1, also known as nPro-Il-16). Precursor IL-16 is cleaved to produce pro-IL-16 and C-terminal mature IL-16. Pro-IL-16 functions as a regulator of T cell growth; mature IL-16 is a CD4 ligand that induces chemotaxis and CD25 expression in CD4+ T cells. IL-16 bioactivity has been closely associated with the progression of several different cancers PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD2-like family PDZ7 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467244 [Multi-domain] Cd Length: 86 Bit Score: 59.55 E-value: 3.28e-11

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 122056614   4 SVTLT-GPGPWGFRLQGGKDF---NMPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKS 71
Cdd:cd06763    3 TVELEkGSAGLGFSLEGGKGSplgDRPLTIKRIFKGGAAEQSgVLQVGDEILQINGTSLQGLTRFEAWNIIKS 75

The second LIM domain of Leupaxin; The second LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188792 [Multi-domain] Cd Length: 52 Bit Score: 56.37 E-value: 1.82e-10

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 500 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 551
Cdd:cd09408    1 CAYCAGPILQNVLTAMDQTWHPEHFFCSHCGELFGDEGFLERDGKPYCRRDF 52

large tegument protein UL36; Provisional

Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 64.19 E-value: 2.23e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  272 TSYSEGPAAPAPKPRVVTTASIRPSVYQPVPASTYSPSPGANYSPTPYTPSPAPAYTPSPAPAyTPSPVPTYTPSPAPAY 351
Cdd:PHA03247 2763 TAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPA-GPLPPPTSAQPTAPPP 2841

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  352 TPSPAPNYNPAPSVAYSGGPA--EPASRPPWVTDDSFSQKFAPGKSTTSISKQTLPRGGPAYTPAGPQVPPLARGTVQRA 429
Cdd:PHA03247 2842 PPGPPPPSLPLGGSVAPGGDVrrRPPSRSPAAKPAAPARPPVRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQP 2921

                         170
                  ....*....|
gi 122056614  430 ERFPASSRTP 439
Cdd:PHA03247 2922 QPPPPPQPQP 2931

The fourth LIM domain of protein PINCH; The fourth LIM domain of protein PINCH: PINCH plays a pivotal role in the assembly of focal adhesions (FAs), regulating diverse functions in cell adhesion, growth, and differentiation through LIM-mediated protein-protein interactions. PINCH comprises an array of five LIM domains that interact with integrin-linked kinase (ILK), Nck2 (also called Nckbeta or Grb4) and other interaction partners. These interactions are essential for triggering the FA assembly and for relaying diverse mechanical and biochemical signals between Cell-extracellular matrix and the actin cytoskeleton. The PINCH LIM4 domain recognizes the third SH3 domain of another adaptor protein, Nck2. This step is an important component of integrin signaling event. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assem bly of multimeric protein complexes.

Pssm-ID: 188720 [Multi-domain] Cd Length: 54 Bit Score: 56.21 E-value: 2.23e-10

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 122056614 439 PLCGHCNNVIRGPFLVAMGRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERCY 492
Cdd:cd09334    1 PICGACRRPIEGRVVTALGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHY 54

PDZ domain 1 of harmonin isoforms a, b, and c, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of harmonin isoforms a, b, and c, and related domains. Harmonin (also known as Usher Type 1C, PDZ-73 and AIE-75) is a key organizer of the Usher (USH) protein interactome. USH syndrome is the leading cause of hereditary sensory deaf-blindness in humans; three clinically distinct types of USH have been identified, type 1 to 3. The gene encoding harmonin (USH1C) is the causative gene for the USH type 1C phenotype. There are at least 10 alternatively spliced isoforms of harmonin, which are divided into three subclasses (a, b, and c). All isoforms contain the first two PDZ domains and the first coiled-coil domain. The a and b isoforms all have a third PDZ domain. The different PDZ domains are responsible for interactions with all known Usher syndrome type 1 proteins, and most Usher syndrome type 2 proteins. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This harmonin family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467219 [Multi-domain] Cd Length: 85 Bit Score: 56.88 E-value: 2.87e-10

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 122056614   8 TGPGPWGFRLQGGKDFNMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASY 74
Cdd:cd06737   10 RGPESLGFSVRGGLEHGCGLFVSHVSPGSQADNKGLRVGDEIVRINGYSISQCTHEEVINLIKTKKT 76

The first LIM domain of LIMK (LIM domain Kinase ); The first LIM domain of LIMK (LIM domain Kinase ): LIMK protein family is comprised of two members LIMK1 and LIMK2. LIMK contains two LIM domains, a PDZ domain and a kinase domain. LIMK is involved in the regulation of actin polymerization and microtubule disassembly. LIMK influences architecture of the actin cytoskeleton by regulating the activity of the cofilin family proteins cofilin1, cofilin2, and destrin. The mechanism of the activation is to phosphorylates cofilin on serine 3 and inactivates its actin-severing activity, and altering the rate of actin depolymerisation. LIMKs can function in both cytoplasm and nucleus and are expressed in all tissues. Both LIMK1 and LIMK2 can act in the nucleus to suppress Rac/Cdc42-dependent cyclin D1 expression. However, LIMK1 and LIMk2 have different cellular locations. While LIMK1 localizes mainly at focal adhesions, LIMK2 is found in cytoplasmic punctae, suggesting that they may have different cellular functions. The LIM domains of LIMK have been shown to play an important role in regulating kinase activity and likely also contribute to LIMK function by acting as sites of protein-to-protein interactions. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188750 [Multi-domain] Cd Length: 53 Bit Score: 55.96 E-value: 3.08e-10

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 122056614 500 CAKCNTKIM-GEVMHALRQTWHTTCFVCAACKKPFGNSLFHmEDGEPYCEKDY 551
Cdd:cd09364    1 CAGCRGKILdSQYVQALNQDWHCDCFRCSVCSDSLSNWYFE-KDGKLYCRKDY 52

The fourth LIM domain of protein PINCH; The fourth LIM domain of protein PINCH: PINCH plays a pivotal role in the assembly of focal adhesions (FAs), regulating diverse functions in cell adhesion, growth, and differentiation through LIM-mediated protein-protein interactions. PINCH comprises an array of five LIM domains that interact with integrin-linked kinase (ILK), Nck2 (also called Nckbeta or Grb4) and other interaction partners. These interactions are essential for triggering the FA assembly and for relaying diverse mechanical and biochemical signals between Cell-extracellular matrix and the actin cytoskeleton. The PINCH LIM4 domain recognizes the third SH3 domain of another adaptor protein, Nck2. This step is an important component of integrin signaling event. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assem bly of multimeric protein complexes.

Pssm-ID: 188720 [Multi-domain] Cd Length: 54 Bit Score: 55.82 E-value: 3.12e-10

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 122056614 498 PLCAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 551
Cdd:cd09334    1 PICGACRRPIEGRVVTALGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHY 54

The second LIM domain of paxillin; The second LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188791 [Multi-domain] Cd Length: 52 Bit Score: 55.73 E-value: 3.34e-10

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 500 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 551
Cdd:cd09407    1 CYYCNGPILDKVVTALDRTWHPEHFFCAQCGAFFGPEGFHEKDGKAYCRKDY 52

DNA polymerase III subunit gamma/tau;

Pssm-ID: 237057 [Multi-domain] Cd Length: 700 Bit Score: 62.97 E-value: 3.98e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 165 AIMDAIAGQAQAQGSDFSGSLpiKDLAVD-SASPVYQAVIKSQNKPEDEADEWARRSSNLQSRSFRILAQMTGT---EFM 240
Cdd:PRK12323 267 AALLAIADEMAGRSLSFAGAL--QDLASLlQKIALAQVVPAAVQDDWPEADDIRRLAGRFDAQEVQLFYQIANLgrsELA 344

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 241 QDPDEEA------LR------------------RSRPQASSYSPAVAASSAPATHTSYSEGPAAPAPKPRVVTTASIRPS 296
Cdd:PRK12323 345 LAPDEYAgftmtlLRmlafrpgqsgggagpataAAAPVAQPAPAAAAPAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPA 424

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 297 VYQPVPAS------TYSPSPGANYSPTPyTPSPAPAYTPSPAPAyTPSPVPTYTPSPAPAYTPSPAPNYNPAPSVAYSGG 370
Cdd:PRK12323 425 RRSPAPEAlaaarqASARGPGGAPAPAP-APAAAPAAAARPAAA-GPRPVAAAAAAAPARAAPAAAPAPADDDPPPWEEL 502

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 122056614 371 PAEPASRPPWVTDDSFSQKFAPGKSTTSISKQTLPRGGPAYTPAGPQVPPLARGTVQR-AERFPASSRTPL 440
Cdd:PRK12323 503 PPEFASPAPAQPDAAPAGWVAESIPDPATADPDDAFETLAPAPAAAPAPRAAAATEPVvAPRPPRASASGL 573

The first LIM domain of Leupaxin; The first LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188790 [Multi-domain] Cd Length: 55 Bit Score: 55.26 E-value: 5.33e-10

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 441 CGHCNNVIRGPFLVAMGRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERCY 492
Cdd:cd09406    3 CASCQKPIAGQVVTALGQTWHPEHFVCCQCGKELGSRPFFERNGQAYCEEDY 54

PDZ domain of Rap guanine nucleotide exchange factor 2 and Rap guanine nucleotide exchange factor 6, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Rap guanine nucleotide exchange factor 2 (RapGEF2, also named RA-GEF-1, PDZ-GEF1, CNrasGEF and nRapGEP) and Rap guanine nucleotide exchange factor 6 (RapGEF6, also named RA-GEF-2 and PDZ-GEF2). RapGEF2 and RapGEF6 constitute a subfamily of guanine nucleotide exchange factors (GEFs) for RAP small GTPases that is characterized by the possession of the PDZ and Ras/Rap-associating domains. They activate Rap small GTPases, by catalyzing the release of GDP from the inactive GDP-bound forms, thereby accelerating GTP loading to yield the active GTP-bound forms. The PDZ domain of RapGEF6 (also known as PDZ-GEF2) binds junctional adhesion molecule A (JAM-A). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This RapGEF2 and RapGEF6 family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467237 [Multi-domain] Cd Length: 83 Bit Score: 56.12 E-value: 5.42e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614   4 SVTLTGPG---PWGFRLQGGKDFNMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYnLSLTL 80
Cdd:cd06755    2 TVTLTRPSresPLHFSLLGGSEKGFGIFVSKVEKGSKAAEAGLKRGDQILEVNGQNFENITLKKALEILRNNTH-LSITV 80

large tegument protein UL36; Provisional

Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 62.65 E-value: 5.91e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  272 TSYSEGPAAPAPKPRVVT-TASIRPsvyqPVPASTYSPSPGANYSPTPYTPSPAPAYTPSPAPAYTPSP--VPTYTPSPA 348
Cdd:PHA03247 2677 SSPPQRPRRRAARPTVGSlTSLADP----PPPPPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAPpaVPAGPATPG 2752

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  349 ----PAYTPSPAPNYNPAPSVAYSGGPAEPASRPPwVTDDSFSQKFAPGKSTTSISKQTLPRGGPAY----TPAGPQVPP 420
Cdd:PHA03247 2753 gparPARPPTTAGPPAPAPPAAPAAGPPRRLTRPA-VASLSESRESLPSPWDPADPPAAVLAPAAALppaaSPAGPLPPP 2831

                         170       180
                  ....*....|....*....|...
gi 122056614  421 L-ARGTVQRAERFPASSRTPLCG 442
Cdd:PHA03247 2832 TsAQPTAPPPPPGPPPPSLPLGG 2854

PDZ domain 2 of the canonical isoform 1 of PDZ domain containing 7 (PDZD7), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of the long isoform 1 of PDZD7, and related domains. PDZD7 is critical for the organization of Usher syndrome type 2 (USH2) complex. Usher syndrome is the leading cause of hereditary sensory deaf-blindness in humans; USH2 is the most common sub-type. Formation of the USH2 complex is based upon heterodimerization between PDZD7 and whirlin (another PDZ domain-containing protein) and a subsequent dynamic interplay between USH2 proteins via their multiple PDZ domains. The PDZD7 PDZ2 domain binds GPR98 (also known as VLGR1) and usherin (USH2A). PDZD7 and whirlin form heterodimers through their multiple PDZ domains; whirlin and PDZD7 interact with usherin and GPR98 to form an interdependent ankle link complex. PDZD7 also interacts with myosin VIIa. PDZD7 also forms homodimers through its PDZ2 domain. Various isoforms of PDZD7 produced by alternative splicing have been identified; this subgroup includes the second PDZ domain of the canonical isoform of PDZD7- isoform 1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD7-like family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467270 [Multi-domain] Cd Length: 85 Bit Score: 55.86 E-value: 7.04e-10

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 122056614  13 WGFRLQGGKDFNMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYnLSLTLQ 81
Cdd:cd10834   15 LGFNIRGGSEYGLGIYVSKVDPGGLAEQNGIKVGDQILAVNGVSFEDITHSKAVEVLKSQTH-LMLTIK 82

The third LIM domain of actin binding LIM (abLIM) proteins; The third LIM domain of actin binding LIM (abLIM) proteins: Three homologous members of the abLIM protein family have been identified; abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM consists of four tandem repeats of LIM domains and the C-terminal of acting binding LIM protein is a villin headpiece domain, which has strong actin binding activity. The abLIM-1, which is expressed in retina, brain, and muscle tissue, has been indicated to function as a tumor suppressor. AbLIM-2 and -3, mainly expressed in muscle and neuronal tissue, bind to F-actin strongly. They may serve as a scaffold for signaling modules of the actin cytoskeleton and thereby modulate transcription. It has shown that LIM domains of abLIMs interact with STARS (striated muscle activator of Rho signaling), which directly binds actin and stimulates serum-response factor (SRF)-dependent transcription. All LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188715 [Multi-domain] Cd Length: 52 Bit Score: 54.63 E-value: 7.33e-10

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 122056614 500 CAKCNTKIM-GEVMHALRQTWHTTCFVCAACKKpfgnsLFHME----DGEPYCEKDY 551
Cdd:cd09329    1 CAGCGQEIKnGQALLALDKQWHVWCFKCKECGK-----VLTGEymgkDGKPYCERDY 52

The first LIM domain of actin binding LIM (abLIM) proteins; The first LIM domain of actin binding LIM (abLIM) proteins: Three homologous members of the abLIM protein family have been identified; abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM consists of four tandem repeats of LIM domains and the C-terminal of acting binding LIM protein is a villin headpiece domain, which has strong actin binding activity. The abLIM-1, which is expressed in retina, brain, and muscle tissue, has been indicated to function as a tumor suppressor. AbLIM-2 and -3, mainly expressed in muscle and neuronal tissue, bind to F-actin strongly. They may serve as a scaffold for signaling modules of the actin cytoskeleton and thereby modulate transcription. It has shown that LIM domains of abLIMs interact with STARS (striated muscle activator of Rho signaling), which directly binds actin and stimulates serum-response factor (SRF)-dependent transcription. All LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188713 [Multi-domain] Cd Length: 52 Bit Score: 54.57 E-value: 7.44e-10

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 500 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 551
Cdd:cd09327    1 CYKCGKKCKGEVLRVQDKYFHIKCFTCKVCGCDLAQGGFFVKEGEYYCTDDY 52

The second LIM domain of the paxillin like protein family; The second LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188723 [Multi-domain] Cd Length: 52 Bit Score: 54.70 E-value: 7.86e-10

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 441 CGHCNNVIRGPFLVAMGRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERCY 492
Cdd:cd09337    1 CAYCNGPILDKCVTALDKTWHPEHFFCAQCGKPFGDEGFHEKDGKPYCREDY 52

The first LIM domain of paxillin; The first LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight cons erved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188789 [Multi-domain] Cd Length: 54 Bit Score: 54.63 E-value: 8.25e-10

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 122056614 440 LCGHCNNVIRGPFLVAMGRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERCY 492
Cdd:cd09405    1 VCGACKKPIAGQVVTAMGKTWHPEHFVCTHCQEEIGSRNFFERDGQPYCEKDY 53

The second LIM domain of Four and a half LIM domains protein (FHL); The second LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 int eracts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188731 [Multi-domain] Cd Length: 54 Bit Score: 53.45 E-value: 2.17e-09

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 559 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKK 610
Cdd:cd09345    1 CKACGKAIMPGSKKMEYKGKFWHEKCFTCSECKKPIGTKSFIPKDDKIYCVP 52

PDZ domain of syntrophins, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of syntrophins (including alpha-1-syntrophin, beta-1-syntrophin, beta-2-syntrophin, gamma-1-syntrophin, and gamma-2-syntrophin), and related domains. Syntrophins play a role in recruiting various signaling molecules into signaling complexes and help provide appropriate spatiotemporal regulation of signaling pathways. They function in cytoskeletal organization and maintenance; as components of the dystrophin-glycoprotein complex (DGC), they help maintain structural integrity of skeletal muscle fibers. They link voltage-gated sodium channels to the actin cytoskeleton and the extracellular matrix, and control the localization and activity of the actin reorganizing proteins such as PI3K, PI(3,4)P2 and TAPP1. Through association with various cytoskeletal proteins within the cells, they are involved in processes such as regulation of focal adhesions, myogenesis, calcium homeostasis, and cell migration. They also have roles in synapse formation and in the organization of utrophin, acetylcholine receptor, and acetylcholinesterase at the neuromuscular synapse. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This syntrophin-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467262 [Multi-domain] Cd Length: 83 Bit Score: 54.12 E-value: 2.98e-09

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 122056614  14 GFRLQGGKDFNMPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQ 81
Cdd:cd06801   14 GISIKGGAEHKMPILISKIFKGQAADQTgQLFVGDAILSVNGENLEDATHDEAVQALKNAGDEVTLTVK 82

The first LIM domain of lipoma preferred partner (LPP); The first LIM domain of lipoma preferred partner (LPP): LPP is a member of the zyxin LIM protein family and contains three LIM zinc-binding domains at the C-terminal and proline-rich region at the N-terminal. LPP initially identified as the most frequent translocation partner of HMGA2 (High Mobility Group A2) in a subgroup of benign tumors of adipose tissue (lipomas). It was also shown to be rearranged in a number of other soft tissues, as well as in a case of acute monoblastic leukemia. In addition to its involvement in tumors, LPP was inedited as a smooth muscle restricted LIM protein that plays an important role in SMC migration. LPP is localized at sites of cell adhesion, cell-cell contacts and transiently in the nucleus. In nucleus, it acts as a coactivator for the ETS domain transcription factor PEA3. In addition to PEA3, it interacts with alpha-actinin,vasodilator stimulated phosphoprotein (VASP),Palladin, and Scrib. The LIM domains are the main focal adhesion targeting elements and that the proline- rich region, which harbors binding sites for alpha-actinin and vasodilator- stimulated phosphoprotein (VASP), has a weak targeting capacity. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188737 [Multi-domain] Cd Length: 54 Bit Score: 53.20 E-value: 3.08e-09

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 122056614 500 CAKCNTKIMGEVM--HALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 551
Cdd:cd09351    1 CVKCGEKVLGEGSgcTAMDQVYHISCFTCHQCQINLQGKPFYALDGKPYCEEDY 54

The Lim domain of DA1; The Lim domain of DA1: DA1 contains one copy of LIM domain and a domain of unknown function. DA1 is predicted as an ubiquitin receptor, which sets final seed and organ size by restricting the period of cell proliferation. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188782 [Multi-domain] Cd Length: 53 Bit Score: 53.03 E-value: 3.42e-09

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 122056614 500 CAKCNTKIM-GEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPY 546
Cdd:cd09396    1 CAGCKSEIGhGRFLSALGAVWHPECFRCHACRKPIAEHEFSVSGNDPY 48

The first LIM domain of the paxillin like protein family; The first LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 259830 [Multi-domain] Cd Length: 53 Bit Score: 52.39 E-value: 4.98e-09

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 122056614 559 CHGCDFPVeAGdKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKKHAH 613
Cdd:cd09336    1 CAACNKPI-VG-QVVTALGKTWHPEHFVCVHCQTELGTSNFFERDGKPYCEKDYH 53

ZASP-like motif; Short motif (26 amino acids) present in an alpha-actinin-binding protein, ZASP, and similar molecules.

Pssm-ID: 128974 Cd Length: 26 Bit Score: 51.83 E-value: 5.40e-09

                           10        20
                   ....*....|....*....|....*.
gi 122056614   148 TIIHAQYNTPISMYSQDAIMDAIAGQ 173
Cdd:smart00735   1 RVVHKQYNSPIGLYSSENIAETLQGQ 26

The third LIM domain of Leupaxin; The third LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188794 [Multi-domain] Cd Length: 53 Bit Score: 52.13 E-value: 5.93e-09

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 500 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 551
Cdd:cd09410    1 CSGCGRPVKENYLSAANGVWHPECFVCSDCLKPFTDGSFFELDGRPLCELHY 52

The third LIM domain of paxillin; The third LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188793 [Multi-domain] Cd Length: 53 Bit Score: 51.77 E-value: 8.09e-09

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 500 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 551
Cdd:cd09409    1 CGGCARAILENYISALNTLWHPECFVCRECFTPFVNGSFFEHDGQPYCEAHY 52

The fourth LIM domain of Leupaxin; The fourth LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188796 [Multi-domain] Cd Length: 52 Bit Score: 51.66 E-value: 8.60e-09

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 441 CGHCNNVIRGPFLVAMGRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERCY 492
Cdd:cd09412    1 CGSCGLPITGRCISALGRKFHPEHFVCAFCLRPLTQGSFKEQSGKPYCSTCF 52

The second LIM domain of Testin-like family; The second LIM domain of Testin-like family: This family includes testin, prickle, dyxin and LIMPETin. Structurally, testin and prickle proteins contain three LIM domains at C-terminal; LIMPETin has six LIM domains; and dyxin presents only two LIM domains. However, all members of the family contain a PET protein-protein interaction domain. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). Dyxin involves in lung and heart development by interaction with GATA6 and blocking GATA6 activated target genes. LIMPETin might be the recombinant product of genes coding testin and four and half LIM proteins and its function is not well understood. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188727 Cd Length: 56 Bit Score: 51.45 E-value: 1.05e-08

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 122056614 439 PLCGHCNNVI-RGPFLVAMGRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERCYE 493
Cdd:cd09341    1 PRCAACDELIfSGEYTQAEGKNWHLKHFCCFQCDEPLGGQRYVLREGKPYCLDCYE 56

The second LIM domain of the filamin-binding LIM protein-1 (FBLP-1); The second LIM domain of the filamin-binding LIM protein-1 (FBLP-1): Fblp-1 contains a proline-rich domain near its N terminus and two LIM domains at its C terminus. FBLP-1 mRNA was detected in a variety of tissues and cells including platelets and endothelial cells. FBLP-1 binds to Filamins. The association between filamin B and FBLP-1 may play an unknown role in cytoskeletal function, cell adhesion, and cell motility. As in other LIM domains, this domain family is 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188758 [Multi-domain] Cd Length: 53 Bit Score: 51.66 E-value: 1.08e-08

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 122056614 500 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHM-EDGEPYCEKDY 551
Cdd:cd09372    1 CAKCQGVITEHIIRALGKGYHPPCFTCVTCGRRIGDESFAVdEQNEVYCLDDY 53

The fourth LIM domain of Paxillin; The fourth LIM domain of Paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188795 [Multi-domain] Cd Length: 52 Bit Score: 51.49 E-value: 1.12e-08

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 441 CGHCNNVIRGPFLVAMGRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERCY 492
Cdd:cd09411    1 CSGCQKPITGRCITAMGKKFHPEHFVCAFCLKQLNKGTFKEQNDKPYCHNCF 52

PDZ domain of PDZ domain-containing protein 11, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of PDZD11, and related domains. PDZD11 (also known as ATPase-interacting PDZ protein, plasma membrane calcium ATPase-interacting single-PDZ protein, PMCA-interacting single-PDZ protein, PISP) is involved in the dynamic assembly of apical junctions (AJs). It is recruited by PLEKHA7 to AJs to promote the efficient junctional recruitment and stabilization of nectins, and the efficient early phases of assembly of AJs in epithelial cells. The PDZD11 PDZ domain binds nectin-1 and nectin-3. PDZD11 also binds to a PDZ binding motif located in the C-terminal tail of the human sodium-dependent multivitamin transporter, to the cytoplasmic tail of the Menkes copper ATPase ATP7A, and to the cytoplasmic tail of all plasma membrane Ca2+-ATPase b-splice variants. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD11-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467234 [Multi-domain] Cd Length: 83 Bit Score: 52.32 E-value: 1.13e-08

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 122056614  14 GFRLQGGKDFNMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSA 72
Cdd:cd06752   14 GFNIRGGKASGLGIFISKVIPDSDAHRLGLKEGDQILSVNGVDFEDIEHSEAVKVLKTA 72

The second LIM domain of Lrg1p, a LIM and RhoGap domain containing protein; The second LIM domain of Lrg1p, a LIM and RhoGap domain containing protein: The members of this family contain three tandem repeats of LIM domains and a Rho-type GTPase activating protein (RhoGap) domain. Lrg1p is a Rho1 GTPase-activating protein required for efficient cell fusion in yeast. Lrg1p-GAP domain strongly and specifically stimulates the GTPase activity of Rho1p, a regulator of beta (1-3)-glucan synthase in vitro. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188778 [Multi-domain] Cd Length: 53 Bit Score: 51.21 E-value: 1.30e-08

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 122056614 441 CGHCNNVIRGPFLVAMGRSWHPEEFTCAYCKTSL-ADVCFVEEQNNVYCERCY 492
Cdd:cd09392    1 CFKCGGALRGSYITALGRKYHVEHFTCSVCPTVFgPNDSYYEHEGKIYCHYHY 53

DNA polymerase III subunits gamma and tau; Validated

Pssm-ID: 236090 [Multi-domain] Cd Length: 824 Bit Score: 58.07 E-value: 1.41e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 278 PAAPAPKPRVVTTASIRPSVYQ---PVPASTYSPSPGANYSPTPYTPSPAPAYTPSPAPAYTPSPVPTYTPSPAPAYTPS 354
Cdd:PRK07764 408 AAPAPAAAAPAAAAAPAPAAAPqpaPAPAPAPAPPSPAGNAPAGGAPSPPPAAAPSAQPAPAPAAAPEPTAAPAPAPPAA 487

                         90       100
                 ....*....|....*....|....*....
gi 122056614 355 PAPNYNPAP---SVAYSGGPAEPASRPPW 380
Cdd:PRK07764 488 PAPAAAPAApaaPAAPAGADDAATLRERW 516

The second LIM domain of the filamin-binding LIM protein-1 (FBLP-1); The second LIM domain of the filamin-binding LIM protein-1 (FBLP-1): Fblp-1 contains a proline-rich domain near its N terminus and two LIM domains at its C terminus. FBLP-1 mRNA was detected in a variety of tissues and cells including platelets and endothelial cells. FBLP-1 binds to Filamins. The association between filamin B and FBLP-1 may play an unknown role in cytoskeletal function, cell adhesion, and cell motility. As in other LIM domains, this domain family is 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188758 [Multi-domain] Cd Length: 53 Bit Score: 51.27 E-value: 1.43e-08

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 122056614 441 CGHCNNVIRGPFLVAMGRSWHPEEFTCAYCKTSLADVCF-VEEQNNVYC 488
Cdd:cd09372    1 CAKCQGVITEHIIRALGKGYHPPCFTCVTCGRRIGDESFaVDEQNEVYC 49

The second LIM domain of Enigma; The second LIM domain of Enigma: Enigma was initially characterized in humans as a protein containing three LIM domains at the C-terminus and a PDZ domain at N-terminus. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. Enigma is expressed in multiple tissues, such as skeletal muscle, heart, bone and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188840 [Multi-domain] Cd Length: 52 Bit Score: 50.77 E-value: 1.98e-08

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 441 CGHCNNVIRGPFLVAMGRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERCY 492
Cdd:cd09456    1 CAKCKKKITGEIMHALKMTWHVHCFTCAACKTPIRNRAFYMEEGAPYCERDY 52

The first LIM domain of Lrg1p, a LIM and RhoGap domain containing protein; The first LIM domain of Lrg1p, a LIM and RhoGap domain containing protein: The members of this family contain three tandem repeats of LIM domains and a Rho-type GTPase activating protein (RhoGap) domain. Lrg1p is a Rho1 GTPase-activating protein required for efficient cell fusion in yeast. Lrg1p-GAP domain strongly and specifically stimulates the GTPase activity of Rho1p, a regulator of beta (1-3)-glucan synthase in vitro. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188777 Cd Length: 57 Bit Score: 50.76 E-value: 2.34e-08

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 122056614 500 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGE-----PYCEKDY 551
Cdd:cd09391    1 CAKCGKPITGQFVRALGDVYHLDCFTCHDCGKPVASKFFPVDDPDtseqvPLCETDY 57

The second LIM domain on actin binding LIM (abLIM) proteins; The second LIM domain of actin binding LIM (abLIM) proteins: Three homologous members of the abLIM protein family have been identified; abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM consists of four tandem repeats of LIM domains and the C-terminal of acting binding LIM protein is a villin headpiece domain, which has strong actin binding activity. The abLIM-1, which is expressed in retina, brain, and muscle tissue, has been indicated to function as a tumor suppressor. AbLIM-2 and -3, mainly expressed in muscle and neuronal tissue, bind to F-actin strongly. They may serve as a scaffold for signaling modules of the actin cytoskeleton and thereby modulate transcription. It has shown that LIM domains of abLIMs interact with STARS (striated muscle activator of Rho signaling), which directly binds actin and stimulates serum-response factor (SRF)-dependent transcription. All LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188714 Cd Length: 56 Bit Score: 50.04 E-value: 3.41e-08

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                 ....*....|....*....|....*....|....*....|....*....|.
gi 122056614 500 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPF-GNSLFHMEDGEPYCEK 549
Cdd:cd09328    4 CDSCQDFVEGEVVSALGKTYHPKCFVCSVCRQPFpPGDRVTFNGKECLCQK 54

The first LIM domain of LIMK1 (LIM domain Kinase 1); The first LIM domain of LIMK1 (LIM domain Kinase 1): LIMK1 belongs to the LIMK protein family, which comprises LIMK1 and LIMK2. LIMK contains two LIM domains, a PDZ domain, and a kinase domain. LIMK is involved in the regulation of actin polymerization and microtubule disassembly. LIMK influences architecture of the actin cytoskeleton by regulating the activity of the cofilin family proteins cofilin1, cofilin2, and destrin. The mechanism of the activation is to phosphorylates cofilin on serine 3 and inactivates its actin-severing activity, and altering the rate of actin depolymerization. LIMKs can function in both cytoplasm and nucleus. Both LIMK1 and LIMK2 can act in the nucleus to suppress Rac/Cdc42-dependent cyclin D1 expression. LIMK1 is expressed in all tissues and is localized to focal adhesions in the cell. LIMK1 can form homodimers upon binding of HSP90 and is activated by Rho effector Rho kinase and MAPKAPK2. LIMK1 is important for normal central nervous system development, and its deletion has been implicated in the development of the human genetic disorder Williams syndrome. Moreover, LIMK1 up-regulates the promoter activity of urokinase type plasminogen activator and induces its mRNA and protein expression in breast cancer cells. The LIM domains have been shown to play an important role in regulating kinase activity and likely also contribute to LIMK function by acting as sites of protein-to-protein interactions. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188846 [Multi-domain] Cd Length: 74 Bit Score: 50.65 E-value: 3.54e-08

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 122056614 498 PLCAKCNTKIM-GEVMHALRQTWHTTCFVCAACkkpfGNSLFHM---EDGEPYCEKDY 551
Cdd:cd09462   20 PVCASCGQSIYdGQYLQALNSDWHADCFRCCEC----GASLSHWyyeKDGRLFCKKDY 73

PDZ domain of protein Lin-7 and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Lin-7 (also known as LIN-7 or LIN7), and related domains. Lin-7 targets and organize protein complexes to epithelial and synaptic plasma membranes. There are three mammalian Lin-7 homologs: Lin-7A (protein lin-7 homolog A, also known as mammalian lin-seven protein 1 (MALS-1), vertebrate lin-7 homolog 1 (Veli-1), tax interaction protein 33); Lin-7B (also known as MALS-2, Veli-2); and Lin-7C (also known as MALS-3, Veli-3). Lin-7 is involved in localization of the Let-23 growth factor receptor to the basolateral membrane of epithelial cells, in tight junction localization of insulin receptor substrate p53 (IRSp53), in retaining gamma-aminobutyric (GABA) transporter (BGT-1) at the basolateral surface of epithelial cells, and in regulating recruitment of neurotransmitter receptors to the postsynaptic density (PSD). The Lin7 PDZ domain binds Let-23, BGT and beta-catenin, and NMDA (N-methyl-D-aspartate) receptor NR2B. Lin-7 also binds to the PDZ binding motif located in the C-terminal tail of Rhotekin, an effector protein for small GTPase Rho. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Lin-7-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467258 [Multi-domain] Cd Length: 86 Bit Score: 50.90 E-value: 3.97e-08

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 122056614  14 GFRLQGGKDFNMPLTISRITPGSKA-AQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLT 79
Cdd:cd06796   15 GFNVMGGKEQNSPIYISRIIPGGVAdRHGGLKRGDQLLSVNGVSVEGEHHEKAVELLKAAQGSVKLV 81

The first LIM domain of Four and a half LIM domains protein 1; The first LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188730 Cd Length: 54 Bit Score: 49.75 E-value: 4.10e-08

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 559 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKK 610
Cdd:cd09344    1 CAECRKPIGADSKELHHKNRYWHETCFRCAKCYKPLANEPFVAKDNKILCGK 52

The Lim domain of DA1; The Lim domain of DA1: DA1 contains one copy of LIM domain and a domain of unknown function. DA1 is predicted as an ubiquitin receptor, which sets final seed and organ size by restricting the period of cell proliferation. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188782 [Multi-domain] Cd Length: 53 Bit Score: 49.17 E-value: 7.11e-08

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                 ....*....|....*....|....*....|....*....|....*....|...
gi 122056614 441 CGHCNNVI-RGPFLVAMGRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERCY 492
Cdd:cd09396    1 CAGCKSEIgHGRFLSALGAVWHPECFRCHACRKPIAEHEFSVSGNDPYHKSCY 53

The third LIM domain of the paxillin like protein family; The third LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188724 [Multi-domain] Cd Length: 53 Bit Score: 49.26 E-value: 7.13e-08

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                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 441 CGHCNNVIRGPFLVAMGRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERCY 492
Cdd:cd09338    1 CGGCNKPILENYISALNTQWHPECFVCRECHKPFINGSFFEHEGLPYCETHY 52

The LIM domains of thymus LIM protein (TLP); The LIM domain of thymus LIM protein (TLP) like proteins: This family includes the LIM domains of TLP and CRIP (Cysteine-Rich Intestinal Protein). TLP is the distant member of the CRP family of proteins. TLP has two isomers (TLP-A and TLP-B) and sharing approximately 30% with each of the three other CRPs. Like CRP1, CRP2 and CRP3/MLP, TLP has two LIM domains, connected by a flexible linker region. Unlike the CRPs, TLP lacks the nuclear targeting signal (K/R-K/R-Y-G-P-K) and is localized solely in the cytoplasm. TLP is specifically expressed in the thymus in a subset of cortical epithelial cells. TLP has a role in development of normal thymus and in controlling the development and differentiation of thymic epithelial cells. CRIP is a short LIM protein with only one LIM domain. CRIP gene is developmentally regulated and can be induced by glucocorticoid hormones during the first three postnatal weeks. The domain shows close sequence homology to LIM domain of thymus LIM protein. However, unlike the TLP proteins which have two LIM domains, the members of this family have only one LIM domain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188785 [Multi-domain] Cd Length: 53 Bit Score: 49.26 E-value: 7.53e-08

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                 ....*....|....*....|....*....|....*....|....*....|...
gi 122056614 500 CAKCNTKI-MGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 551
Cdd:cd09401    1 CPKCGKPVyFAEKKTSLGRDWHKPCLRCEKCKKTLTPGQHSEHEGKPYCNKCY 53

PDZ domain of rhophilin-1, rhophilin-2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of rhophilin-1, rhophilin-2, and related domains. Rhophilin-1 (RHPN1, also known as GTP-Rho-binding protein 1) and rhophilin-2 (RHPN2, also known as GTP-Rho-binding protein 2) are Rho-GTP binding proteins involved in cytoskeletal dynamics. Rhophilin-2 inhibits RhoA's activity to induce F-actin stress fibers. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This rhophilin-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467196 [Multi-domain] Cd Length: 78 Bit Score: 49.51 E-value: 1.11e-07

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                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 122056614   4 SVTLT-GPGPWGFRLQGGKdfnmPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNlSLTLQ 81
Cdd:cd06712    3 TVHLTkEEGGFGFTLRGDS----PVQVASVDPGSCAAEAGLKEGDYIVSVGGVDCKWSKHSEVVKLLKSAGEE-GLELQ 76

PDZ domain 4 of membrane-associated guanylate kinase inverted 1 (MAGI-1), MAGI-2, and MAGI-3, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 4 of MAGI1, 2, 3 (MAGI is also known as Membrane-associated guanylate kinase, WW and PDZ domain-containing protein) and related domains. MAGI proteins have been implicated in the control of cell migration and invasion through altering the activity of phosphatase and tensin homolog (PTEN) and modulating Akt signaling. Four MAGI proteins have been identified (MAGI1-3 and MAGIX). MAGI1-3 have 6 PDZ domains and bind to the C-terminus of PTEN via their PDZ2 domain. MAGIX has a single PDZ domain that is related to MAGI1-3 PDZ domain 5. Other binding partners for MAGI1 include JAM4, C-terminal tail of high risk HPV-18 E6, megalin, TRAF6, Kir4.1 (basolateral K+ channel subunit), and cadherin 23; for MAGI2, include DASM1, dendrin, axin, beta- and delta-catenin, neuroligin, hyperpolarization-activated cation channels, beta1-adrenergic receptors, NMDA receptor, and TARPs; and for MAGI3 includes LPA2. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MAGI family PDZ4 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as beta-strands A, -B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467216 [Multi-domain] Cd Length: 84 Bit Score: 48.76 E-value: 2.48e-07

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                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614   3 YSVTLT---GPGpWGFRLQGGKDFNMPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSL 78
Cdd:cd06734    2 YDVTLTrreNEG-FGFVIISSVNKKSGSKIGRIIPGSPADRCgQLKVGDRILAVNGISILNLSHGDIVNLIKDSGLSVTL 80


                 ....
gi 122056614  79 TLQK 82
Cdd:cd06734   81 TIVP 84

The second LIM domain of Ajuba-like proteins; The second LIM domain of Ajuba-like proteins: Ajuba like LIM protein family includes three highly homologous proteins Ajuba, Limd1, and WTIP. Members of the family contain three tandem C-terminal LIM domains and a proline-rich N-terminal region. This family of proteins functions as scaffolds, participating in the assembly of numerous protein complexes. In the cytoplasm, Ajuba binds Grb2 to modulate serum-stimulated ERK activation. Ajuba also recruits the TNF receptor-associated factor 6 (TRAF6) to p62 and activates PKCKappa activity. Ajuba interacts with alpha-catenin and F-actin to contribute to the formation or stabilization of adheren junctions by linking adhesive receptors to the actin cytoskeleton. Although Ajuba is a cytoplasmic protein, it can shuttle into the nucleus. In nucleus, Ajuba functions as a corepressor for the zinc finger-protein Snail. It binds to the SNAG repression domain of Snail through its LIM region. Arginine methyltransferase-5 (Prmt5), a protein in the complex, is recruited to Snai l through an interaction with Ajuba. This ternary complex functions to repress E-cadherin, a Snail target gene. In addition, Ajuba contains functional nuclear-receptor interacting motifs and selectively interacts with retinoic acid receptors (RARs) and rexinoid receptor (RXRs) to negatively regulate retinoic acid signaling. Wtip, the Wt1-interacting protein, was originally identified as an interaction partner of the Wilms tumour protein 1 (WT1). Wtip is involved in kidney and neural crest development. Wtip interacts with the receptor tyrosine kinase Ror2 and inhibits canonical Wnt signaling. LIMD1 was reported to inhibit cell growth and metastases. The inhibition may be mediated through an interaction with the protein barrier-to-autointegration (BAF), a component of SWI/SNF chromatin-remodeling protein; or through the interaction with retinoblastoma protein (pRB), resulting in inhibition of E2F-mediated transcription, and expression of the majority of genes with E2F1- responsive elements. Recently, Limd1 was shown to interact with the p62/sequestosome protein and influence IL-1 and RANKL signaling by facilitating the assembly of a p62/TRAF6/a-PKC multi-protein complex. The Limd1-p62 interaction affects both NF-kappaB and AP-1 activity in epithelial cells and osteoclasts. Moreover, LIMD1 functions as tumor repressor to block lung tumor cell line in vitro and in vivo. Recent studies revealed that LIM proteins Wtip, LIMD1 and Ajuba interact with components of RNA induced silencing complexes (RISC) as well as eIF4E and the mRNA m7GTP cap-protein complex and are required for microRNA-mediated gene silencing. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188741 [Multi-domain] Cd Length: 53 Bit Score: 47.72 E-value: 2.51e-07

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                 ....*....|....*....|....*....|....*....|....*....|...
gi 122056614 441 CGHCNNVIRGPFLVAMGRSWHPEEFTCAYCKTSLADVCF-VEEQNNVYCERCY 492
Cdd:cd09355    1 CAVCGHLIMEMILQALGKSYHPGCFRCCVCNECLDGVPFtVDVENNIYCVKDY 53

The fourth LIM domain of Four and a half LIM domains protein (FHL); The fourth LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 interacts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188733 Cd Length: 56 Bit Score: 47.34 E-value: 2.98e-07

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                 ....*....|....*....|....*....|....*....|....*....|....
gi 122056614 559 CHGCDFPVEA--GDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKK 610
Cdd:cd09347    1 CAACTKPITGlgGAKFISFEERQWHSDCFNCGKCSVSLVGQGFLTQRDEILCPE 54

PDZ domain 12 of multi-PDZ-domain protein 1 (MUPP1), PDZ domain 10 of protein-associated tight junction (PATJ, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 12 of MUPP1, PDZ domain 10 of PATJ, and related domains. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, 9, and 13; consequently, MUPP1 PDZ7 and 8 align with PATJ PDZ6 and 7; and MUPP1 PDZ domains 10-12 align with PATJ PDZ domains 8-10. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like PDZ12 family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F

Pssm-ID: 467163 [Multi-domain] Cd Length: 86 Bit Score: 48.13 E-value: 3.62e-07

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                 ....*....|....*....|....*....|....*....|....*....|....*
gi 122056614  26 PLTISRITPGSKAAQSQ-LSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLT 79
Cdd:cd06675   29 PVFIAMIQPNGVAAQTGkLKVGDRIVSINGQSTDGLTHSEAVNLLKNASGTIILQ 83

The first LIM domain of Ajuba-like proteins; The first LIM domain of Ajuba-like proteins: Ajuba like LIM protein family includes three highly homologous proteins Ajuba, Limd1, and WTIP. Members of the family contain three tandem C-terminal LIM domains and a proline-rich N-terminal region. This family of proteins functions as scaffolds, participating in the assembly of numerous protein complexes. In the cytoplasm, Ajuba binds Grb2 to modulate serum-stimulated ERK activation. Ajuba also recruits the TNF receptor-associated factor 6 (TRAF6) to p62 and activates PKCKappa activity. Ajuba interacts with alpha-catenin and F-actin to contribute to the formation or stabilization of adheren junctions by linking adhesive receptors to the actin cytoskeleton. Although Ajuba is a cytoplasmic protein, it can shuttle into the nucleus. In nucleus, Ajuba functions as a corepressor for the zinc finger-protein Snail. It binds to the SNAG repression domain of Snail through its LIM region. Arginine methyltransferase-5 (Prmt5), a protein in the complex, is recruited to Snai l through an interaction with Ajuba. This ternary complex functions to repress E-cadherin, a Snail target gene. In addition, Ajuba contains functional nuclear-receptor interacting motifs and selectively interacts with retinoic acid receptors (RARs) and rexinoid receptor (RXRs) to negatively regulate retinoic acid signaling. Wtip, the Wt1-interacting protein, was originally identified as an interaction partner of the Wilms tumour protein 1 (WT1). Wtip is involved in kidney and neural crest development. Wtip interacts with the receptor tyrosine kinase Ror2 and inhibits canonical Wnt signaling. LIMD1 was reported to inhibit cell growth and metastases. The inhibition may be mediated through an interaction with the protein barrier-to-autointegration (BAF), a component of SWI/SNF chromatin-remodeling protein; or through the interaction with retinoblastoma protein (pRB), resulting in inhibition of E2F-mediated transcription, and expression of the majority of genes with E2F1- responsive elements. Recently, Limd1 was shown to interact with the p62/sequestosome protein and influence IL-1 and RANKL signaling by facilitating the assembly of a p62/TRAF6/a-PKC multi-protein complex. The Limd1-p62 interaction affects both NF-kappaB and AP-1 activity in epithelial cells and osteoclasts. Moreover, LIMD1 functions as tumor repressor to block lung tumor cell line in vitro and in vivo. Recent studies revealed that LIM proteins Wtip, LIMD1 and Ajuba interact with components of RNA induced silencing complexes (RISC) as well as eIF4E and the mRNA m7GTP cap-protein complex and are required for microRNA-mediated gene silencing. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188738 Cd Length: 54 Bit Score: 47.04 E-value: 4.23e-07

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                 ....*....|....*....|....*....|....*....|....*....|....
gi 122056614 500 CAKCNTKIMG--EVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 551
Cdd:cd09352    1 CVKCGKGVYGasQACQAMGNLYHTNCFTCCSCGRTLRGKAFYNVNGKVYCEEDY 54

The fourth LIM domain of protein PINCH; The fourth LIM domain of protein PINCH: PINCH plays a pivotal role in the assembly of focal adhesions (FAs), regulating diverse functions in cell adhesion, growth, and differentiation through LIM-mediated protein-protein interactions. PINCH comprises an array of five LIM domains that interact with integrin-linked kinase (ILK), Nck2 (also called Nckbeta or Grb4) and other interaction partners. These interactions are essential for triggering the FA assembly and for relaying diverse mechanical and biochemical signals between Cell-extracellular matrix and the actin cytoskeleton. The PINCH LIM4 domain recognizes the third SH3 domain of another adaptor protein, Nck2. This step is an important component of integrin signaling event. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assem bly of multimeric protein complexes.

Pssm-ID: 188720 [Multi-domain] Cd Length: 54 Bit Score: 46.96 E-value: 4.46e-07

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 122056614 559 CHGCDFPVEagDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKKH 611
Cdd:cd09334    3 CGACRRPIE--GRVVTALGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETH 53

The fifth LIM domain of protein PINCH; The fifth LIM domain of protein PINCH: PINCH plays pivotal roles in the assembly of focal adhesions (FAs), regulating diverse functions in cell adhesion, growth, and differentiation through LIM-mediated protein-protein interactions. PINCH comprises an array of five LIM domains that interact with integrin-linked kinase (ILK), Nck2 (also called Nckbeta or Grb4) and other interaction partners. These interactions are essential for triggering the FA assembly and for relaying diverse mechanical and biochemical signals between Cell-extracellular matrix and the actin cytoskeleton. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188721 [Multi-domain] Cd Length: 54 Bit Score: 46.96 E-value: 4.53e-07

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 122056614 500 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFG-NSLFHMEDGEPYCEKDY 551
Cdd:cd09335    1 CYHCNQVIEGDVVSALNKTWCVDHFSCSFCDTKLTlKSKFYEFDMKPVCKKCY 53

The second LIM domain of Leupaxin; The second LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188792 [Multi-domain] Cd Length: 52 Bit Score: 46.74 E-value: 5.58e-07

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 122056614 441 CGHCNNVIRGPFLVAMGRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCER 490
Cdd:cd09408    1 CAYCAGPILQNVLTAMDQTWHPEHFFCSHCGELFGDEGFLERDGKPYCRR 50

DNA polymerase III subunit gamma/tau;

Pssm-ID: 237874 [Multi-domain] Cd Length: 614 Bit Score: 52.47 E-value: 5.93e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 284 KPRVVTTASIRPSVYQPVPAstYSPSPGANYSPTP---YTPSPAPAYTPSPAPAYTPSPVPTYTPSPAPAYTPSPAPNYN 360
Cdd:PRK14971 370 SGGRGPKQHIKPVFTQPAAA--PQPSAAAAASPSPsqsSAAAQPSAPQSATQPAGTPPTVSVDPPAAVPVNPPSTAPQAV 447


                 ....*.
gi 122056614 361 PAPSVA 366
Cdd:PRK14971 448 RPAQFK 453

The LIM domain of ALP (actinin-associated LIM protein) family; This family represents the LIM domain of ALP (actinin-associated LIM protein) family. Four proteins: ALP, CLP36, RIL, and Mystique have been classified into the ALP subfamily of LIM domain proteins. Each member of the subfamily contains an N-terminal PDZ domain and a C-terminal LIM domain. Functionally, these proteins bind to alpha-actinin through their PDZ domains and bind or other signaling molecules through their LIM domains. ALP proteins have been implicated in cardiac and skeletal muscle structure, function and disease, platelet, and epithelial cell motility. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188746 [Multi-domain] Cd Length: 52 Bit Score: 46.21 E-value: 6.79e-07

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 122056614 441 CGHCNNVIRGPFLVAMGRSWHPEEFTCAYCKTSLADVC--FVEEQnnVYCE 489
Cdd:cd09360    1 CDKCGNGIVGVVVKARDKNRHPECFVCADCGLNLKNKGyfFIEDE--LYCE 49

The third LIM domain of Four and a half LIM domains protein 2 (FHL2); The third LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung to a lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to s upport the assembly of multimeric protein complexes.

Pssm-ID: 188815 Cd Length: 57 Bit Score: 46.52 E-value: 8.00e-07

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 122056614 500 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDYINLFS 556
Cdd:cd09431    1 CVQCKKPITTGGVTYRDQPWHKECFVCTGCKKQLSGQRFTSRDDFAYCLNCFCNLYA 57

The first LIM domain of Testin-like family; The first LIM domain of Testin_like family: This family includes testin, prickle, dyxin and LIMPETin. Structurally, testin and prickle proteins contain three LIM domains at C-terminal; LIMPETin has six LIM domains; and dyxin presents only two LIM domains. However, all members of the family contain a PET protein-protein interaction domain. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). Dyxin involves in lung and heart development by interaction with GATA6 and blocking GATA6 activated target genes. LIMPETin might be the recombinant product of genes coding testin and four and half LIM proteins and its function is not well understood. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188726 Cd Length: 58 Bit Score: 46.44 E-value: 8.12e-07

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 122056614 500 CAKCNTKI-MGEV-----MHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 551
Cdd:cd09340    1 CEKCKEPInPGEVavfaeRAGEDACWHPGCFVCETCNELLVDLIYFYHDGKIYCGRHY 58

The first LIM domain of Lmx1b; The first LIM domain of Lmx1b: Lmx1b belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. In mouse, Lmx1b functions in the developing limbs and eyes, the kidneys, the brain, and in cranial mesenchyme. The disruption of Lmx1b gene results kidney and limb defects. In the brain, Lmx1b is important for generation of mesencephalic dopamine neurons and the differentiation of serotonergic neurons. In the mouse eye, Lmx1b regulates anterior segment (cornea, iris, ciliary body, trabecular meshwork, and lens) development. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188757 [Multi-domain] Cd Length: 53 Bit Score: 46.22 E-value: 8.27e-07

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 122056614 559 CHGCDFPVEagDKFI-EALGHTWHDTCFICAVCHVNLEGQPFYskKDRPL-CKK 610
Cdd:cd09371    1 CAGCQRPIS--DRYLlRVNERSWHEECLQCSVCQQPLTTSCYF--RDRKLyCKQ 50

PDZ domain 2 of Discs Large 5 (Dlg5) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of Drosophila and mammalian Dlg5, and related domains. Dlg5 is a scaffold protein with multiple conserved functions that are independent of each other in regulating growth, cell polarity, and cell adhesion. It has a coiled-coil domain, 4 PDZ domains and a MAGUK domain (an SH3 domain next to a non-catalytically active guanylate kinase domain). Deregulation of Dlg5 has been implicated in the malignancy of several cancer types. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Dlg5-like family PSZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467246 [Multi-domain] Cd Length: 77 Bit Score: 46.96 E-value: 9.17e-07

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 122056614  17 LQGGKDFNMPLT----ISRITPGSKAA-QSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQKSK 84
Cdd:cd06765    4 LSGQKDSGISLEngvfISRIVPGSPAAkEGSLTVGDRIIAINGIALDNKSLSECEALLRSCRDSLSLSLMKVF 76

The second LIM domain of Four and a half LIM domains protein 1 (FHL1); The second LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188808 Cd Length: 58 Bit Score: 46.29 E-value: 9.24e-07

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 122056614 559 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLC 608
Cdd:cd09424    1 CKGCYKDILAGDQNVEYKGNVWHKDCFTCSNCKQPIGTKSFFPKGEDFYC 50

DNA polymerase III subunits gamma and tau; Provisional

Pssm-ID: 237865 [Multi-domain] Cd Length: 618 Bit Score: 51.64 E-value: 9.80e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 300 PVPASTYSPSPganysPTPYTPSPAPAYTPSPAPAYTPSPVPTYTPSPAPAYTPSPAPNYNPAPSVAYSGGPAEPASRPP 379
Cdd:PRK14951 373 AAPAEKKTPAR-----PEAAAPAAAPVAQAAAAPAPAAAPAAAASAPAAPPAAAPPAPVAAPAAAAPAAAPAAAPAAVAL 447

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 122056614 380 WVTDDSfsqkfAPGKSTTSISKQTLPRGG---PAYTPAGPQVPPLARGT 425
Cdd:PRK14951 448 APAPPA-----QAAPETVAIPVRVAPEPAvasAAPAPAAAPAAARLTPT 491

DNA polymerase III subunits gamma and tau; Validated

Pssm-ID: 236090 [Multi-domain] Cd Length: 824 Bit Score: 51.91 E-value: 1.07e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 300 PVPASTYSPSPGANYSPTPYTPSPAPAYTPSPAPAYTPSPVPTytPSPAPAYTPSPAPNYNPAPSVAYSGGPAEPASRPP 379
Cdd:PRK07764 392 GAPAAAAPSAAAAAPAAAPAPAAAAPAAAAAPAPAAAPQPAPA--PAPAPAPPSPAGNAPAGGAPSPPPAAAPSAQPAPA 469

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 122056614 380 WVtddsfsqkfAPGKSTTSISKQTLPRGGPAYTPAGPQVPPLARG 424
Cdd:PRK07764 470 PA---------AAPEPTAAPAPAPPAAPAPAAAPAAPAAPAAPAG 505

The first LIM domain of LIMK2 (LIM domain Kinase 2); The first LIM domain of LIMK2 (LIM domain Kinase 2): LIMK2 is a member of the LIMK protein family, which comprises LIMK1 and LIMK2. LIMK contains two LIM domains, a PDZ domain, and a kinase domain. LIMK is involved in the regulation of actin polymerization and microtubule disassembly. LIMK influences architecture of the actin cytoskeleton by regulating the activity of the cofilin family proteins cofilin1, cofilin2, and destrin. The mechanism of the activation is to phosphorylates cofilin on serine 3 and inactivates its actin-severing activity, altering the rate of actin depolymerization. LIMK activity is activated by phosphorylation of a threonine residue within the activation loop of the kinase by p21-activated kinases 1 and 4 and by Rho kinase. LIMKs can function in both cytoplasm and nucleus. Both LIMK1 and LIMK2 can act in the nucleus to suppress Rac/Cdc42-dependent cyclin D1 expression. LIMK2 is expressed in all tissues. While LIMK1 localizes mainly at focal adhesions, LIMK2 is found in cytoplasmic punctae, suggesting that they may have different cellular functions. The activity of LIM kinase 2 to regulate cofilin phosphorylation is inhibited by the direct binding of Par-3. LIMK2 activation promotes cell cycle progression. The phenotype of Limk2 knockout mice shows a defect in spermatogenesis. The LIM domains have been shown to play an important role in regulating kinase activity and likely also contribute to LIMK function by acting as sites of protein-to-protein interactions. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188847 [Multi-domain] Cd Length: 53 Bit Score: 45.63 E-value: 1.11e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 122056614 500 CAKCNTKIM-GEVMHALRQTWHTTCFVCAACKKPFGNSLFHmEDGEPYCEKDY 551
Cdd:cd09463    1 CTGCGGRIQdSFHYRVVQEAWHNSCFQCSVCQDLLTNWYYE-KDGKLYCHKHY 52

PDZ domain 2 of glutamate receptor-interacting protein 1 (GRIP1) and GRIP2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) binding proteins GRIP1 (ABP/GRIP2) and GRIP2, and related domains. GRIP1 and GRIP2 each have 7 PDZ domains. The interaction of GRIP1 and GRIP2 with GluA2/3 (AMPAR subunit) regulates AMPAR trafficking and synaptic targeting. GRIP1 has an essential role in regulating AMPAR trafficking during synaptic plasticity and learning and memory. GRIP1 and GRIP2 interact with a variety of other proteins associated with protein trafficking and internalization, for example GRIP1 also interacts with KIF5 (also known as kinesin 1), EphB receptors, scaffold protein liprin-alpha, and the rasGEF GRASP-1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This GRIP family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467169 [Multi-domain] Cd Length: 89 Bit Score: 46.84 E-value: 1.11e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614   5 VTLT-GPGPWGFRLQGG----KDFNMPLTISRITPGSKAA-QSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSL 78
Cdd:cd06681    5 VTLEkEGNSFGFVIRGGahedRNKSRPLTVTHVRPGGPADrEGTIKPGDRLLSVDGISLHGATHAEAMSILKQCGQEATL 84


                 .
gi 122056614  79 T 79
Cdd:cd06681   85 L 85

PDZ domain 4 of human Ligand of Numb protein X 1 (LNX1) and LNX2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 4 of LNX1 (also known as PDZ domain-containing RING finger protein 2, PDZRN2)and LNX2 (also known as PDZ domain-containing RING finger protein 1, PDZRN1), and related domains. LNX1 and LNX2 are Ring (Really Interesting New Gene) finger and PDZ domain-containing E3 ubiquitin ligases that bind to the cell fate determinant protein NUMB and mediate its ubiquitination. LNX1 can ubiquitinate a number of other ligands including PPFIA1, KLHL11, KIF7 and ERC2. LNX1 and LNX2 each have four PDZ domains. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This LNX family PDZ4 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467168 [Multi-domain] Cd Length: 89 Bit Score: 46.96 E-value: 1.18e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614   4 SVTL--TGPGPWGFRLQGGKDF---NMPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLS 77
Cdd:cd06680    2 DITLrrSSSGSLGFSIVGGYEEshgNQPFFVKSIVPGTPAYNDgRLKCGDIILAVNGVSTVGMSHAALVPLLKEQRGRVT 81


                 ..
gi 122056614  78 LT 79
Cdd:cd06680   82 LT 83

The third LIM domain of Leupaxin; The third LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188794 [Multi-domain] Cd Length: 53 Bit Score: 45.58 E-value: 1.18e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 441 CGHCNNVIRGPFLVAMGRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERCY 492
Cdd:cd09410    1 CSGCGRPVKENYLSAANGVWHPECFVCSDCLKPFTDGSFFELDGRPLCELHY 52

The third LIM domain of protein LIMPETin; The third LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188805 Cd Length: 59 Bit Score: 46.02 E-value: 1.19e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 122056614 555 FSTKCHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLC 608
Cdd:cd09421    1 FANQCEECSKIIGIDSKDLSYKDKHWHEACFLCSKCKISLVDKPFGSKADRIYC 54

large tegument protein UL36; Provisional

Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 51.86 E-value: 1.28e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  249 RRSRPQASSYSPAVAASSAPATHTSYSEGPAAPAPKPrvvTTASIRPSVYQPVPASTYSP-----SPGANYS--PTPYTP 321
Cdd:PHA03247 2795 RESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPP---TSAQPTAPPPPPGPPPPSLPlggsvAPGGDVRrrPPSRSP 2871

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  322 SPAPAYTPSP------APAYTPSPVPTYTPSPAPAYTPSPAPNYNPAPSVAYSGGPAE-PASRPPWVTDdsfsqkfAPGK 394
Cdd:PHA03247 2872 AAKPAAPARPpvrrlaRPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPqPPPPPPPRPQ-------PPLA 2944

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 122056614  395 STTSISKQTLPRGGPAYTPAGPQVP-----PLARGTVQRAER-FPASSRTPLCGH 443
Cdd:PHA03247 2945 PTTDPAGAGEPSGAVPQPWLGALVPgrvavPRFRVPQPAPSReAPASSTPPLTGH 2999

PDZ domain 2 of tyrosine kinase PTPN13, FERM and PDZ domain-containing protein 2 (FRMPD2), and similar domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of human PTPN13, and related domains. PTPN13, also known as Fas-associated protein-tyrosine phosphatase 1 (FAP-1), protein-tyrosine phosphatase 1E (PTP-E1), and protein-tyrosine phosphatase (PTPL1), negatively regulates FAS-mediated apoptosis and NGFR-mediated pro-apoptotic signaling, and may also regulate phosphoinositide 3-kinase (PI3K) signaling. It contains 5 PDZ domains; interaction partners of its second PDZ domain (PDZ2) include the Fas receptor (TNFRSF6) and thyroid receptor-interacting protein 6 (TRIP6). The second PDZ (PDZ2) domain, but not PDZ1 or PDZ3, of FRMPD2 binds to GluN2A and GluN2B, two subunits of N-methyl-d-aspartic acid (NMDA) receptors. Other binding partners of the FRMPDZ2 PDZ2 domain include NOD2, and catenin family members, delta catenin (CTNND2), armadillo repeat gene deleted in velo-cardio-facial syndrome (ARVCF) and p0071 (also known as plakophilin 4; PKP4). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PTPN13-like family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467254 [Multi-domain] Cd Length: 87 Bit Score: 46.44 E-value: 1.33e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614   3 YSVTLT-GPGPWGFRLQGGKDFNMPLT---ISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLS 77
Cdd:cd06792    3 FEVELSkKDGSLGISVTGGINTSVRHGgiyVKSLVPGGAAEQDgRIQKGDRLLEVNGVSLEGVTHKQAVECLKNAGQVVT 82


                 ....*
gi 122056614  78 LTLQK 82
Cdd:cd06792   83 LVLER 87

The third LIM domain of Leupaxin; The third LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188794 [Multi-domain] Cd Length: 53 Bit Score: 45.58 E-value: 1.41e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 122056614 559 CHGCDFPVEagDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKKHAH 613
Cdd:cd09410    1 CSGCGRPVK--ENYLSAANGVWHPECFVCSDCLKPFTDGSFFELDGRPLCELHYH 53

The first LIM domain of protein LIMPETin; The first LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the Testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188798 [Multi-domain] Cd Length: 58 Bit Score: 45.47 E-value: 1.44e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 122056614 441 CGHCNNVI-RGPFLVAMGRS-----WHPEEFTCAYCKTSLADVCFVEEQNNVYCERCY 492
Cdd:cd09414    1 CGGCSEPLkYGELAVTAPKFgesllWHPACFRCSTCEELLVDLTYCVHDDQIYCERHY 58

LIM domain in proteins of unknown function; The first Lim domain of a LIM domain containing protein: The functions of the proteins are unknown. The members of this family contain two copies of LIM domain. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188783 [Multi-domain] Cd Length: 58 Bit Score: 45.33 E-value: 1.56e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 122056614 500 CAKCNTKIMGEVMH----ALRQTWHTTCFVCAACKKPF-GNSLFHMEDGEPYCEKDY 551
Cdd:cd09397    1 CRKCGLEIEGKSISskdgELSGQWHRECFVCTTCGCPFqFSVPCYVLDDKPYCQQHY 57

Hedgehog signalling target; TALPID3 is a family of eukaryotic proteins that are targets for Hedgehog signalling. Mutations in this gene noticed first in chickens lead to multiple abnormalities of development.

Pssm-ID: 434634 [Multi-domain] Cd Length: 1288 Bit Score: 51.43 E-value: 1.65e-06

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614   280 APAPKPRVVTTASIRPSVYQPVPASTYSPSP---GANYSPTPYTPSPAPAYT-PSPAPAYTPSPVPTytPSPAPAYTPSP 355
Cdd:pfam15324  986 TPVPTPQPTPPCSPPSPLKEPSPVKTPDSSPcvsEHDFFPVKEIPPEKGADTgPAVSLVITPTVTPI--ATPPPAATPTP 1063

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614   356 APNYNPAPSVAYSggpaEPASRPPWVTDD---------SFSQKFAPGKSTTSISKQTLPRG--GPAYTPAGPQVPPLARG 424
Cdd:pfam15324 1064 PLSENSIDKLKSP----SPELPKPWEDSDlpleeenpnSEQEELHPRAVVMSVARDEEPESvvLPASPPEPKPLAPPPLG 1139

                          170
                   ....*....|....*
gi 122056614   425 TvqraeRFPASSRTP 439
Cdd:pfam15324 1140 A-----APPSPPQSP 1149

DNA polymerase III subunits gamma and tau; Provisional

Pssm-ID: 237864 [Multi-domain] Cd Length: 585 Bit Score: 50.96 E-value: 1.66e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 279 AAPAPKPRVVTTASIRPSVYQPVPASTYSPSPGANYSPTPYTPSPAPAYTPSPAPAYTPSPVPtytPSPAPAYTPSPApn 358
Cdd:PRK14950 362 PVPAPQPAKPTAAAPSPVRPTPAPSTRPKAAAAANIPPKEPVRETATPPPVPPRPVAPPVPHT---PESAPKLTRAAI-- 436

                         90
                 ....*....|....*...
gi 122056614 359 ynPAPSVAYSGGPAEPAS 376
Cdd:PRK14950 437 --PVDEKPKYTPPAPPKE 452

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.

Pssm-ID: 282904 [Multi-domain] Cd Length: 886 Bit Score: 51.07 E-value: 1.91e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  272 TSYSEGPAAPAPKPRVVTTASIRP-------SVYQPVPASTySPSPGANySPTPYTPSPAPAYTPSPAPAYTPSPVPTyt 344
Cdd:pfam05109 481 TTSGASPVTPSPSPRDNGTESKAPdmtsptsAVTTPTPNAT-SPTPAVT-TPTPNATSPTLGKTSPTSAVTTPTPNAT-- 556

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  345 pSPAPAYTpSPAPNYNpAPSVaysgGPAEPASRPPWVTDDSFSQKFAPGKSTTSISKQTLprGGPAYTPAGPQVPPLARG 424
Cdd:pfam05109 557 -SPTPAVT-TPTPNAT-IPTL----GKTSPTSAVTTPTPNATSPTVGETSPQANTTNHTL--GGTSSTPVVTSPPKNATS 627

                         170
                  ....*....|....
gi 122056614  425 TVQRAERFPASSRT 438
Cdd:pfam05109 628 AVTTGQHNITSSST 641

The first LIM domain of Zyxin; The first LIM domain of Zyxin: Zyxin exhibits three copies of the LIM domain, an extensive proline-rich domain and a nuclear export signal. Localized at sites of cell substratum adhesion in fibroblasts, Zyxin interacts with alpha-actinin, members of the cysteine-rich protein (CRP) family, proteins that display Src homology 3 (SH3) domains and Ena/VASP family members. Zyxin and its partners have been implicated in the spatial control of actin filament assembly as well as in pathways important for cell differentiation. In addition to its functions at focal adhesion plaques, recent work has shown that zyxin moves from the sites of cell contacts to the nucleus, where it directly participates in the regulation of gene expression. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188735 [Multi-domain] Cd Length: 87 Bit Score: 46.00 E-value: 1.96e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 122056614 559 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCK 609
Cdd:cd09349   34 CGICGQPLSRTQPAVRALGHLFHVTCFTCHQCEQQLQGQQFYSLEGKPYCE 84

DNA translocase FtsK; Provisional

Pssm-ID: 236669 [Multi-domain] Cd Length: 1355 Bit Score: 51.24 E-value: 2.02e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  278 PAAPAPKPRVVTTASIRPSV-YQPVPAsTYSPSPGANYSPTPYTPSPAPAYTPSPAPAYTPSPVPTYTPSPAPAY-TPSP 355
Cdd:PRK10263  339 PVTQTPPVASVDVPPAQPTVaWQPVPG-PQTGEPVIAPAPEGYPQQSQYAQPAVQYNEPLQQPVQPQQPYYAPAAeQPAQ 417

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  356 APNYNPAPSVA-----YSGGPAEPASRPPWVTDDSfSQKFAPGKSTTSISKQTLPRGGPAYTPAGPQVPP 420
Cdd:PRK10263  418 QPYYAPAPEQPaqqpyYAPAPEQPVAGNAWQAEEQ-QSTFAPQSTYQTEQTYQQPAAQEPLYQQPQPVEQ 486

The third LIM domain of Four and a half LIM domains protein (FHL); The third LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 int eracts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188732 Cd Length: 52 Bit Score: 45.01 E-value: 2.04e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 122056614 500 CAKCNTKI-MGEVMHAlRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 551
Cdd:cd09346    1 CAKCKKAItSGGVTYR-DQPWHKECFVCTGCKKQLAGQRFTSRDEYPYCVDCF 52

EBNA-3B; Provisional

Pssm-ID: 223065 [Multi-domain] Cd Length: 991 Bit Score: 50.84 E-value: 2.50e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 295 PSVYQPVPASTYSPSPGANYSPTPYTPS--------PAPAYTPSPAPAYTPSPVPTYTPSPAPAYTPSPAPNYNPAPSVA 366
Cdd:PHA03378 655 PQVEITPYKPTWTQIGHIPYQPSPTGANtmlpiqwaPGTMQPPPRAPTPMRPPAAPPGRAQRPAAATGRARPPAAAPGRA 734

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 122056614 367 YSGGPAEPASRPPWVTDDSFSQkfaPGKSTTSISKQTLPRGGPAYTPAgPQVPPLARgtvQRAERFPASSRTP 439
Cdd:PHA03378 735 RPPAAAPGRARPPAAAPGRARP---PAAAPGRARPPAAAPGAPTPQPP-PQAPPAPQ---QRPRGAPTPQPPP 800

The second LIM domain of Prickle; The second LIM domain of Prickle: Prickle contains three C-terminal LIM domains and a N-terminal PET domain. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). PCP establishment requires the conserved Frizzled/Dishevelled PCP pathway. Prickle interacts with Dishevelled, thereby modulating Frizzled/Dishevelled activity and PCP signaling. Two forms of prickles have been identified; namely prickle 1 and prickle 2. Prickle 1 and prickle 2 are differentially expressed. While prickle 1 is expressed in fetal heart and hematological malignancies, prickle 2 is found in fetal brain, adult cartilage, pancreatic islet, and some types of timorous cells. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188802 Cd Length: 56 Bit Score: 44.73 E-value: 2.56e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 122056614 498 PLCAKCNTKIMG-EVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYC 547
Cdd:cd09418    1 PRCSACDEIIFAdECTEAEGRHWHMKHFCCFECECQLGGQRYIMREGRPYC 51

The second LIM domain of Zyxin; The second LIM domain of Zyxin: Zyxin exhibits three copies of the LIM domain, an extensive proline-rich domain and a nuclear export signal. Localized at sites of cellsubstratum adhesion in fibroblasts, Zyxin interacts with alpha-actinin, members of the cysteine-rich protein (CRP) family, proteins that display Src homology 3 (SH3) domains and Ena/VASP family members. Zyxin and its partners have been implicated in the spatial control of actin filament assembly as well as in pathways important for cell differentiation. In addition to its functions at focal adhesion plaques, recent work has shown that zyxin moves from the sites of cell contacts to the nucleus, where it directly participates in the regulation of gene expression. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors o r scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188739 [Multi-domain] Cd Length: 60 Bit Score: 44.92 E-value: 2.59e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 122056614 441 CGHCNNVIRGPFLVAMGRSWHPEEFTCAYCKTSLADVCFVEEQNNV-YCERCYEQFFAP 498
Cdd:cd09353    1 CAVCDQKITDRMLKATGKSYHPQCFTCVVCKCPLEGESFIVDQANQpHCVNDYHRRYAP 59

DNA polymerase III subunits gamma and tau; Provisional

Pssm-ID: 237865 [Multi-domain] Cd Length: 618 Bit Score: 50.10 E-value: 2.98e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 198 VYQAVIKSQNKPED-EADEWARRSSNLQSRSFRILAQMT---GTEFMQDPDEEA------LR--RSRPQASSYSPAVAAs 265
Cdd:PRK14951 299 VLQAVPQAAAAATDpEAAEVARLAALMPADETQLLYSIClhgRAELGLAPDEYAaltmvlLRllAFKPAAAAEAAAPAE- 377

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 266 sapaTHTSYSEGPAAPAPKPRVVTTASIRPSVyqPVPASTYSPSPGANYSPTPYTPSPAP-AYTPSPAPAYTPSPVPTYT 344
Cdd:PRK14951 378 ----KKTPARPEAAAPAAAPVAQAAAAPAPAA--APAAAASAPAAPPAAAPPAPVAAPAAaAPAAAPAAAPAAVALAPAP 451

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 122056614 345 PSPAPAYTPSPAPNYNPAPSVAYSGGPAEPASRPPWVTD 383
Cdd:PRK14951 452 PAQAAPETVAIPVRVAPEPAVASAAPAPAAAPAAARLTP 490

The first LIM domain of Four and a half LIM domains protein (FHL); The first LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 int eracts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188729 Cd Length: 59 Bit Score: 44.74 E-value: 3.11e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 122056614 555 FSTKCHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLC 608
Cdd:cd09343    1 FANTCEECKKKIGCDSKDLSYKDRHWHEGCFKCFKCQRSLVDKPFAAKDEDLLC 54

The first LIM domain of LIMK (LIM domain Kinase ); The first LIM domain of LIMK (LIM domain Kinase ): LIMK protein family is comprised of two members LIMK1 and LIMK2. LIMK contains two LIM domains, a PDZ domain and a kinase domain. LIMK is involved in the regulation of actin polymerization and microtubule disassembly. LIMK influences architecture of the actin cytoskeleton by regulating the activity of the cofilin family proteins cofilin1, cofilin2, and destrin. The mechanism of the activation is to phosphorylates cofilin on serine 3 and inactivates its actin-severing activity, and altering the rate of actin depolymerisation. LIMKs can function in both cytoplasm and nucleus and are expressed in all tissues. Both LIMK1 and LIMK2 can act in the nucleus to suppress Rac/Cdc42-dependent cyclin D1 expression. However, LIMK1 and LIMk2 have different cellular locations. While LIMK1 localizes mainly at focal adhesions, LIMK2 is found in cytoplasmic punctae, suggesting that they may have different cellular functions. The LIM domains of LIMK have been shown to play an important role in regulating kinase activity and likely also contribute to LIMK function by acting as sites of protein-to-protein interactions. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188750 [Multi-domain] Cd Length: 53 Bit Score: 44.40 E-value: 3.24e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 122056614 441 CGHCNNVIR-GPFLVAMGRSWHPEEFTCAYCKTSLADVCFvEEQNNVYCERCY 492
Cdd:cd09364    1 CAGCRGKILdSQYVQALNQDWHCDCFRCSVCSDSLSNWYF-EKDGKLYCRKDY 52

The third LIM domain of paxillin; The third LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188793 [Multi-domain] Cd Length: 53 Bit Score: 44.45 E-value: 3.26e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 122056614 559 CHGCDFPVEagDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKKHAH 613
Cdd:cd09409    1 CGGCARAIL--ENYISALNTLWHPECFVCRECFTPFVNGSFFEHDGQPYCEAHYH 53

DNA polymerase III subunits gamma and tau; Validated

Pssm-ID: 236090 [Multi-domain] Cd Length: 824 Bit Score: 49.98 E-value: 3.71e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 277 GPAAPAPKPRVVTTASIRPSVYQPVPASTYSPSPGANYSPTPYTPSPAPAYTPSPAPAytpsPVPTYTPSPAPAYTPSPA 356
Cdd:PRK07764 637 AEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKAGGAAPAAPPPAPAPAAPAAPA----GAAPAQPAPAPAATPPAG 712

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 122056614 357 PNYNPAPSVAysgGPAEPASRPPWVTDDSFSQKFAPGKSTTSISKQTLPRGGPAYTPAGPQVPPLARGTVQRAERFPA 434
Cdd:PRK07764 713 QADDPAAQPP---QAAQGASAPSPAADDPVPLPPEPDDPPDPAGAPAQPPPPPAPAPAAAPAAAPPPSPPSEEEEMAE 787

The first LIM domain of Lhx3b; The first LIM domain of Lhx3b. Lhx3b is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx3b is one of the two isoforms of Lhx3. The Lhx3 gene is expressed in the ventral spinal cord, the pons, the medulla oblongata, and the pineal gland of the developing nervous system during mouse embryogenesis, and transcripts are found in the emergent pituitary gland. Lhx3 functions in concert with other transcription factors to specify interneuron and motor neuron fates during development. Lhx3 proteins have been demonstrated to directly bind to the promoters of several pituitary hormone gene promoters. The Lhx3 gene encodes two isoforms, LHX3a and LHX3b that differ in their amino-terminal sequences, where Lhx3a has longer N-terminal. They show differential activation of pituitary hormone genes and distinct DNA binding properties. In human, Lhx3a trans-activated the alpha-glycoprotein subunit promoter and genes containing a high-affinity Lhx3 binding site more effectively than the hLhx3b isoform. In addition, hLhx3a induce transcription of the TSHbeta-subunit gene by acting on pituitary POU domain factor, Pit-1, while hLhx3b does not. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188851 [Multi-domain] Cd Length: 55 Bit Score: 44.16 E-value: 4.07e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 122056614 498 PLCAKCNTKIMGE-VMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGePYCEKDY 551
Cdd:cd09467    2 PLCAGCNQHIVDRfILKVLDRHWHSKCLKCSDCQTQLAEKCFSRGDS-VYCKDDF 55

ORF080 virion core protein; Provisional

Pssm-ID: 177464 [Multi-domain] Cd Length: 280 Bit Score: 48.70 E-value: 4.20e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 294 RPSVYQPVPASTYSPSPgANYSPTPYTPSPAPAYT-PSPAPAYTPSPVPTytpSPAPAYTPSPAPNYNPAPSVAYSGGPA 372
Cdd:PHA02682  75 RPSGQSPLAPSPACAAP-APACPACAPAAPAPAVTcPAPAPACPPATAPT---CPPPAVCPAPARPAPACPPSTRQCPPA 150

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 122056614 373 EPASRP-------PWVTDDSFSQKFAPGKSTTSIskQTLPRGGPAYTPAGP 416
Cdd:PHA02682 151 PPLPTPkpapaakPIFLHNQLPPPDYPAASCPTI--ETAPAASPVLEPRIP 199

The second LIM domain of paxillin; The second LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188791 [Multi-domain] Cd Length: 52 Bit Score: 44.18 E-value: 4.27e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 441 CGHCNNVIRGPFLVAMGRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERCY 492
Cdd:cd09407    1 CYYCNGPILDKVVTALDRTWHPEHFFCAQCGAFFGPEGFHEKDGKAYCRKDY 52

PDZ domains of the Na+/H+ exchange regulatory cofactor (NHERF) family (NHERF1-4), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of the Na+/H+ exchange regulatory cofactor (NHERF) family of multi-PDZ-domain-containing scaffolding proteins (NHERF1-4), and related domains. The NHERF family includes NHERF1 (also known as EBP50), NHERF2 (also known as E3KARP; TKA-1; SIP-1), NHERF3 (also known as CAP70; CLAMP; Napi-Cap-1; PDZD1) and NHERF4 (also known as IKEPP; PDZK2; Napi-Cap-2). NHERF1 and NHERF2 have tandem PDZ domains (PDZ1-2); NHERF3 and NHERF4 have four PDZ domains (PDZ1-4). NHERFs are involved in the regulation of multiple receptors or transporters, such as type II sodium-phosphate cotransporter (Npt2a), purinergic P2Y1 receptor P2Y1R, the beta2-adrenergic receptor (beta2-AR), parathyroid hormone receptor type 1 (PTHR), the lysophosphatidic acid receptors (LPARs), sodium-hydrogen exchanger 3 (NHE3), and cystic fibrosis transmembrane conductance regulator (CFTR). NHERF-PDZ1 domain interaction partners include Npt2a, purinergic P2Y1 receptor, beta2-AR, CFTR, PTHR, NH3, G-protein-coupled receptor kinase 6 (GRK6A), platelet-derived growth factor receptor (PDGFR), B1 subunit of the H+ATPase, cholesterol, receptor for activated C-kinase RACK1, aquaporin 9, among others. The NHERF PDZ2 domain interacts with fewer proteins: NHERF1 PDZ2 binds Npt2a, PTHR, beta-catenin, aquaporin 9, and RACK1; NHERF2 PDZ2 binds LPA2, P2Y1R, and NHE3, cGMP-dependent protein kinase type II (cGKII). NHERF4 PDZ1 and PDZ4 bind the epithelial Ca(2+) channels TRPV5 and TRPV6. NHERF2/NHERF3 heterodimerization is mediated by PDZ domains of NHERF2 and the C-terminal PDZ domain recognition motif of NHERF3. NHERF4 regulates several transporters mediating influx of xenobiotics and nutrients in the small intestine. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This NHERF-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467249 [Multi-domain] Cd Length: 80 Bit Score: 44.74 E-value: 4.41e-06

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 122056614   9 GPGPWGFRLQGGKD----FnmpltISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTL 80
Cdd:cd06768    8 GPEGYGFNLHAEKGrpghF-----IREVDPGSPAERAGLKDGDRLVEVNGENVEGESHEQVVEKIKASGNQVTLLV 78

The fourth LIM domain of Four and a half LIM domains protein 2 (FHL2); The fourth LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung to a lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to s upport the assembly of multimeric protein complexes.

Pssm-ID: 188817 Cd Length: 58 Bit Score: 44.21 E-value: 4.48e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 559 CHGCDFPVEA--GDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLC 608
Cdd:cd09433    1 CAGCTNPISGlgGTKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILC 52

The first LIM domain of lipoma preferred partner (LPP); The first LIM domain of lipoma preferred partner (LPP): LPP is a member of the zyxin LIM protein family and contains three LIM zinc-binding domains at the C-terminal and proline-rich region at the N-terminal. LPP initially identified as the most frequent translocation partner of HMGA2 (High Mobility Group A2) in a subgroup of benign tumors of adipose tissue (lipomas). It was also shown to be rearranged in a number of other soft tissues, as well as in a case of acute monoblastic leukemia. In addition to its involvement in tumors, LPP was inedited as a smooth muscle restricted LIM protein that plays an important role in SMC migration. LPP is localized at sites of cell adhesion, cell-cell contacts and transiently in the nucleus. In nucleus, it acts as a coactivator for the ETS domain transcription factor PEA3. In addition to PEA3, it interacts with alpha-actinin,vasodilator stimulated phosphoprotein (VASP),Palladin, and Scrib. The LIM domains are the main focal adhesion targeting elements and that the proline- rich region, which harbors binding sites for alpha-actinin and vasodilator- stimulated phosphoprotein (VASP), has a weak targeting capacity. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188737 [Multi-domain] Cd Length: 54 Bit Score: 43.95 E-value: 4.57e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 122056614 559 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCK 609
Cdd:cd09351    1 CVKCGEKVLGEGSGCTAMDQVYHISCFTCHQCQINLQGKPFYALDGKPYCE 51

The second LIM domain of Lhx1 (also known as Lim1) and Lhx5; The second LIM domain of Lhx1 (also known as Lim1) and Lhx5. Lhx1 and Lhx5 are closely related members of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx1 is required for regulating the vertebrate head organizer, the nervous system, and female reproductive tract development. During embryogenesis in the mouse, Lhx1 is expressed early in mesodermal tissue, then later during urogenital, kidney, liver, and nervous system development. In the adult, expression is restricted to the kidney and brain. A mouse embryos with Lhx1 gene knockout cannot grow normal anterior head structures, kidneys, and gonads, but with normally developed trunk and tail morphology. In the developing nervous system, Lhx1 is required to direct the trajectories of motor axons in the limb. Lhx1 null female mice lack the oviducts and uterus. Lhx5 protein may play complementary or overlapping roles with Lhx1. The expression of Lhx5 in the anterior portion of the mouse neural tube suggests a role in patterning of the forebrain. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188761 Cd Length: 56 Bit Score: 44.27 E-value: 4.73e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 122056614 500 CAKCNTKIMGE--VMHALRQTWHTTCFVCAACKKPF--GNSLFHMEDGEPYCEKDY 551
Cdd:cd09375    1 CAGCDQGISPNdlVRRARDKVFHLNCFTCMVCRKQLstGEELYILDENKFICKEDY 56

The first LIM domain of Leupaxin; The first LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188790 [Multi-domain] Cd Length: 55 Bit Score: 44.09 E-value: 4.74e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 122056614 559 CHGCDFPVeAGdKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKKHAH 613
Cdd:cd09406    3 CASCQKPI-AG-QVVTALGQTWHPEHFVCCQCGKELGSRPFFERNGQAYCEEDYH 55

The second LIM domain of Four and a half LIM domains protein 3 (FHL3); The second LIM domain of Four and a half LIM domains protein 3 (FHL3): FHL3 is highly expressed in the skeleton and cardiac muscles and possesses the transactivation and repression activities. FHL3 interacts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. Moreover, FHL3 interacts with alpha- and beta-subunits of the muscle alpha7beta1 integrin receptor. FHL3 was also proved to possess the auto-activation ability and was confirmed that the second zinc finger motif in fourth LIM domain was responsible for the auto-activation of FHL3. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188811 Cd Length: 58 Bit Score: 44.07 E-value: 5.13e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 122056614 556 STKCHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLC 608
Cdd:cd09427    1 SSKCVACGKTVMPGSRKLEYEGQTWHEHCFICHGCEQPIGSRSFIPDKDEHYC 53

The first LIM domain of Enigma-like family; The first LIM domain of Enigma-like family: The Enigma LIM domain family is comprised of three members: Enigma, ENH, and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. Enigma was initially characterized in humans and is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. The second member, ENH protein, was first identified in rat brain. It has been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188747 [Multi-domain] Cd Length: 52 Bit Score: 43.89 E-value: 5.16e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 122056614 559 CHGCDFPVEagDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKKH 611
Cdd:cd09361    1 CAHCNQVIR--GPFLVALGRSWHPEEFTCSHCHCSLAEIGFVEEKGSLYCELC 51

The second LIM domain of Four and a half LIM domains protein (FHL); The second LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 int eracts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188731 [Multi-domain] Cd Length: 54 Bit Score: 43.82 E-value: 5.31e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 122056614 500 CAKCNTKIMGEV--MHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 551
Cdd:cd09345    1 CKACGKAIMPGSkkMEYKGKFWHEKCFTCSECKKPIGTKSFIPKDDKIYCVPCY 54

DNA polymerase III subunits gamma and tau; Validated

Pssm-ID: 236090 [Multi-domain] Cd Length: 824 Bit Score: 49.60 E-value: 5.41e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 275 SEGPAAPAPKP-RVVTTASIRPSVYQPVPASTYSPSPGAnySPTPYTPSPAPAYTPSPAPAYTPSPVPtytPSPAPAYTP 353
Cdd:PRK07764 675 GAAPAAPPPAPaPAAPAAPAGAAPAQPAPAPAATPPAGQ--ADDPAAQPPQAAQGASAPSPAADDPVP---LPPEPDDPP 749

                         90       100
                 ....*....|....*....|....*....
gi 122056614 354 SPAPNYNPAPSVAYSGGPAEPASRPPWVT 382
Cdd:PRK07764 750 DPAGAPAQPPPPPAPAPAAAPAAAPPPSP 778

The second LIM domain of protein PINCH; The second LIM domain of protein PINCH: PINCH plays a pivotal role in the assembly of focal adhesions (FAs), regulating diverse functions in cell adhesion, growth, and differentiation through LIM-mediated protein-protein interactions. PINCH comprises an array of five LIM domains that interact with integrin-linked kinase (ILK), Nck2 (also called Nckbeta or Grb4) and other interaction partners. These interactions are essential for triggering the FA assembly and for relaying diverse mechanical and biochemical signals between Cell-extracellular matrix and the actin cytoskeleton. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188718 [Multi-domain] Cd Length: 52 Bit Score: 43.86 E-value: 5.41e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 122056614 500 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEK 549
Cdd:cd09332    1 CGKCGEFVIGRVIKAMNNNWHPDCFRCEICNKELADIGFVKNAGRALCHP 50

DNA polymerase III subunit gamma/tau;

Pssm-ID: 237057 [Multi-domain] Cd Length: 700 Bit Score: 49.49 E-value: 5.57e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 278 PAAPAPKPRVVTTASIrPSVYQPVPASTYSPS--------PGANYSPTPYTPSPAPA---YTPSPAPAYTPSPVPTYTPS 346
Cdd:PRK12323 464 PAAAGPRPVAAAAAAA-PARAAPAAAPAPADDdpppweelPPEFASPAPAQPDAAPAgwvAESIPDPATADPDDAFETLA 542

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 122056614 347 PAPAYTPSPAPNYNPAPSVAySGGPAEPASRPPWVTD 383
Cdd:PRK12323 543 PAPAAAPAPRAAAATEPVVA-PRPPRASASGLPDMFD 578

The LIM domain of N-RAP; The LIM domain of N-RAP: N-RAP is a muscle-specific protein concentrated at myotendinous junctions in skeletal muscle and intercalated disks in cardiac muscle. LIM domain is found at the N-terminus of N-RAP and the C-terminal of N-RAP contains a region with multiple of nebulin repeats. N-RAP functions as a scaffolding protein that organizes alpha-actinin and actin into symmetrical I-Z-I structures in developing myofibrils. Nebulin repeat is known as actin binding domain. The N-RAP is hypothesized to form antiparallel dimerization via its LIM domain. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188830 Cd Length: 53 Bit Score: 43.75 E-value: 5.97e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 122056614 559 CHGCDFPVEAGDKfIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKKH 611
Cdd:cd09446    1 CARCGYGVYPAEK-INCIDQTWHKACFHCEVCKMMLTVNNFVSHQKKPYCQAH 52

The first LIM domain of Four and a half LIM domains protein 2 (FHL2); The first LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung at lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188806 Cd Length: 62 Bit Score: 43.74 E-value: 6.58e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 122056614 555 FSTKCHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLC 608
Cdd:cd09422    1 YSNTCEECKKPIGCDCKDLSYKDRHWHESCFHCFQCKNSLVDKPFAAKEEHLLC 54

envelope glycoprotein C; Provisional

Pssm-ID: 165527 [Multi-domain] Cd Length: 566 Bit Score: 48.96 E-value: 7.00e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 271 HTSYSEGPAAPAPKPRVVTTASIRPSVyqpVPASTYSPSPGANYSPTPYT---PSPAPAYTPSPAPAYTPSPVPTY--TP 345
Cdd:PHA03269  32 HTSAATQKPDPAPAPHQAASRAPDPAV---APTSAASRKPDLAQAPTPAAsekFDPAPAPHQAASRAPDPAVAPQLaaAP 108

                         90       100       110
                 ....*....|....*....|....*....|....
gi 122056614 346 SPAPAYTPSPAPNYNPAPSVAysggPAEPASRPP 379
Cdd:PHA03269 109 KPDAAEAFTSAAQAHEAPADA----GTSAASKKP 138

The third LIM domain of Four and a half LIM domains protein 1 (FHL1); The third LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188813 Cd Length: 53 Bit Score: 43.65 E-value: 7.09e-06

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 122056614 500 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYC 547
Cdd:cd09429    1 CVKCNKPITSGGVTYQDQPWHSECFVCSSCSKKLAGQRFTAVEDQYYC 48

PDZ domain of synaptojanin-2-binding protein (SYNJ2BP), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of SYNJ2BP, and related domains. SYNJ2BP (also known as mitochondrial outer membrane protein 25, OMP25) regulates endocytosis of activin type 2 receptor kinases through the Ral/RALBP1-dependent pathway and may be involved in suppression of activin-induced signal transduction. Binding partners of the SYNJ2BP PDZ domain include activin type II receptors (ActR-II), and SYNJ2. SYNJ2BP interacts with the PDZ binding motif of the Notch Delta-like ligand 1 (DLL1) and DLL4, promoting Delta-Notch signaling, and inhibiting sprouting angiogenesis. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This SYNJ2BP-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467193 [Multi-domain] Cd Length: 86 Bit Score: 44.59 E-value: 7.43e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614   5 VTLT-GPGPWGFRLQGGKDfnMPLT-------ISRITP-GSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYN 75
Cdd:cd06709    3 ITLKrGPSGLGFNIVGGTD--QPYIpndsgiyVAKIKEdGAAAIDGRLQEGDKILEINGQSLENLTHQDAVELFRNAGED 80


                 ....*.
gi 122056614  76 LSLTLQ 81
Cdd:cd06709   81 VKLKVQ 86

The second LIM domain of Cysteine Rich Protein 2 (CRP2); The second LIM domain of Cysteine Rich Protein 2 (CRP2): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network.CRP3 also called Muscle LIM Protein (MLP), which is a striated muscle-specific factor that enhances myogenic differentiation. The second LIM domain of CRP3/MLP interacts with cytoskeletal protein beta-spectrin. CRP3/MLP also interacts with the basic helix-loop-helix myogenic transcription factors MyoD, myogenin, and MRF4 thereby increasing their affinity for specific DNA regulatory elements. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188871 [Multi-domain] Cd Length: 54 Bit Score: 43.56 E-value: 7.50e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 122056614 441 CGHCNN-VIRGPFLVAMGRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERCY 492
Cdd:cd09840    1 CSRCGDsVYAAEKIMGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCY 53

PDZ domain 3 of PDZ domain containing 2 (PDZD2), PDZ domain 1 of human pro-interleukin-16 (isoform 1, 1332 AA), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of PDZD2, also known as KIAA0300, PIN-1, activated in prostate cancer (AIPC) and PDZ domain-containing protein 3 (PDZK3). PDZD2 has seven PDZ domains. PDZD2 is expressed at exceptionally high levels in the pancreas and certain cancer tissues, such as prostate cancer. It promotes the proliferation of insulinoma cells and is upregulated during prostate tumorigenesis. In osteosarcoma (OS), the microRNA miR-363 acts as a tumor suppressor by inhibiting PDZD2. This family also includes the first PDZ domain (PDZ1) of human pro-interleukin-16 (isoform 1, also known as nPro-Il-16; 1332 amino-acid protein). Precursor IL-16 is cleaved to produce pro-IL-16 and mature IL-16 (derived from the C-terminal 121 AA). Pro-IL-16 functions as a regulator of T cell growth; mature IL-16 is a CD4 ligand that induces chemotaxis and CD25 expression in CD4+ T cells. IL-16 bioactivity has been closely associated with the progression of several different cancers. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD2-like family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467240 [Multi-domain] Cd Length: 87 Bit Score: 44.57 E-value: 7.78e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 122056614  14 GFRLQGGKDF---NMPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKS 71
Cdd:cd06759   15 GFSIVGGRDSprgPMGIYVKTIFPGGAAAEDgRLKEGDEILEVNGESLQGLTHQEAIQKFKQ 76

large tegument protein UL36; Provisional

Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 49.17 E-value: 7.92e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  300 PVPASTYSPSPGANYSPTPYTPSPAPAYTPSPAPAYTPSPVPTYTPspapayTPSPAPNYNPAPSVAYSGGPAEPASRPP 379
Cdd:PHA03247  389 RHAATPFARGPGGDDQTRPAAPVPASVPTPAPTPVPASAPPPPATP------LPSAEPGSDDGPAPPPERQPPAPATEPA 462

                          90
                  ....*....|
gi 122056614  380 WVTDDSFSQK 389
Cdd:PHA03247  463 PDDPDDATRK 472

large tegument protein UL36; Provisional

Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 49.17 E-value: 7.99e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  272 TSYSEGPAAPAPKPRVVTTASIRPSVYQPVPASTYSPSPGANYSPTPYTPSPAPAYTPS-------PAPAYTPSPVPT-- 342
Cdd:PHA03247 2636 NEPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAAQASSPPQRPRRRAARPTVGSltsladpPPPPPTPEPAPHal 2715

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  343 -----YTPSPAPAYTPSPAPNYNPAPSvAYSGGPAEPASRPPwvtddsfsqkfAPGKSTTSISKQTLPRGGPAYTPAGPQ 417
Cdd:PHA03247 2716 vsatpLPPGPAAARQASPALPAAPAPP-AVPAGPATPGGPAR-----------PARPPTTAGPPAPAPPAAPAAGPPRRL 2783

                         170
                  ....*....|....*....
gi 122056614  418 VPPLARGTVQRAERFPASS 436
Cdd:PHA03247 2784 TRPAVASLSESRESLPSPW 2802

The fifth LIM domain of protein LIMPETin; The fifth LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188814 Cd Length: 52 Bit Score: 43.23 E-value: 8.11e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 441 CGHCNNVIRGPFLVAMGRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERCY 492
Cdd:cd09430    1 CSKCNKIINSGGVTYKNEPWHRECFTCTNCSKSLAGQRFTSRDEKPYCADCF 52

The LIM domains of thymus LIM protein (TLP); The LIM domain of thymus LIM protein (TLP) like proteins: This family includes the LIM domains of TLP and CRIP (Cysteine-Rich Intestinal Protein). TLP is the distant member of the CRP family of proteins. TLP has two isomers (TLP-A and TLP-B) and sharing approximately 30% with each of the three other CRPs. Like CRP1, CRP2 and CRP3/MLP, TLP has two LIM domains, connected by a flexible linker region. Unlike the CRPs, TLP lacks the nuclear targeting signal (K/R-K/R-Y-G-P-K) and is localized solely in the cytoplasm. TLP is specifically expressed in the thymus in a subset of cortical epithelial cells. TLP has a role in development of normal thymus and in controlling the development and differentiation of thymic epithelial cells. CRIP is a short LIM protein with only one LIM domain. CRIP gene is developmentally regulated and can be induced by glucocorticoid hormones during the first three postnatal weeks. The domain shows close sequence homology to LIM domain of thymus LIM protein. However, unlike the TLP proteins which have two LIM domains, the members of this family have only one LIM domain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188785 [Multi-domain] Cd Length: 53 Bit Score: 43.48 E-value: 8.35e-06

                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 122056614 454 VAMGRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERCY 492
Cdd:cd09401   15 TSLGRDWHKPCLRCEKCKKTLTPGQHSEHEGKPYCNKCY 53

The third LIM domain of Four and a half LIM domains protein (FHL); The third LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 int eracts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188732 Cd Length: 52 Bit Score: 43.09 E-value: 9.25e-06

                         10        20
                 ....*....|....*....|....*....
gi 122056614 580 WHDTCFICAVCHVNLEGQPFYSKKDRPLC 608
Cdd:cd09346   20 WHKECFVCTGCKKQLAGQRFTSRDEYPYC 48

The first LIM domain of Lhx2 and Lhx9 family; The first LIM domain of Lhx2 and Lhx9 family: Lhx2 and Lhx9 are highly homologous LHX regulatory proteins. They belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Although Lhx2 and Lhx9 are highly homologous, they seems to play regulatory roles in different organs. In animals, Lhx2 plays important roles in eye, cerebral cortex, limb, the olfactory organs, and erythrocyte development. Lhx2 gene knockout mice exhibit impaired patterning of the cortical hem and the telencephalon of the developing brain, and a lack of development in olfactory structures. Lhx9 is expressed in several regions of the developing mouse brain , the spinal cord, the pancreas, in limb mesenchyme, and in the urogenital region. Lhx9 plays critical roles in gonad development. Homozygous mice lacking functional Lhx9 alleles exhibit numerous urogenital defects, such as gonadal agenesis, infertility, and undetectable levels of testosterone and estradiol coupled with high FSH levels. Lhx9 null mice are phenotypically female, even those that are genotypically male. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188755 [Multi-domain] Cd Length: 54 Bit Score: 43.10 E-value: 9.74e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 122056614 500 CAKCNTKIMGE-VMHALRQTWHTTCFVCAACKKPFG--NSLFhMEDGEPYCEKDY 551
Cdd:cd09369    1 CAGCGEKIQDRfYLLAVDRQWHASCLKCCECRLPLDseLSCF-SRDGNIYCKEDY 54

The sixth LIM domain of protein LIMPETin; The sixth LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188816 Cd Length: 56 Bit Score: 43.23 E-value: 1.04e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 559 CHGCDFPVEA--GDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLC 608
Cdd:cd09432    1 CAACGKPITGigGTKFISFEDRHWHNDCFNCAGCRTSLVGKGFITDGGRILC 52

This family represents the LIM domain of ALP, actinin-associated LIM protein; This family represents the LIM domain of ALP, actinin-associated LIM protein. ALP contains an N-terminal PDZ domain, a C-terminal LIM domain and an ALP-subfamily-specific 34-amino-acid motif termed ALP-like motif (AM), which contains a putative consensus protein kinase C (PKC) phosphorylation site and two alpha-helices. ALP proteins are found in heart and in skeletal muscle. ALP may act as a signaling molecule which is regulated by PKC-dependent signaling. ALP plays an essential role in the development of RV (right ventricle) chamber. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188834 [Multi-domain] Cd Length: 53 Bit Score: 42.97 E-value: 1.13e-05

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 122056614 500 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCE 548
Cdd:cd09450    1 CDKCGSGIVGTVVKARDKYRHPECFVCSDCNLNLKQKGYFFVEGQLYCE 49

The LIM domain of ALP (actinin-associated LIM protein) family; This family represents the LIM domain of ALP (actinin-associated LIM protein) family. Four proteins: ALP, CLP36, RIL, and Mystique have been classified into the ALP subfamily of LIM domain proteins. Each member of the subfamily contains an N-terminal PDZ domain and a C-terminal LIM domain. Functionally, these proteins bind to alpha-actinin through their PDZ domains and bind or other signaling molecules through their LIM domains. ALP proteins have been implicated in cardiac and skeletal muscle structure, function and disease, platelet, and epithelial cell motility. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188746 [Multi-domain] Cd Length: 52 Bit Score: 42.74 E-value: 1.16e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 122056614 500 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEK 549
Cdd:cd09360    1 CDKCGNGIVGVVVKARDKNRHPECFVCADCGLNLKNKGYFFIEDELYCET 50

large tegument protein UL36; Provisional

Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 48.78 E-value: 1.21e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  278 PAAPAPKPR--VVTTASIRPSVyQPVPASTYSP-----SPGANYSPTPYTPSPAPAYTPSPAP-------------AYTP 337
Cdd:PHA03247 2570 PPRPAPRPSepAVTSRARRPDA-PPQSARPRAPvddrgDPRGPAPPSPLPPDTHAPDPPPPSPspaanepdphpppTVPP 2648

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  338 SPVPTYTPSPAPAYTPSPAPNYN-PAPSVAYSGGPAEPASRPPWVTDDSFSQKFAPGKSTTSISKQTLP----------- 405
Cdd:PHA03247 2649 PERPRDDPAPGRVSRPRRARRLGrAAQASSPPQRPRRRAARPTVGSLTSLADPPPPPPTPEPAPHALVSatplppgpaaa 2728

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 122056614  406 RGGPAYTPAGPQVPPLARGTVQRA-ERFPASSRTP 439
Cdd:PHA03247 2729 RQASPALPAAPAPPAVPAGPATPGgPARPARPPTT 2763

The second LIM domain on actin binding LIM (abLIM) proteins; The second LIM domain of actin binding LIM (abLIM) proteins: Three homologous members of the abLIM protein family have been identified; abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM consists of four tandem repeats of LIM domains and the C-terminal of acting binding LIM protein is a villin headpiece domain, which has strong actin binding activity. The abLIM-1, which is expressed in retina, brain, and muscle tissue, has been indicated to function as a tumor suppressor. AbLIM-2 and -3, mainly expressed in muscle and neuronal tissue, bind to F-actin strongly. They may serve as a scaffold for signaling modules of the actin cytoskeleton and thereby modulate transcription. It has shown that LIM domains of abLIMs interact with STARS (striated muscle activator of Rho signaling), which directly binds actin and stimulates serum-response factor (SRF)-dependent transcription. All LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188714 Cd Length: 56 Bit Score: 42.72 E-value: 1.25e-05

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 122056614 557 TKCHGCDFPVEagDKFIEALGHTWHDTCFICAVChvnleGQPF 599
Cdd:cd09328    2 TKCDSCQDFVE--GEVVSALGKTYHPKCFVCSVC-----RQPF 37

The first LIM domain of Lhx3b; The first LIM domain of Lhx3b. Lhx3b is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx3b is one of the two isoforms of Lhx3. The Lhx3 gene is expressed in the ventral spinal cord, the pons, the medulla oblongata, and the pineal gland of the developing nervous system during mouse embryogenesis, and transcripts are found in the emergent pituitary gland. Lhx3 functions in concert with other transcription factors to specify interneuron and motor neuron fates during development. Lhx3 proteins have been demonstrated to directly bind to the promoters of several pituitary hormone gene promoters. The Lhx3 gene encodes two isoforms, LHX3a and LHX3b that differ in their amino-terminal sequences, where Lhx3a has longer N-terminal. They show differential activation of pituitary hormone genes and distinct DNA binding properties. In human, Lhx3a trans-activated the alpha-glycoprotein subunit promoter and genes containing a high-affinity Lhx3 binding site more effectively than the hLhx3b isoform. In addition, hLhx3a induce transcription of the TSHbeta-subunit gene by acting on pituitary POU domain factor, Pit-1, while hLhx3b does not. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188851 [Multi-domain] Cd Length: 55 Bit Score: 43.00 E-value: 1.30e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 439 PLCGHCNNVIRGPFLV-AMGRSWHPEEFTCAYCKTSLADVCFvEEQNNVYCE 489
Cdd:cd09467    2 PLCAGCNQHIVDRFILkVLDRHWHSKCLKCSDCQTQLAEKCF-SRGDSVYCK 52

The fourth LIM domain of Four and a half LIM domains protein (FHL); The fourth LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 interacts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188733 Cd Length: 56 Bit Score: 42.72 E-value: 1.36e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 122056614 441 CGHCNNVIRGP----FLVAMGRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERC 491
Cdd:cd09347    1 CAACTKPITGLggakFISFEERQWHSDCFNCGKCSVSLVGQGFLTQRDEILCPEC 55

DNA polymerase III subunits gamma and tau; Validated

Pssm-ID: 236090 [Multi-domain] Cd Length: 824 Bit Score: 48.06 E-value: 1.42e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 308 PSPGANYSPTPYTPSPAPAYTPSPAPAYTPSPVPTYTPSPAPAYTPSPAPNYNPAPSVAYSGGPAEPASRPPWVTDDSFS 387
Cdd:PRK07764 590 PAPGAAGGEGPPAPASSGPPEEAARPAAPAAPAAPAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGW 669

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 388 QKFAPGKSTTSISKQTLPRGGPAYTPAGPQVPPLARGTVQRAERFPASSRTP 439
Cdd:PRK07764 670 PAKAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPAGQADDPAAQP 721

The first LIM domain of Lhx4; The first LIM domain of Lhx4. Lhx4 belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. LHX4 plays essential roles in pituitary gland and nervous system development. In mice, the lhx4 gene is expressed in the developing hindbrain, cerebral cortex, pituitary gland, and spinal cord. LHX4 shows significant sequence similarity to LHX3, particularly to isoforms Lhx3a. In gene regulation experiments, the LHX4 protein exhibits regulation roles towards pituitary genes, acting on their promoters/enhancers. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188852 Cd Length: 52 Bit Score: 42.65 E-value: 1.47e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 122056614 500 CAKCNTKIMGE-VMHALRQTWHTTCFVCAACKKPFGNSLFHmEDGEPYCEKDY 551
Cdd:cd09468    1 CAGCNQHILDKfILKVLDRHWHSSCLKCADCQMQLAERCFS-RAGNVYCKEDF 52

DNA polymerase III subunits gamma and tau; Provisional

Pssm-ID: 237864 [Multi-domain] Cd Length: 585 Bit Score: 47.88 E-value: 1.47e-05

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 122056614 300 PVPASTysPSPGANYSPTPYTPSPAPAYTPSPAPAYTPSPVPTyTPSPAPAYTPSPAPNYNPAPSVAYSGGPAEPASRP 378
Cdd:PRK14950 362 PVPAPQ--PAKPTAAAPSPVRPTPAPSTRPKAAAAANIPPKEP-VRETATPPPVPPRPVAPPVPHTPESAPKLTRAAIP 437

The third LIM domain of protein PINCH; The third LIM domain of protein PINCH: PINCH plays pivotal roles in the assembly of focal adhesions (FAs), regulating diverse functions in cell adhesion, growth, and differentiation through LIM-mediated protein-protein interactions. PINCH comprises an array of five LIM domains that interact with integrin-linked kinase (ILK), Nck2 (also called Nckbeta or Grb4) and other interaction partners. These interactions are essential for triggering the FA assembly and for relaying diverse mechanical and biochemical signals between Cell-extracellular matrix and the actin cytoskeleton. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188719 Cd Length: 51 Bit Score: 42.36 E-value: 1.58e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 441 CGHCNNVIRGPFLVAMGRSWHPEEFTCAYCKTSLADVCfVEEQNNVYCERCY 492
Cdd:cd09333    1 CQKCHAIIEEQHLKFKGDPYHPYHFNCANCGKELTADA-RELKGELYCLRCH 51

The fourth LIM domain of Four and a half LIM domains protein 3 (FHL3); The fourth LIM domain of Four and a half LIM domains protein 3 (FHL3): FHL3 is highly expressed in the skeleton and cardiac muscles and possesses the transactivation and repression activities. FHL3 interacts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. Moreover, FHL3 interacts with alpha- and beta-subunits of the muscle alpha7beta1 integrin receptor. FHL3 was also proved to possess the auto-activation ability and was confirmed that the second zinc finger motif in fourth LIM domain was responsible for the auto-activation of FHL3. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188818 Cd Length: 56 Bit Score: 42.44 E-value: 1.62e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 122056614 559 CHGCDFPVEA--GDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCK 609
Cdd:cd09434    1 CAACNKPITGfgGGKYVSFEDRQWHQPCFKCSRCSVSLVGAGFFPDGDQILCR 53

The first LIM domain of protein PINCH; The first LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188717 Cd Length: 59 Bit Score: 42.70 E-value: 1.63e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 122056614 559 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKKHAHT 614
Cdd:cd09331    1 CERCREGFEPDEKIVNSNGELYHEQCFVCAQCFQPFPDGLFYEFEGRKYCEHDFQV 56

transcriptional regulator ICP4; Provisional

Pssm-ID: 223039 [Multi-domain] Cd Length: 1352 Bit Score: 48.24 E-value: 1.71e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  277 GPAAPAPKPRVVTTASIRPSVYQPV-PASTYSPSPGANySPTPYTPSPAP--AYTPSPAPAYTPSPVPTYTPSPAPAYTP 353
Cdd:PHA03307   74 GPGTEAPANESRSTPTWSLSTLAPAsPAREGSPTPPGP-SSPDPPPPTPPpaSPPPSPAPDLSEMLRPVGSPGPPPAASP 152

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  354 SPAPNYNPAP--SVAYSGGPAEPASRPPWVTDDSFSQKFAPGKSTTSISKQTLP--RGGPAYTPAGPQVPPLARGTVQRA 429
Cdd:PHA03307  153 PAAGASPAAVasDAASSRQAALPLSSPEETARAPSSPPAEPPPSTPPAAASPRPprRSSPISASASSPAPAPGRSAADDA 232

                         170       180
                  ....*....|....*....|.
gi 122056614  430 ERFPASSRTPLCGHCNNVIRG 450
Cdd:PHA03307  233 GASSSDSSSSESSGCGWGPEN 253

PDZ domain 1 of glutamate receptor-interacting protein 1 (GRIP1) and GRIP2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) binding proteins GRIP1 (ABP/GRIP2) and GRIP2, and related domains. GRIP1 and GRIP2 each have 7 PDZ domains. The interaction of GRIP1 and GRIP2 with GluA2/3 (AMPAR subunit) regulates AMPAR trafficking and synaptic targeting. GRIP1 has an essential role in regulating AMPAR trafficking during synaptic plasticity and learning and memory. GRIP1 and GRIP2 interact with a variety of other proteins associated with protein trafficking and internalization, for example GRIP1 also interacts with KIF5 (also known as kinesin 1), EphB receptors, scaffold protein liprin-alpha, and the rasGEF GRASP-1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This GRIP family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467175 [Multi-domain] Cd Length: 83 Bit Score: 43.17 E-value: 1.78e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 122056614  12 PWGFRLQGGKDFNMPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSL 78
Cdd:cd06687   12 TLGLTVSGGIDKDGKPRVSNLRPGGIAARSdQLNVGDYIKSVNGIRTTKLRHDEIISLLKNVGERVVL 79

The second LIM domain of LIMK2 (LIM domain Kinase 2); The second LIM domain of LIMK2 (LIM domain Kinase 2): LIMK2 is a member of the LIMK protein family, which comprises LIMK1 and LIMK2. LIMK contains two LIM domains, a PDZ domain, and a kinase domain. LIMK is involved in the regulation of actin polymerization and microtubule disassembly. LIMK influences architecture of the actin cytoskeleton by regulating the activity of the cofilin family proteins cofilin1, cofilin2, and destrin. The mechanism of the activation is to phosphorylates cofilin on serine 3 and inactivates its actin-severing activity, altering the rate of actin depolymerisation. LIMK activity is activated by phosphorylation of a threonine residue within the activation loop of the kinase by p21-activated kinases 1 and 4 and by Rho kinase. LIMKs can function in both cytoplasm and nucleus. Both LIMK1 and LIMK2 can act in the nucleus to suppress Rac/Cdc42-dependent cyclin D1 expression. LIMK2 is expressed in all tissues. While LIMK1 localizes mainly at focal adhesions, LIMK2 is found in cytoplasmic punctae, suggesting that they may have different cellular functions. The activity of LIM kinase 2 to regulate cofilin phosphorylation is inhibited by the direct binding of Par-3. LIMK2 activation promotes cell cycle progression. The phenotype of Limk2 knockout mice shows a defect in spermatogenesis. The LIM domains have been shown to play an important role in regulating kinase activity and likely also contribute to LIMK function by acting as sites of protein-to-protein interactions. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188849 [Multi-domain] Cd Length: 59 Bit Score: 42.62 E-value: 1.78e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 122056614 440 LCGHCNNVIRGPFLVAMGRSWHPEEFTCAYCKTSL--ADVCFVEEQNNVYCERCY 492
Cdd:cd09465    5 LCHGCSLLMTGPAMVAGEYKYHPECFACMSCKVIIedGDTYALVQHTTLYCGKCH 59

The sixth LIM domain of protein LIMPETin; The sixth LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188816 Cd Length: 56 Bit Score: 42.46 E-value: 1.80e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 122056614 441 CGHCNNVIRG----PFLVAMGRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERC 491
Cdd:cd09432    1 CAACGKPITGiggtKFISFEDRHWHNDCFNCAGCRTSLVGKGFITDGGRILCPDC 55

The second LIM domain of Zyxin; The second LIM domain of Zyxin: Zyxin exhibits three copies of the LIM domain, an extensive proline-rich domain and a nuclear export signal. Localized at sites of cellsubstratum adhesion in fibroblasts, Zyxin interacts with alpha-actinin, members of the cysteine-rich protein (CRP) family, proteins that display Src homology 3 (SH3) domains and Ena/VASP family members. Zyxin and its partners have been implicated in the spatial control of actin filament assembly as well as in pathways important for cell differentiation. In addition to its functions at focal adhesion plaques, recent work has shown that zyxin moves from the sites of cell contacts to the nucleus, where it directly participates in the regulation of gene expression. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors o r scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188739 [Multi-domain] Cd Length: 60 Bit Score: 42.61 E-value: 1.83e-05

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 122056614 559 CHGCDFPVEagDKFIEALGHTWHDTCFICAVCHVNLEGQPF 599
Cdd:cd09353    1 CAVCDQKIT--DRMLKATGKSYHPQCFTCVVCKCPLEGESF 39

The third LIM domain of Four and a half LIM domains protein (FHL); The third LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 int eracts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188732 Cd Length: 52 Bit Score: 42.31 E-value: 1.89e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 441 CGHCNNVIRGPFLVAMGRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERCY 492
Cdd:cd09346    1 CAKCKKAITSGGVTYRDQPWHKECFVCTGCKKQLAGQRFTSRDEYPYCVDCF 52

The first LIM domain of Ajuba-like proteins; The first LIM domain of Ajuba-like proteins: Ajuba like LIM protein family includes three highly homologous proteins Ajuba, Limd1, and WTIP. Members of the family contain three tandem C-terminal LIM domains and a proline-rich N-terminal region. This family of proteins functions as scaffolds, participating in the assembly of numerous protein complexes. In the cytoplasm, Ajuba binds Grb2 to modulate serum-stimulated ERK activation. Ajuba also recruits the TNF receptor-associated factor 6 (TRAF6) to p62 and activates PKCKappa activity. Ajuba interacts with alpha-catenin and F-actin to contribute to the formation or stabilization of adheren junctions by linking adhesive receptors to the actin cytoskeleton. Although Ajuba is a cytoplasmic protein, it can shuttle into the nucleus. In nucleus, Ajuba functions as a corepressor for the zinc finger-protein Snail. It binds to the SNAG repression domain of Snail through its LIM region. Arginine methyltransferase-5 (Prmt5), a protein in the complex, is recruited to Snai l through an interaction with Ajuba. This ternary complex functions to repress E-cadherin, a Snail target gene. In addition, Ajuba contains functional nuclear-receptor interacting motifs and selectively interacts with retinoic acid receptors (RARs) and rexinoid receptor (RXRs) to negatively regulate retinoic acid signaling. Wtip, the Wt1-interacting protein, was originally identified as an interaction partner of the Wilms tumour protein 1 (WT1). Wtip is involved in kidney and neural crest development. Wtip interacts with the receptor tyrosine kinase Ror2 and inhibits canonical Wnt signaling. LIMD1 was reported to inhibit cell growth and metastases. The inhibition may be mediated through an interaction with the protein barrier-to-autointegration (BAF), a component of SWI/SNF chromatin-remodeling protein; or through the interaction with retinoblastoma protein (pRB), resulting in inhibition of E2F-mediated transcription, and expression of the majority of genes with E2F1- responsive elements. Recently, Limd1 was shown to interact with the p62/sequestosome protein and influence IL-1 and RANKL signaling by facilitating the assembly of a p62/TRAF6/a-PKC multi-protein complex. The Limd1-p62 interaction affects both NF-kappaB and AP-1 activity in epithelial cells and osteoclasts. Moreover, LIMD1 functions as tumor repressor to block lung tumor cell line in vitro and in vivo. Recent studies revealed that LIM proteins Wtip, LIMD1 and Ajuba interact with components of RNA induced silencing complexes (RISC) as well as eIF4E and the mRNA m7GTP cap-protein complex and are required for microRNA-mediated gene silencing. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188738 Cd Length: 54 Bit Score: 42.42 E-value: 1.91e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 559 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKK 610
Cdd:cd09352    1 CVKCGKGVYGASQACQAMGNLYHTNCFTCCSCGRTLRGKAFYNVNGKVYCEE 52

PDZ domain 3 of the canonical isoform 1 of PDZ domain containing 7 (PDZD7), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of the long isoform 1 of PDZD7, and related domains. PDZD7 is critical for the organization of the Usher syndrome type 2 (USH2) complex. Usher syndrome is the leading cause of hereditary sensory deaf-blindness in humans; USH2 is the most common sub-type. Formation of the USH2 complex is based upon heterodimerization between PDZD7 and whirlin (another PDZ domain-containing protein) and a subsequent dynamic interplay between USH2 proteins via their multiple PDZ domains. The PDZD7 PDZ2 domain binds GPR98 (also known as VLGR1) and usherin (USH2A). PDZD7 and whirlin form heterodimers through their multiple PDZ domains; whirlin and PDZD7 interact with usherin and GPR98 to form an interdependent ankle link complex. PDZD7 also interacts with myosin VIIa and can also form homodimers through its PDZ2 domain. Various isoforms of PDZD7 produced by alternative splicing have been identified; this subgroup includes the third PDZ domain of the canonical isoform of PDZD7- isoform 1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD7-like family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467233 [Multi-domain] Cd Length: 89 Bit Score: 43.58 E-value: 1.92e-05

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 122056614  14 GFRLQGGKDF-NMPLT-ISRITPGSKAAQSQ-LSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNlsltlqKSKRPIPI 89
Cdd:cd06751   14 GISISGGIESkVQPVVkIEKIFPGGAAALSGnLKAGYELVSVDGESLQQVTHQQAVDIIRRAYSN------KSKEPMEI 86

The LIM domains of Cysteine Rich Protein (CRP) family; The LIM domains of Cysteine Rich Protein (CRP) family: Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to a short glycine-rich repeats (GRRs). The known CRP family members include CRP1, CRP2, and CRP3/MLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription control, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. CRP1, CRP2, and CRP3/MLP are involved in promoting protein assembly along the actin-based cytoskeleton. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188712 Cd Length: 53 Bit Score: 42.20 E-value: 1.95e-05

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 122056614 500 CAKCNTKI-MGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYC 547
Cdd:cd09326    1 CPRCGKSVyAAEEVIAAGKSWHKSCFTCAVCNKRLDSTTLAEHDGEIYC 49

The second LIM domain of Lhx2 and Lhx9 family; The second LIM domain of Lhx2 and Lhx9 family: Lhx2 and Lhx9 are highly homologous LHX regulatory proteins. They belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Although Lhx2 and Lhx9 are highly homologous, they seems to play regulatory roles in different organs. In animals, Lhx2 plays important roles in eye, cerebral cortex, limb, the olfactory organs, and erythrocyte development. Lhx2 gene knockout mice exhibit impaired patterning of the cortical hem and the telencephalon of the developing brain, and a lack of development in olfactory structures. Lhx9 is expressed in several regions of the developing mouse brain, the spinal cord, the pancreas, in limb mesenchyme, and in the urogenital region. Lhx9 plays critical roles in gonad development. Homozygous mice lacking functional Lhx9 alleles exhibit numerous urogenital defects, such as gonadal agenesis, infertility, and undetectable levels of testosterone and estradiol coupled with high FSH levels. Lhx9 null mice are phenotypically female, even those that are genotypically male. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188763 Cd Length: 59 Bit Score: 42.26 E-value: 2.27e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 122056614 500 CAKCNTKIMGE--VMHALRQTWHTTCFVCAACKKPF-GNSLFHMEDGEPYCEKDY 551
Cdd:cd09377    5 CARCHLGISASelVMRARDLVFHLNCFTCATCNKPLtKGDHFGMRDGLVYCRLHY 59

PDZ domain 3 of human discs large homolog 1 (Dlg1), Dlg2, and Dlg4, Drosophila disc large (Dlg), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of Drosophila Dlg1, human Dlg1, 2, and 4 and related domains. Dlg1 (also known as synapse-associated protein Dlg197; SAP-97), Dlg2 (also known as channel-associated protein of synapse-110; postsynaptic density protein 93, PSD-93), Dlg4 (also known as postsynaptic density protein 95, PSD-95; synapse-associated protein 90, SAP-90) each have 3 PDZ domains and belong to the membrane-associated guanylate kinase family. Dlg1 regulates antigen receptor signaling and cell polarity in lymphocytes, B-cell proliferation and antibody production, and TGFalpha bioavailability; its PDZ3 domain binds pro-TGFalpha, and its PDZ2 domain binds the TACE metalloprotease responsible for cleaving pro-TGFalpha to a soluble form. Dlg2 is involved in N-methyl-D-aspartate (NMDA) receptor signaling, regulating surface expression of NMDA receptors in dorsal horn neurons of the spinal cord; it interacts with NMDA receptor subunits and with Shaker-type K+ channel subunits to cluster into a channel complex. The Dlg4 PDZ1 domain binds NMDA receptors, and its PDZ2 domain binds neuronal nitric oxide synthase (nNOS), forming a complex in neurons. The Drosophila Scribble complex (Scribble, Dlg, and lethal giant larvae) plays a role in apico-basal cell polarity, and in other forms of polarity, including regulation of the actin cytoskeleton, cell signaling and vesicular trafficking, and in tumor development; postsynaptic targeting of Drosophila DLG requires interactions mediated by the first two PDZ domains. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Dlg-like family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467257 [Multi-domain] Cd Length: 91 Bit Score: 43.11 E-value: 2.29e-05

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 122056614   5 VTLT-GPGPWGFRLQGGKDfNMPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQ 81
Cdd:cd06795    5 IVLHkGSTGLGFNIVGGED-GEGIFISFILAGGPADLSgELRRGDQILSVNGVDLRNATHEQAAAALKNAGQTVTIIAQ 82

large tegument protein UL36; Provisional

Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 48.01 E-value: 2.29e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  278 PAAPAPKPRVVTTASIRPSVYQPvPASTYSPSPGANYSPTPYTPSPA-PAYTPSPAPAYTPSPVPTYTPSPAPAYTPSPA 356
Cdd:PHA03247 2872 AAKPAAPARPPVRRLARPAVSRS-TESFALPPDQPERPPQPQAPPPPqPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPA 2950

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 122056614  357 PNYNPAPSVAYSGGPAEPASR---PPWVTDDSFSQKFAPGKSTTSISKQTLPR 406
Cdd:PHA03247 2951 GAGEPSGAVPQPWLGALVPGRvavPRFRVPQPAPSREAPASSTPPLTGHSLSR 3003

The second LIM domain of Prickle; The second LIM domain of Prickle: Prickle contains three C-terminal LIM domains and a N-terminal PET domain. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). PCP establishment requires the conserved Frizzled/Dishevelled PCP pathway. Prickle interacts with Dishevelled, thereby modulating Frizzled/Dishevelled activity and PCP signaling. Two forms of prickles have been identified; namely prickle 1 and prickle 2. Prickle 1 and prickle 2 are differentially expressed. While prickle 1 is expressed in fetal heart and hematological malignancies, prickle 2 is found in fetal brain, adult cartilage, pancreatic islet, and some types of timorous cells. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188802 Cd Length: 56 Bit Score: 42.03 E-value: 2.31e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 122056614 439 PLCGHCNNVIRGPFLV-AMGRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERCYE 493
Cdd:cd09418    1 PRCSACDEIIFADECTeAEGRHWHMKHFCCFECECQLGGQRYIMREGRPYCCHCFE 56

The first LIM domain of Enigma; The first LIM domain of Enigma: Enigma was initially characterized in humans as a protein containing three LIM domains at the C-terminus and a PDZ domain at N-terminus. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes such as mitogenic activity, insulin related actin organization, and glucose metabolism. Enigma is expressed in multiple tissues, such as skeletal muscle, heart, bone and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188836 [Multi-domain] Cd Length: 52 Bit Score: 42.09 E-value: 2.43e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 500 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 551
Cdd:cd09452    1 CAQCNKIIRGRYLVALGRSYHPEEFTCSQCKKVLDEGGFFEEKGSIFCPKCY 52

The fourth LIM domain of Leupaxin; The fourth LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188796 [Multi-domain] Cd Length: 52 Bit Score: 42.03 E-value: 2.50e-05

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 122056614 500 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYC 547
Cdd:cd09412    1 CGSCGLPITGRCISALGRKFHPEHFVCAFCLRPLTQGSFKEQSGKPYC 48

The fourth LIM domain of protein LIMPETin; The fourth LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the Testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188809 Cd Length: 54 Bit Score: 42.04 E-value: 2.55e-05

                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 122056614 457 GRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERCY 492
Cdd:cd09425   19 GQQWHEKCFCCCECKQPIGTKSFIPKDDDVYCVPCY 54

The second LIM domain of Lrg1p, a LIM and RhoGap domain containing protein; The second LIM domain of Lrg1p, a LIM and RhoGap domain containing protein: The members of this family contain three tandem repeats of LIM domains and a Rho-type GTPase activating protein (RhoGap) domain. Lrg1p is a Rho1 GTPase-activating protein required for efficient cell fusion in yeast. Lrg1p-GAP domain strongly and specifically stimulates the GTPase activity of Rho1p, a regulator of beta (1-3)-glucan synthase in vitro. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188778 [Multi-domain] Cd Length: 53 Bit Score: 41.96 E-value: 2.63e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 122056614 500 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFG-NSLFHMEDGEPYCEKDY 551
Cdd:cd09392    1 CFKCGGALRGSYITALGRKYHVEHFTCSVCPTVFGpNDSYYEHEGKIYCHYHY 53

The first LIM domain of LIMK (LIM domain Kinase ); The first LIM domain of LIMK (LIM domain Kinase ): LIMK protein family is comprised of two members LIMK1 and LIMK2. LIMK contains two LIM domains, a PDZ domain and a kinase domain. LIMK is involved in the regulation of actin polymerization and microtubule disassembly. LIMK influences architecture of the actin cytoskeleton by regulating the activity of the cofilin family proteins cofilin1, cofilin2, and destrin. The mechanism of the activation is to phosphorylates cofilin on serine 3 and inactivates its actin-severing activity, and altering the rate of actin depolymerisation. LIMKs can function in both cytoplasm and nucleus and are expressed in all tissues. Both LIMK1 and LIMK2 can act in the nucleus to suppress Rac/Cdc42-dependent cyclin D1 expression. However, LIMK1 and LIMk2 have different cellular locations. While LIMK1 localizes mainly at focal adhesions, LIMK2 is found in cytoplasmic punctae, suggesting that they may have different cellular functions. The LIM domains of LIMK have been shown to play an important role in regulating kinase activity and likely also contribute to LIMK function by acting as sites of protein-to-protein interactions. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188750 [Multi-domain] Cd Length: 53 Bit Score: 42.09 E-value: 2.68e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 122056614 559 CHGCDFPVEAGDkFIEALGHTWHDTCFICAVCHVNLEGQpfYSKKDRPL-CKKH 611
Cdd:cd09364    1 CAGCRGKILDSQ-YVQALNQDWHCDCFRCSVCSDSLSNW--YFEKDGKLyCRKD 51

The fourth LIM domain of protein LIMPETin; The fourth LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the Testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188809 Cd Length: 54 Bit Score: 42.04 E-value: 2.68e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 122056614 559 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLC 608
Cdd:cd09425    1 CDGCGEIFRAGMKKMEYKGQQWHEKCFCCCECKQPIGTKSFIPKDDDVYC 50

The second LIM domain of Cysteine Rich Protein 3 (CRP3/MLP); The second LIM domain of Cysteine Rich Protein 3 (CRP3/MLP): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network.CRP3 also called Muscle LIM Protein (MLP), which is a striated muscle-specific factor that enhances myogenic differentiation. The second LIM domain of CRP3/MLP interacts with cytoskeletal protein beta-spectrin. CRP3/MLP also interacts with the basic helix-loop-helix myogenic transcription factors MyoD, myogenin, and MRF4 thereby increasing their affinity for specific DNA regulatory elements. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188866 [Multi-domain] Cd Length: 54 Bit Score: 41.92 E-value: 2.79e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 122056614 488 CERCYEQFFAPlcakcnTKIMGEvmhalRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 551
Cdd:cd09482    1 CPRCGKSVYAA------EKVMGG-----GKPWHKTCFRCAICGKSLESTTVTDKDGELYCKVCY 53

DNA polymerase III subunits gamma and tau; Validated

Pssm-ID: 236090 [Multi-domain] Cd Length: 824 Bit Score: 47.29 E-value: 2.83e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 278 PAAPAPKPRVVTTASIRPSVYQPVPASTYSPSPGANYSPTPYTPSPAPAYTPSPAPAYTPSPVPT-YTPSPAPAYTPSPA 356
Cdd:PRK07764 615 PAAPAAPAAPAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKAGGAAPAaPPPAPAPAAPAAPA 694

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 357 PnynPAPSVAYSGGPAEPASRP---PWVTDDSFSQKFAPGKSTTsiSKQTLPRGGPAYTPAGPQVPPLARGTVQRAERFP 433
Cdd:PRK07764 695 G---AAPAQPAPAPAATPPAGQaddPAAQPPQAAQGASAPSPAA--DDPVPLPPEPDDPPDPAGAPAQPPPPPAPAPAAA 769


                 ....*.
gi 122056614 434 ASSRTP 439
Cdd:PRK07764 770 PAAAPP 775

Domain of unknown function (DUF3432); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is about 100 amino acids in length. This domain is found associated with pfam00096. This domain has two conserved sequence motifs: YPSPV and PSP.

Pssm-ID: 403204 [Multi-domain] Cd Length: 98 Bit Score: 43.17 E-value: 2.99e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 122056614  310 PGANYSPTPYTPSPAPAYTPSPAPAYTPSPVPTYTPSPAPAYTPSPAPNYNPAPSVAYSGGPAEPA 375
Cdd:pfam11914   5 PASAVSSISSYSSSVTTSYPSPITTSYPSPVSTSYSSPVPSSYPSPVHTSFPSPSIATTYPSVTTT 70

The fifth LIM domain of protein LIMPETin; The fifth LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188814 Cd Length: 52 Bit Score: 41.69 E-value: 3.08e-05

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 122056614 500 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYC 547
Cdd:cd09430    1 CSKCNKIINSGGVTYKNEPWHRECFTCTNCSKSLAGQRFTSRDEKPYC 48

The second LIM domain of Cysteine Rich Protein 2 (CRP2); The second LIM domain of Cysteine Rich Protein 2 (CRP2): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network.CRP3 also called Muscle LIM Protein (MLP), which is a striated muscle-specific factor that enhances myogenic differentiation. The second LIM domain of CRP3/MLP interacts with cytoskeletal protein beta-spectrin. CRP3/MLP also interacts with the basic helix-loop-helix myogenic transcription factors MyoD, myogenin, and MRF4 thereby increasing their affinity for specific DNA regulatory elements. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188871 [Multi-domain] Cd Length: 54 Bit Score: 41.63 E-value: 3.24e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 122056614 500 CAKCNTKI-MGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 551
Cdd:cd09840    1 CSRCGDSVyAAEKIMGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCY 53

The first LIM domain of Arrowhead (AWH); The first LIM domain of Arrowhead (AWH): Arrowhead belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. During embryogenesis of Drosophila, Arrowhead is expressed in each abdominal segment and in the labial segment. Late in embryonic development, expression of arrowhead is refined to the abdominal histoblasts and salivary gland imaginal ring cells themselves. The Arrowhead gene required for establishment of a subset of imaginal tissues: the abdominal histoblasts and the salivary gland imaginal rings. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188759 [Multi-domain] Cd Length: 54 Bit Score: 41.59 E-value: 3.30e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 122056614 559 CHGCDFPVEagDKFI-EALGHTWHDTCFICAVCHVNLEGQPF-YSKKDRPLCK 609
Cdd:cd09373    1 CTGCGEPIT--DRFLlKVSGRSWHVSCLRCCVCQTPLERQPScFTRDRQIYCK 51

The second LIM domain of Testin-like family; The second LIM domain of Testin-like family: This family includes testin, prickle, dyxin and LIMPETin. Structurally, testin and prickle proteins contain three LIM domains at C-terminal; LIMPETin has six LIM domains; and dyxin presents only two LIM domains. However, all members of the family contain a PET protein-protein interaction domain. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). Dyxin involves in lung and heart development by interaction with GATA6 and blocking GATA6 activated target genes. LIMPETin might be the recombinant product of genes coding testin and four and half LIM proteins and its function is not well understood. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188727 Cd Length: 56 Bit Score: 41.82 E-value: 3.31e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 122056614 498 PLCAKCNTKI-MGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYC 547
Cdd:cd09341    1 PRCAACDELIfSGEYTQAEGKNWHLKHFCCFQCDEPLGGQRYVLREGKPYC 51

The first LIM domain of an Enigma subfamily with unknown function; The first LIM domain of an Enigma subfamily with unknown function: The Enigma LIM domain family is comprised of three characterized members: Enigma, ENH and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. They serve as adaptor proteins, where the PDZ domain tethers the protein to the cytoskeleton and the LIM domains, recruit signaling proteins to implement corresponding functions. The members of the Enigma family have been implicated in regulating or organizing cytoskeletal structure, as well as involving multiple signaling pathways. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188839 Cd Length: 54 Bit Score: 41.67 E-value: 3.38e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 122056614 500 CAKCNTKIMGEVMHALRQTWHTTCFVCA--ACKKPFGNSLFHMEDGEPYCE 548
Cdd:cd09455    1 CESCNQQIRGPFITALGKIWCPDHFICAnaSCRRPLQDIGFVEEKGQLYCE 51

PDZ domain 1 of Drosophila Scribble, human Scribble homolog, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of Drosophila Scribble (also known as LAP4), human Scribble homolog (also known as hScrib, LAP4, CriB1, ScrB1 and Vartul), and related domains. They belong to the LAP family, which describes proteins that contain either one or four PDZ domains and 16 LRRs (leucine-rich repeats) and function in controlling cell shape, size and subcellular protein localization. In Drosophila, the Scribble complex, comprising Scribble, discs large, and lethal giant larvae, plays a role in apico-basal cell polarity, in other forms of polarity, including regulation of the actin cytoskeleton, cell signaling and vesicular trafficking, and in tumor development. Mammalian Scribble is important in many aspects of cancer development. Scribble and its homologs can be downregulated or overexpressed in cancer; they have a role in cancer beyond their function in loss of cell polarity. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Scribble-like family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467188 [Multi-domain] Cd Length: 87 Bit Score: 42.65 E-value: 3.43e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  10 PGPWGFRLQGGKDfNMP-------LTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQK 82
Cdd:cd06704    9 TGGLGISIAGGKG-STPykgddegIFISRVTEGGPAAKAGVRVGDKLLEVNGVDLVDADHHEAVEALKNSGNTVTMVVLR 87

envelope glycoprotein C; Provisional

Pssm-ID: 165527 [Multi-domain] Cd Length: 566 Bit Score: 46.65 E-value: 3.51e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 281 PAPKPRVVTTASIR---PSVyQPVPASTYSPSPG-ANYSPTPYTPSPAPAYTPSPAPAYTPSPVPTY--TPSPAPAYTPS 354
Cdd:PHA03269  25 NIPIPELHTSAATQkpdPAP-APHQAASRAPDPAvAPTSAASRKPDLAQAPTPAASEKFDPAPAPHQaaSRAPDPAVAPQ 103

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 122056614 355 PAPNYNPAPSVAYSGGP-AEPASRPPWVTddSFSQKFAPGKSTTSISKQTL 404
Cdd:PHA03269 104 LAAAPKPDAAEAFTSAAqAHEAPADAGTS--AASKKPDPAAHTQHSPPPFA 152

PDZ domain 3 of Drosophila Scribble, human Scribble homolog, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of Drosophila Scribble (also known as LAP4), human Scribble homolog (also known as hScrib, LAP4, CriB1, ScrB1 and Vartul), and related domains. They belong to the LAP family, which describes proteins that contain either one or four PDZ domains and 16 LRRs (leucine-rich repeats) and function in controlling cell shape, size and subcellular protein localization. In Drosophila, the Scribble complex, comprising Scribble, discs large, and lethal giant larvae, plays a role in apico-basal cell polarity, in other forms of polarity, including regulation of the actin cytoskeleton, cell signaling and vesicular trafficking, and in tumor development. Mammalian Scribble is important in many aspects of cancer development. Scribble and its homologs can be downregulated or overexpressed in cancer; they have a role in cancer beyond their function in loss of cell polarity. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Scribble-like family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467186 [Multi-domain] Cd Length: 89 Bit Score: 42.63 E-value: 3.52e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  11 GPWGFRLQGGKD-----F--NMP-LTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQK 82
Cdd:cd06702   10 GPLGLSIVGGSDhsshpFgvDEPgIFISKVIPDGAAAKSGLRIGDRILSVNGKDLRHATHQEAVSALLSPGQEIKLLVRH 89

The first LIM domain of Thyroid receptor-interacting protein 6 (TRIP6); The first LIM domain of Thyroid receptor-interacting protein 6 (TRIP6): TRIP6 is a member of the zyxin LIM protein family and contains three LIM zinc-binding domains at the C-terminal. TRIP6 protein localizes to focal adhesion sites and along actin stress fibers. Recruitment of this protein to the plasma membrane occurs in a lysophosphatidic acid (LPA)-dependent manner. TRIP6 recruits a number of molecules involved in actin assembly, cell motility, survival and transcriptional control. The function of TRIP6 in cell motility is regulated by Src-dependent phosphorylation at a Tyr residue. The phosphorylation activates the coupling to the Crk SH2 domain, which is required for the function of TRIP6 in promoting lysophosphatidic acid (LPA)-induced cell migration. TRIP6 can shuttle to the nucleus to serve as a coactivator of AP-1 and NF-kappaB transcriptional factors. Moreover, TRIP6 can form a ternary complex with the NHERF2 PDZ protein and LPA2 receptor to regulate LPA-induced activation of ERK and AKT, rendering cells resistant to chemotherapy. Recent evidence shows that TRIP6 antagonizes Fas-Induced apoptosis by enhancing the antiapoptotic effect of LPA in cells. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188736 Cd Length: 54 Bit Score: 41.62 E-value: 3.54e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 122056614 500 CAKCNTKIMGEV--MHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 551
Cdd:cd09350    1 CGRCGENVVGEGtgCTAMDQVFHVDCFTCMTCNGKLRGQPFYAVEKKAYCEPCY 54

The second LIM domain of lipoma preferred partner (LPP); The second LIM domain of lipoma preferred partner (LPP): LPP is a member of the zyxin LIM protein family and contains three LIM zinc-binding domains at the C-terminal and proline-rich region at the N-terminal. LPP initially identified as the most frequent translocation partner of HMGA2 (High Mobility Group A2) in a subgroup of benign tumors of adipose tissue (lipomas). It was also shown to be rearranged in a number of other soft tissues, as well as in a case of acute monoblastic leukemia. In addition to its involvement in tumors, LPP was inedited as a smooth muscle restricted LIM protein that plays an important role in SMC migration. LPP is localized at sites of cell adhesion, cell-cell contacts and transiently in the nucleus. In nucleus, it acts as a coactivator for the ETS domain transcription factor PEA3. In addition to PEA3, it interacts with alpha-actinin,vasodilator stimulated phosphoprotein (VASP),Palladin, and Scrib. The LIM domains are the main focal adhesion targeting elements and that the proline- rich region, which harbors binding sites for alpha-actinin and vasodilator- stimulated phosphoprotein (VASP), has a weak targeting capacity. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188740 [Multi-domain] Cd Length: 60 Bit Score: 41.76 E-value: 3.59e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 122056614 441 CGHCNNVIRGPFLVAMGRSWHPEEFTCAYCKTSLADVCF-VEEQNNVYCERCYEQFFAP 498
Cdd:cd09354    1 CSVCSKPILDRILRATGKPYHPQCFTCVVCGKSLDGIPFtVDATNQIHCIEDFHKKFAP 59

PDZ domain 2 of Zonula Occludens-1 (ZO-1), ZO-2 and ZO-3, and related domains; form domain-swapping dimers; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of ZO-1, -2, -3 and related domains. Zonula occludens proteins (ZO-1, ZO-2, ZO-3) are multi-PDZ domain proteins involved in the maintenance and biogenesis of multi-protein networks at the cytoplasmic surface of intercellular contacts in epithelial and endothelial cells. They have three N-terminal PDZ domains, PDZ1-3, followed by a Src homology-3 (SH3) domain and a guanylate kinase (GuK)-like domain. Among protein-protein interactions for all ZO proteins is the binding of the first PDZ domain (PDZ1) to the C-termini of claudins , and the homo- and hetero-dimerization of ZO-proteins via their second PDZ domain (PDZ2), which takes place by symmetrical domain swapping of the first two beta-strands of PDZ2. At the cell level, ZO-1 and ZO-2 are involved in polarity maintenance, gene transcription, cell proliferation, and tumor cell metastasis. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This ZO family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467210 [Multi-domain] Cd Length: 79 Bit Score: 42.21 E-value: 3.63e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614   3 YSVTLTGPGP---WGFRLqGGKDFnmpltISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSL 78
Cdd:cd06728    1 LKVTLTKSRKndeYGLRL-GSRIF-----VKEITPDSLAAKDgNLQEGDIILKINGTPVENLSLSEAKKLIEKSKDKLQL 74


                 ....
gi 122056614  79 TLQK 82
Cdd:cd06728   75 VVLR 78

The second LIM domain of Four and a half LIM domains protein 1 (FHL1); The second LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188808 Cd Length: 58 Bit Score: 41.67 E-value: 3.70e-05

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 122056614 457 GRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERCYEQFF 496
Cdd:cd09424   19 GNVWHKDCFTCSNCKQPIGTKSFFPKGEDFYCVPCHEKKF 58

The second LIM domain of Enigma; The second LIM domain of Enigma: Enigma was initially characterized in humans as a protein containing three LIM domains at the C-terminus and a PDZ domain at N-terminus. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. Enigma is expressed in multiple tissues, such as skeletal muscle, heart, bone and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188840 [Multi-domain] Cd Length: 52 Bit Score: 41.52 E-value: 3.79e-05

                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 122056614 573 IEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKK 610
Cdd:cd09456   13 MHALKMTWHVHCFTCAACKTPIRNRAFYMEEGAPYCER 50

transcriptional regulator ICP4; Provisional

Pssm-ID: 223039 [Multi-domain] Cd Length: 1352 Bit Score: 47.09 E-value: 3.84e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  278 PAAPAPKPrvvttASIRPSVYQPVPASTYSPSPGANYSPTPYTPSPAPAYTPSPAPAYTPSPVPTYTPSPAPAYT----- 352
Cdd:PHA03307  123 PASPPPSP-----APDLSEMLRPVGSPGPPPAASPPAAGASPAAVASDAASSRQAALPLSSPEETARAPSSPPAEpppst 197

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  353 -PSPAPNYNPAPSVAYSGGPAEPASRPPWVTDDSFSQKFAPGKSTTSISKQTLPRGGPAYTPAGPQVPP-----LARGTV 426
Cdd:PHA03307  198 pPAAASPRPPRRSSPISASASSPAPAPGRSAADDAGASSSDSSSSESSGCGWGPENECPLPRPAPITLPtriweASGWNG 277

                         170
                  ....*....|...
gi 122056614  427 QRAERFPASSRTP 439
Cdd:PHA03307  278 PSSRPGPASSSSS 290

The third LIM domain of Testin-like family; The third LIM domain of Testin_like family: This family includes testin, prickle, dyxin and LIMPETin. Structurally, testin and prickle proteins contain three LIM domains at C-terminal; LIMPETin has six LIM domains; and dyxin presents only two LIM domains. However, all members of the family contain a PET protein-protein interaction domain. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). Dyxin involves in lung and heart development by interaction with GATA6 and blocking GATA6 activated target genes. LIMPETin might be the recombinant product of genes coding testin and four and half LIM proteins and its function is not well understood. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188728 Cd Length: 57 Bit Score: 41.61 E-value: 3.92e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 559 CHGCDFPVEAGDKFIEALGHTWH--DTCFICAVCHVNLEGQPFYSKKDRPLC 608
Cdd:cd09342    1 CDACGEPIGPDVQRVAHNGQHWHatEECFCCSNCKKSLLGQPFLPKNGQIFC 52

The fourth LIM domain of Paxillin; The fourth LIM domain of Paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188795 [Multi-domain] Cd Length: 52 Bit Score: 41.47 E-value: 3.99e-05

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 122056614 500 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCE 548
Cdd:cd09411    1 CSGCQKPITGRCITAMGKKFHPEHFVCAFCLKQLNKGTFKEQNDKPYCH 49

The second LIM domain of LIMK2 (LIM domain Kinase 2); The second LIM domain of LIMK2 (LIM domain Kinase 2): LIMK2 is a member of the LIMK protein family, which comprises LIMK1 and LIMK2. LIMK contains two LIM domains, a PDZ domain, and a kinase domain. LIMK is involved in the regulation of actin polymerization and microtubule disassembly. LIMK influences architecture of the actin cytoskeleton by regulating the activity of the cofilin family proteins cofilin1, cofilin2, and destrin. The mechanism of the activation is to phosphorylates cofilin on serine 3 and inactivates its actin-severing activity, altering the rate of actin depolymerisation. LIMK activity is activated by phosphorylation of a threonine residue within the activation loop of the kinase by p21-activated kinases 1 and 4 and by Rho kinase. LIMKs can function in both cytoplasm and nucleus. Both LIMK1 and LIMK2 can act in the nucleus to suppress Rac/Cdc42-dependent cyclin D1 expression. LIMK2 is expressed in all tissues. While LIMK1 localizes mainly at focal adhesions, LIMK2 is found in cytoplasmic punctae, suggesting that they may have different cellular functions. The activity of LIM kinase 2 to regulate cofilin phosphorylation is inhibited by the direct binding of Par-3. LIMK2 activation promotes cell cycle progression. The phenotype of Limk2 knockout mice shows a defect in spermatogenesis. The LIM domains have been shown to play an important role in regulating kinase activity and likely also contribute to LIMK function by acting as sites of protein-to-protein interactions. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188849 [Multi-domain] Cd Length: 59 Bit Score: 41.46 E-value: 4.14e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 122056614 496 FAPLCAKCNTKIMGEVMHALRQTWHTTCFVCAACKkpfgnslFHMEDGEPYCEKDYINLFSTKCH 560
Cdd:cd09465    2 FGELCHGCSLLMTGPAMVAGEYKYHPECFACMSCK-------VIIEDGDTYALVQHTTLYCGKCH 59

The fourth LIM domain of Four and a half LIM domains protein 1 (FHL1); The fourth LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188734 Cd Length: 64 Bit Score: 41.67 E-value: 4.14e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 122056614 441 CGHCNNVI----RGPFLVAM-GRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERC 491
Cdd:cd09348    5 CSGCQNPItgfgKGTNVVNYeGSSWHDYCFNCKKCSLNLANKRFVFHNGQIYCSDC 60

The Lim domain of DA1; The Lim domain of DA1: DA1 contains one copy of LIM domain and a domain of unknown function. DA1 is predicted as an ubiquitin receptor, which sets final seed and organ size by restricting the period of cell proliferation. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188782 [Multi-domain] Cd Length: 53 Bit Score: 41.47 E-value: 4.15e-05

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 122056614 559 CHGCDFPVEAGDkFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRP 606
Cdd:cd09396    1 CAGCKSEIGHGR-FLSALGAVWHPECFRCHACRKPIAEHEFSVSGNDP 47

The second LIM domain of Testin-like family; The second LIM domain of Testin-like family: This family includes testin, prickle, dyxin and LIMPETin. Structurally, testin and prickle proteins contain three LIM domains at C-terminal; LIMPETin has six LIM domains; and dyxin presents only two LIM domains. However, all members of the family contain a PET protein-protein interaction domain. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). Dyxin involves in lung and heart development by interaction with GATA6 and blocking GATA6 activated target genes. LIMPETin might be the recombinant product of genes coding testin and four and half LIM proteins and its function is not well understood. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188727 Cd Length: 56 Bit Score: 41.44 E-value: 4.19e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 122056614 559 CHGCD---FpveaGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLC 608
Cdd:cd09341    3 CAACDeliF----SGEYTQAEGKNWHLKHFCCFQCDEPLGGQRYVLREGKPYC 51

DNA polymerase III subunit gamma/tau;

Pssm-ID: 237874 [Multi-domain] Cd Length: 614 Bit Score: 46.31 E-value: 4.96e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 300 PVPASTYSPSPGANYSPTPYTPSPAPAYTPSPAPAYTPSPVPTYTPSPAPAytPSPAPNYNPAPSVAySGGPAEPASRPP 379
Cdd:PRK14971 363 TQKGDDASGGRGPKQHIKPVFTQPAAAPQPSAAAAASPSPSQSSAAAQPSA--PQSATQPAGTPPTV-SVDPPAAVPVNP 439

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 380 WVTddsfsqkfAPGKSTTSISKQTLPrggPAYTPAGPQVPPLARGTVQRAER 431
Cdd:PRK14971 440 PST--------APQAVRPAQFKEEKK---IPVSKVSSLGPSTLRPIQEKAEQ 480

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.

Pssm-ID: 282904 [Multi-domain] Cd Length: 886 Bit Score: 46.45 E-value: 5.00e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  274 YSEGPAAPAPKPRVVTTASIRPSVYQPVPASTYSPSPGANYSPTPYTPSPAPAYTPSPAPAYTPSPVPTYTPSPAPAYTP 353
Cdd:pfam05109 421 FSKAPESTTTSPTLNTTGFAAPNTTTGLPSSTHVPTNLTAPASTGPTVSTADVTSPTPAGTTSGASPVTPSPSPRDNGTE 500

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  354 SPAPNYNPAPSVAYSGGPAEPASRP------PWVTDDSFSQKFAPGKSTTSISKQTLPRggPAYTPAGPQ--VPPLARGT 425
Cdd:pfam05109 501 SKAPDMTSPTSAVTTPTPNATSPTPavttptPNATSPTLGKTSPTSAVTTPTPNATSPT--PAVTTPTPNatIPTLGKTS 578

                         170
                  ....*....|...
gi 122056614  426 VQRAERFPASSRT 438
Cdd:pfam05109 579 PTSAVTTPTPNAT 591

UV excision repair protein Rad23; All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]

Pssm-ID: 273167 [Multi-domain] Cd Length: 378 Bit Score: 46.04 E-value: 5.11e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 122056614  284 KPRVVTTASIRPSvyqPVPASTYSPSPGANYSPTPyTPSPAPAYTPSPAPAyTPSPVPTYTPSPAPAYTPSPAP 357
Cdd:TIGR00601  76 KPKTGTGKVAPPA---ATPTSAPTPTPSPPASPAS-GMSAAPASAVEEKSP-SEESATATAPESPSTSVPSSGS 144

PDZ domain 3 of protein tyrosine phosphatase non-receptor type 13 (PTPN13), FERM and PDZ domain-containing protein 2 (FRMPD2), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of PTPN13 [also known as Fas-associated protein-tyrosine phosphatase 1 (FAP-1), protein-tyrosine phosphatase 1E (PTP-E1), and protein-tyrosine phosphatase (PTPL1)], FRMPD2 (also known as PDZ domain-containing protein 4; PDZ domain-containing protein 5C), and related domains. PTPN13 regulates negative apoptotic signaling and mediates phosphoinositide 3-kinase (PI3K) signaling. PTPN13 has five PDZ domains. Proteins known to interact with PTPN13 PDZ domains include: PLEKHA1 and PLEKHA2 via PTPN13-PDZ domain 1, Fas receptor and thyroid receptor-interacting protein 6 via PTPN13-PDZ domain 2, nerve growth factor receptor and protein kinase N2 via PTPN13-PDZ domain 3, PDZ and LIM domain 4 (PDLIM4) via PTPN13-PDZ domains 2 and 4, and brain calpain-2 via PTPN13-PDZ domains 3, 4 and 5. Calpain-2-mediated PTPN13 fragments may be involved in abnormal tau aggregation and increased risk for Alzheimer's disease. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). FRMPD2 is localized in the basolateral membranes of polarized epithelial cells and is associated with tight junction formation and immune response; it contains 3 PDZ domains). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PTPN13 family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467181 [Multi-domain] Cd Length: 90 Bit Score: 42.25 E-value: 5.11e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614   3 YSVTLT-GPGPWGFRLQGGK------DFNMPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASY 74
Cdd:cd06695    2 FEVKLTkGSSGLGFSFLGGEnnspedPFSGLVRIKKLFPGQPAAESgLIQEGDVILAVNGEPLKGLSYQEVLSLLRGAPP 81

                         90
                 ....*....|..
gi 122056614  75 NLSLTLqksKRP 86
Cdd:cd06695   82 EVTLLL---CRP 90

The fifth LIM domain of protein PINCH; The fifth LIM domain of protein PINCH: PINCH plays pivotal roles in the assembly of focal adhesions (FAs), regulating diverse functions in cell adhesion, growth, and differentiation through LIM-mediated protein-protein interactions. PINCH comprises an array of five LIM domains that interact with integrin-linked kinase (ILK), Nck2 (also called Nckbeta or Grb4) and other interaction partners. These interactions are essential for triggering the FA assembly and for relaying diverse mechanical and biochemical signals between Cell-extracellular matrix and the actin cytoskeleton. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188721 [Multi-domain] Cd Length: 54 Bit Score: 41.18 E-value: 5.19e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 122056614 441 CGHCNNVIRGPFLVAMGRSWHPEEFTCAYCKTSLA-DVCFVEEQNNVYCERCYE 493
Cdd:cd09335    1 CYHCNQVIEGDVVSALNKTWCVDHFSCSFCDTKLTlKSKFYEFDMKPVCKKCYD 54

PDZ domain of tamalin, cytohesin-1-interacting protein (CYTIP), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of tamalin, cytohesin-1-interacting protein, and related domains. Tamalin (trafficking regulator and scaffold protein tamalin, also known as general receptor for phosphoinositides 1-associated scaffold protein, GRASP) functions to link receptors, including group 1 metabotropic glutamate receptors (mGluRs), to neuronal proteins. The tamalin PDZ domain binds the C-terminal domains of group I mGluRs; it also binds potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2 (HCN2), neurotrophin-3 (NT3) TrkCT1-truncated receptor, SAP90/PSD-95-associated protein, and tamalin itself. CYTIP (cytohesin-1-interacting protein, also known as Pleckstrin homology Sec7 and coiled-coil domain-binding protein) sequesters cytohesin-1 in the cytoplasm, limiting its interaction with beta2 integrins; cytohesin-1 binds the CYTIP coiled coil domain. The CYTIP PDZ domain can bind the C-terminal peptide of protocadherin alpha-1 (PCDHA1), indicating a possible interaction between the two. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This tamalin-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467197 [Multi-domain] Cd Length: 91 Bit Score: 42.23 E-value: 5.21e-05

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 122056614  11 GPWGFRLQ----GGKDFN---MPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSL 78
Cdd:cd06713   14 ETFGFEIQtyglHHKNSNeveMCTYVCRVHEDSPAYLAGLTAGDVILSVNGVSVEGASHQEIVELIRSSGNTLRL 88

The third LIM domain of actin binding LIM (abLIM) proteins; The third LIM domain of actin binding LIM (abLIM) proteins: Three homologous members of the abLIM protein family have been identified; abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM consists of four tandem repeats of LIM domains and the C-terminal of acting binding LIM protein is a villin headpiece domain, which has strong actin binding activity. The abLIM-1, which is expressed in retina, brain, and muscle tissue, has been indicated to function as a tumor suppressor. AbLIM-2 and -3, mainly expressed in muscle and neuronal tissue, bind to F-actin strongly. They may serve as a scaffold for signaling modules of the actin cytoskeleton and thereby modulate transcription. It has shown that LIM domains of abLIMs interact with STARS (striated muscle activator of Rho signaling), which directly binds actin and stimulates serum-response factor (SRF)-dependent transcription. All LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188715 [Multi-domain] Cd Length: 52 Bit Score: 40.77 E-value: 5.62e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 122056614 441 CGHCNNVIR-GPFLVAMGRSWHPEEFTCAYCKTSLAdvcfvEE---QNNV-YCERCY 492
Cdd:cd09329    1 CAGCGQEIKnGQALLALDKQWHVWCFKCKECGKVLT-----GEymgKDGKpYCERDY 52

The first LIM domain of Zyxin; The first LIM domain of Zyxin: Zyxin exhibits three copies of the LIM domain, an extensive proline-rich domain and a nuclear export signal. Localized at sites of cell substratum adhesion in fibroblasts, Zyxin interacts with alpha-actinin, members of the cysteine-rich protein (CRP) family, proteins that display Src homology 3 (SH3) domains and Ena/VASP family members. Zyxin and its partners have been implicated in the spatial control of actin filament assembly as well as in pathways important for cell differentiation. In addition to its functions at focal adhesion plaques, recent work has shown that zyxin moves from the sites of cell contacts to the nucleus, where it directly participates in the regulation of gene expression. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188735 [Multi-domain] Cd Length: 87 Bit Score: 42.15 E-value: 5.76e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 122056614 499 LCAKCNTKIM--GEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 551
Cdd:cd09349   33 LCGICGQPLSrtQPAVRALGHLFHVTCFTCHQCEQQLQGQQFYSLEGKPYCEECY 87

DNA polymerase III subunits gamma and tau; Validated

Pssm-ID: 236090 [Multi-domain] Cd Length: 824 Bit Score: 46.13 E-value: 5.81e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 277 GPAAPAPKPRVVTTASIRPSVYQPVPASTYSPSPGANY----SPTPYTPSPAPAYTPSPAPAYTPSPVPTYTPSPAPAYT 352
Cdd:PRK07764 635 APAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKaggaAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPAGQA 714

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 122056614 353 PSPAPNYNPAPSVAYSGGPAEPASRPPWVTDDSFSQKFAPGKSttsiSKQTLPRGGPAYTPAGPQVPP 420
Cdd:PRK07764 715 DDPAAQPPQAAQGASAPSPAADDPVPLPPEPDDPPDPAGAPAQ----PPPPPAPAPAAAPAAAPPPSP 778

LIM domain in proteins of unknown function; LIM domain in proteins of unknown function: LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation, and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. The LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid).

Pssm-ID: 188784 Cd Length: 61 Bit Score: 41.26 E-value: 5.97e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 122056614 558 KCHGCDFPVEAGDKfIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLC 608
Cdd:cd09400    4 PCASCGLPVFLAER-LLIEGKVYHRTCFKCARCGVQLTPGSFYETEYGSYC 53

The first LIM domain of Lmx1b; The first LIM domain of Lmx1b: Lmx1b belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. In mouse, Lmx1b functions in the developing limbs and eyes, the kidneys, the brain, and in cranial mesenchyme. The disruption of Lmx1b gene results kidney and limb defects. In the brain, Lmx1b is important for generation of mesencephalic dopamine neurons and the differentiation of serotonergic neurons. In the mouse eye, Lmx1b regulates anterior segment (cornea, iris, ciliary body, trabecular meshwork, and lens) development. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188757 [Multi-domain] Cd Length: 53 Bit Score: 40.82 E-value: 7.28e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 122056614 441 CGHCNNVIRGPFLV-AMGRSWHPEEFTCAYCKTSLADVCFVEEQnNVYCERCYE 493
Cdd:cd09371    1 CAGCQRPISDRYLLrVNERSWHEECLQCSVCQQPLTTSCYFRDR-KLYCKQDYQ 53

The second LIM domain of Four and a half LIM domains protein 2 (FHL2); The second LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung to a lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to s upport the assembly of multimeric protein complexes.

Pssm-ID: 188810 Cd Length: 57 Bit Score: 40.80 E-value: 7.38e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 122056614 500 CAKCNTKIM--GEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYC 547
Cdd:cd09426    1 CSECKKTIMpgTRKMEYKGNSWHETCFICQRCQQPIGTKSFIPKDNQNFC 50

C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, protein turnover, chaperones];

Pssm-ID: 440556 [Multi-domain] Cd Length: 341 Bit Score: 45.25 E-value: 7.50e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  14 GFRLQGGKDFnmpLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSAS-YNLSLTLQK--SKRPIPIS 90
Cdd:COG0793   63 GAELGEEDGK---VVVVSVIPGSPAEKAGIKPGDIILAIDGKSVAGLTLDDAVKLLRGKAgTKVTLTIKRpgEGEPITVT 139


                 ..
gi 122056614  91 TT 92
Cdd:COG0793  140 LT 141

The second LIM domain of the paxillin like protein family; The second LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188723 [Multi-domain] Cd Length: 52 Bit Score: 40.45 E-value: 8.09e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 559 CHGCDFPVEagDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKK 610
Cdd:cd09337    1 CAYCNGPIL--DKCVTALDKTWHPEHFFCAQCGKPFGDEGFHEKDGKPYCRE 50

The first LIM domain of Lmx1a; The first LIM domain of Lmx1a: Lmx1a belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Mouse Lmx1a is expressed in multiple tissues, including the roof plate of the neural tube, the developing brain, the otic vesicles, the notochord, and the pancreas. Human Lmx1a can be found in pancreas, skeletal muscle, adipose tissue, developing brain, mammary glands, and pituitary. The functions of Lmx1a in the developing nervous system were revealed by studies of mutant mouse. In mouse, mutations in Lmx1a result in failure of the roof plate to develop. Lmx1a may act upstream of other roof plate markers such as MafB, Gdf7, Bmp 6, and Bmp7. Further characterization of these mice reveals numerous defects including disorganized cerebellum, hippocampus, and cortex; altered pigmentation; female sterility; skeletal defects; and behavioral abnormalities. Within pancreatic cells, the Lmx1a protein interacts synergistically with the bHLH transcription factor E47 to activate the insulin gene enhancer/promoter. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188756 [Multi-domain] Cd Length: 52 Bit Score: 40.52 E-value: 8.40e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 122056614 441 CGHCNNVIRGPFLVAMGRS-WHPEEFTCAYCKTSLADVCFVEEQnNVYCERCY 492
Cdd:cd09370    1 CEGCNRVIQDRFLLRVNDSlWHERCLQCASCKEPLETTCFYRDK-KLYCKEDY 52

The first LIM domain of Lhx4; The first LIM domain of Lhx4. Lhx4 belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. LHX4 plays essential roles in pituitary gland and nervous system development. In mice, the lhx4 gene is expressed in the developing hindbrain, cerebral cortex, pituitary gland, and spinal cord. LHX4 shows significant sequence similarity to LHX3, particularly to isoforms Lhx3a. In gene regulation experiments, the LHX4 protein exhibits regulation roles towards pituitary genes, acting on their promoters/enhancers. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188852 Cd Length: 52 Bit Score: 40.34 E-value: 9.63e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 122056614 441 CGHCNNVIRGPFLV-AMGRSWHPEEFTCAYCKTSLADVCFvEEQNNVYCE 489
Cdd:cd09468    1 CAGCNQHILDKFILkVLDRHWHSSCLKCADCQMQLAERCF-SRAGNVYCK 49

The first LIM domain of LIMK1 (LIM domain Kinase 1); The first LIM domain of LIMK1 (LIM domain Kinase 1): LIMK1 belongs to the LIMK protein family, which comprises LIMK1 and LIMK2. LIMK contains two LIM domains, a PDZ domain, and a kinase domain. LIMK is involved in the regulation of actin polymerization and microtubule disassembly. LIMK influences architecture of the actin cytoskeleton by regulating the activity of the cofilin family proteins cofilin1, cofilin2, and destrin. The mechanism of the activation is to phosphorylates cofilin on serine 3 and inactivates its actin-severing activity, and altering the rate of actin depolymerization. LIMKs can function in both cytoplasm and nucleus. Both LIMK1 and LIMK2 can act in the nucleus to suppress Rac/Cdc42-dependent cyclin D1 expression. LIMK1 is expressed in all tissues and is localized to focal adhesions in the cell. LIMK1 can form homodimers upon binding of HSP90 and is activated by Rho effector Rho kinase and MAPKAPK2. LIMK1 is important for normal central nervous system development, and its deletion has been implicated in the development of the human genetic disorder Williams syndrome. Moreover, LIMK1 up-regulates the promoter activity of urokinase type plasminogen activator and induces its mRNA and protein expression in breast cancer cells. The LIM domains have been shown to play an important role in regulating kinase activity and likely also contribute to LIMK function by acting as sites of protein-to-protein interactions. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188846 [Multi-domain] Cd Length: 74 Bit Score: 41.02 E-value: 9.71e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 122056614 561 GCDFPVEAG-------DKFIEALGHTWHDTCFICAVCHVNLEGQpFYSKKDRPLCKKH 611
Cdd:cd09462   16 GNVLPVCAScgqsiydGQYLQALNSDWHADCFRCCECGASLSHW-YYEKDGRLFCKKD 72

The first LIM domain of Four and a half LIM domains protein (FHL); The first LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 int eracts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188729 Cd Length: 59 Bit Score: 40.50 E-value: 1.01e-04

                         10        20        30
                 ....*....|....*....|....*....|....*
gi 122056614 458 RSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERCY 492
Cdd:cd09343   24 RHWHEGCFKCFKCQRSLVDKPFAAKDEDLLCTECY 58

EBNA-3A; Provisional

Pssm-ID: 223066 [Multi-domain] Cd Length: 935 Bit Score: 45.43 E-value: 1.02e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 272 TSYSEGPAApAPKPRVVTTASIRP----SVYQPVPASTYSPSPGANYSPTPYTP----SPAPAYTPSPAPA--------Y 335
Cdd:PHA03379 433 TATSHGSAQ-VPEPPPVHDLEPGPlhdqHSMAPCPVAQLPPGPLQDLEPGDQLPgvvqDGRPACAPVPAPAgpivrpweA 511

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 336 TPSPVP-----TYTPSPAP-AYTPSPAPNYN----PAPSVAYSGGPAEPAS---------RPPWVTDdsfsqkfaPGKST 396
Cdd:PHA03379 512 SLSQVPgvafaPVMPQPMPvEPVPVPTVALErpvcPAPPLIAMQGPGETSGivrvrerwrPAPWTPN--------PPRSP 583

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 122056614 397 TSIS-KQTLPRGGP---AYT-------PAGPQVP---PLARGTVQRAERFPASSRTPLCghcnNVIRGPFLVAM 456
Cdd:PHA03379 584 SQMSvRDRLARLRAeaqPYQasvevqpPQLTQVSpqqPMEYPLEPEQQMFPGSPFSQVA----DVMRAGGVPAM 653

The second LIM domain of protein PINCH; The second LIM domain of protein PINCH: PINCH plays a pivotal role in the assembly of focal adhesions (FAs), regulating diverse functions in cell adhesion, growth, and differentiation through LIM-mediated protein-protein interactions. PINCH comprises an array of five LIM domains that interact with integrin-linked kinase (ILK), Nck2 (also called Nckbeta or Grb4) and other interaction partners. These interactions are essential for triggering the FA assembly and for relaying diverse mechanical and biochemical signals between Cell-extracellular matrix and the actin cytoskeleton. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188718 [Multi-domain] Cd Length: 52 Bit Score: 40.40 E-value: 1.02e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 122056614 559 CHGC-DFPVeagDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKK 610
Cdd:cd09332    1 CGKCgEFVI---GRVIKAMNNNWHPDCFRCEICNKELADIGFVKNAGRALCHP 50

ORF080 virion core protein; Provisional

Pssm-ID: 177464 [Multi-domain] Cd Length: 280 Bit Score: 44.47 E-value: 1.05e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 278 PAAPAPKPrvvttASIRPSVYQPVPASTYSPSPGANYSPTPYTPSPA-PAYTPSPAPAYTPSPVPTYTPSPAPAYTPSPA 356
Cdd:PHA02682  93 PACPACAP-----AAPAPAVTCPAPAPACPPATAPTCPPPAVCPAPArPAPACPPSTRQCPPAPPLPTPKPAPAAKPIFL 167

                         90       100
                 ....*....|....*....|....*
gi 122056614 357 PNYNPAPSVAYSGGP---AEPASRP 378
Cdd:PHA02682 168 HNQLPPPDYPAASCPtieTAPAASP 192

sec-independent translocase; Provisional

Pssm-ID: 135173 [Multi-domain] Cd Length: 214 Bit Score: 44.03 E-value: 1.09e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 279 AAPAPKPRVVTTASIRPSVYQPVPASTyspSPGANYSPTPyTPSPAP----AYTPSPAPAYT--PSPVPTYTPSPAPAYT 352
Cdd:PRK04654 105 ATPVATPLELAHADLSASAQVDAAAGA---EPGAGQAHTP-VPAPAPviaqAQPIAPAPHQTlvPAPHDTIVPAPHAAHL 180

                         90       100
                 ....*....|....*....|....*...
gi 122056614 353 PS-PAPNYNPAPSVAysGGPAEPASRPP 379
Cdd:PRK04654 181 PSaPATPVSVAPVDA--GTSASPTPSEP 206

The second LIM domain of Four and a half LIM domains protein 2 (FHL2); The second LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung to a lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to s upport the assembly of multimeric protein complexes.

Pssm-ID: 188810 Cd Length: 57 Bit Score: 40.42 E-value: 1.09e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 122056614 559 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLC 608
Cdd:cd09426    1 CSECKKTIMPGTRKMEYKGNSWHETCFICQRCQQPIGTKSFIPKDNQNFC 50

The second LIM domain of Arrowhead (AWH); The second LIM domain of Arrowhead (AWH): Arrowhead belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs such as the pituitary gland and the pancreas. During embryogenesis of Drosophila, Arrowhead is expressed in each abdominal segment and in the labial segment. Late in embryonic development, expression of arrowhead is refined to the abdominal histoblasts and salivary gland imaginal ring cells themselves. The Arrowhead gene required for establishment of a subset of imaginal tissues: the abdominal histoblasts and the salivary gland imaginal rings. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188765 Cd Length: 55 Bit Score: 40.10 E-value: 1.10e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 122056614 559 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLE-GQPFYSKKDRPLCKKH 611
Cdd:cd09379    1 CAKCSRNISASDWVRRARDHVYHLACFACDACKRQLStGEEFALIEDRVLCKAH 54

The fifth LIM domain of protein LIMPETin; The fifth LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188814 Cd Length: 52 Bit Score: 40.15 E-value: 1.16e-04

                         10        20        30
                 ....*....|....*....|....*....|..
gi 122056614 577 GHTWHDTCFICAVCHVNLEGQPFYSKKDRPLC 608
Cdd:cd09430   17 NEPWHRECFTCTNCSKSLAGQRFTSRDEKPYC 48

Fibronectin-attachment protein (FAP); This family contains bacterial fibronectin-attachment proteins (FAP). Family members are rich in alanine and proline, are approximately 300 long, and seem to be restricted to mycobacteria. These proteins contain a fibronectin-binding motif that allows mycobacteria to bind to fibronectin in the extracellular matrix.

Pssm-ID: 429334 Cd Length: 301 Bit Score: 44.53 E-value: 1.17e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  300 PVPASTYSPSPGANYSPTPYTPSPAPAyTPSPAPAytpSPVPTytpsPAPAYTPSPAPNYNPAPSVAYSGGPAEPASRPP 379
Cdd:pfam07174  32 ALPAVAHADPEPAPPPPSTATAPPAPP-PPPPAPA---APAPP----PPPAAPNAPNAPPPPADPNAPPPPPADPNAPPP 103


                  ....
gi 122056614  380 WVTD 383
Cdd:pfam07174 104 PAVD 107

circularly permuted PDZ domain of C-terminal processing peptidase (CPP), a serine protease, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of CPP (also known as tail-specific protease, PRC protein, Protease Re, and Photosystem II D1 protein processing peptidase), and related domains. CPP belongs to the peptidase S41A family. It cleaves a C-terminal 11 residue peptide from the precursor form of penicillin-binding protein 3, and may have a role in protecting bacterium from thermal and osmotic stresses. In the plant chloroplast, the enzyme removes the C-terminal extension of the D1 polypeptide of photosystem II. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This CPP-like PDZ domain is a circularly permuted PDZ domain which places beta-strand A on the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus.

Pssm-ID: 467623 [Multi-domain] Cd Length: 88 Bit Score: 40.93 E-value: 1.25e-04

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 122056614  27 LTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIK 70
Cdd:cd06782   16 LVVVSPIPGGPAEKAGIKPGDVIVAVDGESVRGMSLDEVVKLLR 59

The first LIM domain of LMO2 (LIM domain only protein 2); The first LIM domain of LMO2 (LIM domain only protein 2): LMO2 is a nuclear protein that plays important roles in transcriptional regulation and development. The two tandem LIM domains of LMO2 support the assembly of a crucial cell-regulatory complex by interacting with both the TAL1-E47 and GATA1 transcription factors to form a DNA-binding complex that is capable of transcriptional activation. LMOs have also been shown to be involved in oncogenesis. LMO1 and LMO2 are activated in T-cell acute lymphoblastic leukemia by distinct chromosomal translocations. LMO2 was also shown to be involved in erythropoiesis and is required for the hematopoiesis in the adult animals. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188770 Cd Length: 56 Bit Score: 40.22 E-value: 1.33e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 122056614 559 CHGCDFPVeaGDK-FIEALGHTWHDTCFICAVCHVNLE--GQPFYSKKDRPLCKK 610
Cdd:cd09384    1 CGGCQQNI--GDRyFLKAIDQYWHEDCLSCDLCGCRLGevGRRLYYKLGRKLCRR 53

ORF080 virion core protein; Provisional

Pssm-ID: 177464 [Multi-domain] Cd Length: 280 Bit Score: 44.08 E-value: 1.33e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 276 EGPAAPAPKPRVVTTASIRPSVYQPVPASTySPSPGANYSPTPYTPSPAPAYTPSPAPAYTPSPVPTYTPSPAPAY-TPS 354
Cdd:PHA02682  79 QSPLAPSPACAAPAPACPACAPAAPAPAVT-CPAPAPACPPATAPTCPPPAVCPAPARPAPACPPSTRQCPPAPPLpTPK 157

                         90       100
                 ....*....|....*....|....*
gi 122056614 355 PAPNYNPAPSVAYSGGPAEPASRPP 379
Cdd:PHA02682 158 PAPAAKPIFLHNQLPPPDYPAASCP 182

cell division protein DamX; Validated

Pssm-ID: 236792 [Multi-domain] Cd Length: 328 Bit Score: 44.54 E-value: 1.35e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 278 PAAPAPKPRVVTT------ASIRPSVYQPVPASTYSPSPGanyspTPYTPSPAPAYTPSPAPAYTPSPVPTYTPSPAPAY 351
Cdd:PRK10905 142 TAKTQTAERPATTrparkqAVIEPKKPQATAKTEPKPVAQ-----TPKRTEPAAPVASTKAPAATSTPAPKETATTAPVQ 216

                         90
                 ....*....|....*....
gi 122056614 352 TPSPAPNYNPAPSVAYSGG 370
Cdd:PRK10905 217 TASPAQTTATPAAGGKTAG 235

The fourth LIM domain of Four and a half LIM domains protein 1 (FHL1); The fourth LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188734 Cd Length: 64 Bit Score: 40.13 E-value: 1.39e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 122056614 558 KCHGCDFPVEA---GDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLC 608
Cdd:cd09348    4 KCSGCQNPITGfgkGTNVVNYEGSSWHDYCFNCKKCSLNLANKRFVFHNGQIYC 57

DNA polymerase III subunit gamma/tau;

Pssm-ID: 235906 [Multi-domain] Cd Length: 830 Bit Score: 44.84 E-value: 1.40e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 247 ALRRSRPQASSYSPAVAASSAPATHTSYSEGPAAPAPKPRVVTTASIRPSVYQPVPASTYSPSPGANYSPTPyTPSPAPA 326
Cdd:PRK07003 379 AVPAPGARAAAAVGASAVPAVTAVTGAAGAALAPKAAAAAAATRAEAPPAAPAPPATADRGDDAADGDAPVP-AKANARA 457

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 122056614 327 YTPSPAPAYTPSPVPTYTPSPAPAY-TPSPAPNyNPAPSVAYSGGPAEPASRPP 379
Cdd:PRK07003 458 SADSRCDERDAQPPADSGSASAPASdAPPDAAF-EPAPRAAAPSAATPAAVPDA 510

putative acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated

Pssm-ID: 235540 [Multi-domain] Cd Length: 153 Bit Score: 42.54 E-value: 1.41e-04

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 122056614 316 PTPYTPSPAPAYTPSPAPAYTPSPVPTYTPSPAPAytpSPAPNYNPAP 363
Cdd:PRK05641  46 SAVQEQVPTPAPAPAPAVPSAPTPVAPAAPAPAPA---SAGENVVTAP 90

The first LIM domain of Thyroid receptor-interacting protein 6 (TRIP6); The first LIM domain of Thyroid receptor-interacting protein 6 (TRIP6): TRIP6 is a member of the zyxin LIM protein family and contains three LIM zinc-binding domains at the C-terminal. TRIP6 protein localizes to focal adhesion sites and along actin stress fibers. Recruitment of this protein to the plasma membrane occurs in a lysophosphatidic acid (LPA)-dependent manner. TRIP6 recruits a number of molecules involved in actin assembly, cell motility, survival and transcriptional control. The function of TRIP6 in cell motility is regulated by Src-dependent phosphorylation at a Tyr residue. The phosphorylation activates the coupling to the Crk SH2 domain, which is required for the function of TRIP6 in promoting lysophosphatidic acid (LPA)-induced cell migration. TRIP6 can shuttle to the nucleus to serve as a coactivator of AP-1 and NF-kappaB transcriptional factors. Moreover, TRIP6 can form a ternary complex with the NHERF2 PDZ protein and LPA2 receptor to regulate LPA-induced activation of ERK and AKT, rendering cells resistant to chemotherapy. Recent evidence shows that TRIP6 antagonizes Fas-Induced apoptosis by enhancing the antiapoptotic effect of LPA in cells. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188736 Cd Length: 54 Bit Score: 39.69 E-value: 1.42e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 122056614 559 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCK 609
Cdd:cd09350    1 CGRCGENVVGEGTGCTAMDQVFHVDCFTCMTCNGKLRGQPFYAVEKKAYCE 51

PDZ domain 13 of multi-PDZ-domain protein 1 (MUPP1) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 13 of MUPP1. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, PDZ9, and PDZ13. This MuPP1-like PDZ13 domain is therefore absent from PATJ. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like family PDZ13 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467164 [Multi-domain] Cd Length: 83 Bit Score: 40.79 E-value: 1.47e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614   4 SVTLT-GPGPWGFRLQGGKDF---NMPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSL 78
Cdd:cd06676    1 TITLErGSDGLGFSIVGGFGSphgDLPIYVKTVFEKGAAAEDgRLKRGDQILAVNGESLEGVTHEEAVNILKKTKGTVTL 80


                 ..
gi 122056614  79 TL 80
Cdd:cd06676   81 TV 82

The fourth LIM domain of protein LIMPETin; The fourth LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the Testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188809 Cd Length: 54 Bit Score: 39.73 E-value: 1.62e-04

                         10        20        30
                 ....*....|....*....|....*....|....*
gi 122056614 517 QTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 551
Cdd:cd09425   20 QQWHEKCFCCCECKQPIGTKSFIPKDDDVYCVPCY 54

The second LIM domain of Four and a half LIM domains protein 3 (FHL3); The second LIM domain of Four and a half LIM domains protein 3 (FHL3): FHL3 is highly expressed in the skeleton and cardiac muscles and possesses the transactivation and repression activities. FHL3 interacts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. Moreover, FHL3 interacts with alpha- and beta-subunits of the muscle alpha7beta1 integrin receptor. FHL3 was also proved to possess the auto-activation ability and was confirmed that the second zinc finger motif in fourth LIM domain was responsible for the auto-activation of FHL3. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188811 Cd Length: 58 Bit Score: 39.83 E-value: 1.65e-04

                         10        20        30
                 ....*....|....*....|....*....|.
gi 122056614 517 QTWHTTCFVCAACKKPFGNSLFHMEDGEPYC 547
Cdd:cd09427   23 QTWHEHCFICHGCEQPIGSRSFIPDKDEHYC 53

The second LIM domain of LIMK (LIM domain Kinase ); The second LIM domain of LIMK (LIM domain Kinase ): LIMK protein family is comprised of two members LIMK1 and LIMK2. LIMK contains two LIM domains, a PDZ domain and a kinase domain. LIMK is involved in the regulation of actin polymerization and microtubule disassembly. LIMK influences architecture of the actin cytoskeleton by regulating the activity of the cofilin family proteins cofilin1, cofilin2, and destrin. The mechanism of the activation is to phosphorylates cofilin on serine 3 and inactivates its actin-severing activity, and altering the rate of actin depolymerization. LIMKs can function in both cytoplasm and nucleus and are expressed in all tissues. Both LIMK1 and LIMK2 can act in the nucleus to suppress Rac/Cdc42-dependent cyclin D1 expression. However, LIMK1 and LIMk2 have different cellular locations. While LIMK1 localizes mainly at focal adhesions, LIMK2 is found in cytoplasmic punctae, suggesting that they may have different cellular functions. The LIM domains of LIMK have been shown to play an important role in regulating kinase activity and likely also contribute to LIMK function by acting as sites of protein-to-protein interactions. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188751 [Multi-domain] Cd Length: 54 Bit Score: 39.66 E-value: 1.70e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 122056614 441 CGHCNNVIRGPFLVAMGRSWHPEEFTCAYCKTSLAD---VCFVeEQNNVYCERCY 492
Cdd:cd09365    1 CHGCSQIITGPVMVAGDHKFHPECFSCSSCKAFIGDgdsYALV-ERSKLYCGVCY 54

The first LIM domain of Four and a half LIM domains protein 1; The first LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188730 Cd Length: 54 Bit Score: 39.74 E-value: 1.78e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 500 CAKCNTKIMGEV--MHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEK 549
Cdd:cd09344    1 CAECRKPIGADSkeLHHKNRYWHETCFRCAKCYKPLANEPFVAKDNKILCGK 52

The LIM domain of LIM and SH3 Protein (LASP)-like proteins; The LIM domain of LIM and SH3 Protein (LASP) like proteins: This family contains two types of LIM containing proteins; LASP and N-RAP. LASP family contains two highly homologous members, LASP-1 and LASP-2. LASP contains a LIM motif at its amino terminus, a src homology 3 (SH3) domains at its C-terminal part, and a nebulin-like region in the middle. LASP-1 and -2 are highly conserved in their LIM, nebulin-like, and SH3 domains, but differ significantly at their linker regions. Both proteins are ubiquitously expressed and involved in cytoskeletal architecture, especially in the organization of focal adhesions. LASP-1 and LASP-2, are important during early embryo- and fetogenesis and are highly expressed in the central nervous system of the adult. However, only LASP-1 seems to participate significantly in neuronal differentiation and plays an important functional role in migration and proliferation of certain cancer cells while the role of LASP-2 is more structural. The expression of LASP-1 in breast tumors is increased significantly. N-RAP is a muscle-specific protein concentrated at myotendinous junctions in skeletal muscle and intercalated disks in cardiac muscle. LIM domain is found at the N-terminus of N-RAP and the C-terminal of N-RAP contains a region with multiple of nebulin repeats. N-RAP functions as a scaffolding protein that organizes alpha-actinin and actin into symmetrical I-Z-I structures in developing myofibrils. Nebulin repeat is known as actin binding domain. The N-RAP is hypothesized to form antiparallel dimerization via its LIM domain. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188745 Cd Length: 53 Bit Score: 39.56 E-value: 1.78e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 122056614 559 CHGCDFPVEAGDKfIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKKH 611
Cdd:cd09359    1 CARCGKIVYPTEK-VNCLDKTWHKACFHCEVCKMTLNMNNYKGYQKKPYCNAH 52

sec-independent translocase; Provisional

Pssm-ID: 135173 [Multi-domain] Cd Length: 214 Bit Score: 43.26 E-value: 1.80e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 306 YSPSPGANySPTPYTPSPAPAYTPSPAPAYTPSPVPTYTPSPAPAYTPSPAPNYNPAPSVAY-SGGPAEPASRPPwvTDD 384
Cdd:PRK04654 119 LSASAQVD-AAAGAEPGAGQAHTPVPAPAPVIAQAQPIAPAPHQTLVPAPHDTIVPAPHAAHlPSAPATPVSVAP--VDA 195

                         90
                 ....*....|....*...
gi 122056614 385 SFSQKFAPGKSTTSISKQ 402
Cdd:PRK04654 196 GTSASPTPSEPTKIQEKQ 213

multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine pyrophosphate-binding subunit/dihydrolipoyllysine-residue succinyltransferase subunit;

Pssm-ID: 237030 [Multi-domain] Cd Length: 1228 Bit Score: 44.88 E-value: 1.80e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  299 QPVPASTYSPSPGANYSPTPYTPSPAPAYTPSPAPAYTPSPVPTYTPSPAPAYTPSPAPNYNPAPSVAYSGGPAEPASRP 378
Cdd:PRK12270   40 STAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAAAAAAAAAPAAPPAAAAAAAPAAAAVEDEVTP 119

The first LIM domain of paxillin; The first LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight cons erved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188789 [Multi-domain] Cd Length: 54 Bit Score: 39.61 E-value: 1.85e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 122056614 559 CHGCDFPVeAGdKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKKHAH 613
Cdd:cd09405    2 CGACKKPI-AG-QVVTAMGKTWHPEHFVCTHCQEEIGSRNFFERDGQPYCEKDYH 54

The third LIM domain of actin binding LIM (abLIM) proteins; The third LIM domain of actin binding LIM (abLIM) proteins: Three homologous members of the abLIM protein family have been identified; abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM consists of four tandem repeats of LIM domains and the C-terminal of acting binding LIM protein is a villin headpiece domain, which has strong actin binding activity. The abLIM-1, which is expressed in retina, brain, and muscle tissue, has been indicated to function as a tumor suppressor. AbLIM-2 and -3, mainly expressed in muscle and neuronal tissue, bind to F-actin strongly. They may serve as a scaffold for signaling modules of the actin cytoskeleton and thereby modulate transcription. It has shown that LIM domains of abLIMs interact with STARS (striated muscle activator of Rho signaling), which directly binds actin and stimulates serum-response factor (SRF)-dependent transcription. All LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188715 [Multi-domain] Cd Length: 52 Bit Score: 39.61 E-value: 1.92e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 122056614 559 CHGCDFPVEAGDKFIeALGHTWHDTCFICAVCHVNLEGQpfYSKKDR-PLCKK 610
Cdd:cd09329    1 CAGCGQEIKNGQALL-ALDKQWHVWCFKCKECGKVLTGE--YMGKDGkPYCER 50

The second LIM domain of Lhx3-Lhx4 family; The second LIM domain of Lhx3-Lhx4 family: Lhx3 and Lhx4 belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. The LHX3 and LHX4 LIM-homeodomain transcription factors play essential roles in pituitary gland and nervous system development. Although LHX3 and LHX4 share marked sequence homology, the genes have different expression patterns. They play overlapping, but distinct functions during the establishment of the specialized cells of the mammalian pituitary gland and the nervous system. Lhx3 proteins have been demonstrated the ability to directly bind to the promoters/enhancers of several pituitary hormone gene promoters to cause increased transcription.Lhx3a and Lhx3b, whose mRNAs have distinct temporal expression profiles during development, are two isoforms of Lhx3. LHX4 plays essential roles in pituitary gland and nervous system development. In mice, the lhx4 gene is expressed in the developing hindbrain, cerebral cortex, pituitary gland, and spinal cord. LHX4 shows significant sequence similarity to LHX3, particularly to isoforms Lhx3a. In gene regulation experiments, the LHX4 protein exhibits regulation roles towards pituitary genes, acting on their promoters/enhancers. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188762 Cd Length: 56 Bit Score: 39.64 E-value: 1.96e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 122056614 559 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLE-GQPFYSKKDRPL-CKK 610
Cdd:cd09376    1 CAGCDEGIPPTQVVRRAQDNVYHLECFACFMCKRQLEtGDEFYLMEDDRLvCKK 54

Chitinase [Carbohydrate transport and metabolism];

Pssm-ID: 442692 [Multi-domain] Cd Length: 534 Bit Score: 44.36 E-value: 2.00e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 270 THTSYSEGPAAPAPKPRVVTTASIRPSVYQPVPASTYSPSPGANYSPTPYTPSPAPA-YTPSPAPAYTPSPVPTYTPSPA 348
Cdd:COG3469  103 SGANTGTSTVTTTSTGAGSVTSTTSSTAGSTTTSGASATSSAGSTTTTTTVSGTETAtGGTTTTSTTTTTTSASTTPSAT 182

                         90       100       110
                 ....*....|....*....|....*....|.
gi 122056614 349 PAYTPSPAPNYNPAPSVAYSGGPAEPASRPP 379
Cdd:COG3469  183 TTATATTASGATTPSATTTATTTGPPTPGLP 213

The second LIM domain of Ajuba-like proteins; The second LIM domain of Ajuba-like proteins: Ajuba like LIM protein family includes three highly homologous proteins Ajuba, Limd1, and WTIP. Members of the family contain three tandem C-terminal LIM domains and a proline-rich N-terminal region. This family of proteins functions as scaffolds, participating in the assembly of numerous protein complexes. In the cytoplasm, Ajuba binds Grb2 to modulate serum-stimulated ERK activation. Ajuba also recruits the TNF receptor-associated factor 6 (TRAF6) to p62 and activates PKCKappa activity. Ajuba interacts with alpha-catenin and F-actin to contribute to the formation or stabilization of adheren junctions by linking adhesive receptors to the actin cytoskeleton. Although Ajuba is a cytoplasmic protein, it can shuttle into the nucleus. In nucleus, Ajuba functions as a corepressor for the zinc finger-protein Snail. It binds to the SNAG repression domain of Snail through its LIM region. Arginine methyltransferase-5 (Prmt5), a protein in the complex, is recruited to Snai l through an interaction with Ajuba. This ternary complex functions to repress E-cadherin, a Snail target gene. In addition, Ajuba contains functional nuclear-receptor interacting motifs and selectively interacts with retinoic acid receptors (RARs) and rexinoid receptor (RXRs) to negatively regulate retinoic acid signaling. Wtip, the Wt1-interacting protein, was originally identified as an interaction partner of the Wilms tumour protein 1 (WT1). Wtip is involved in kidney and neural crest development. Wtip interacts with the receptor tyrosine kinase Ror2 and inhibits canonical Wnt signaling. LIMD1 was reported to inhibit cell growth and metastases. The inhibition may be mediated through an interaction with the protein barrier-to-autointegration (BAF), a component of SWI/SNF chromatin-remodeling protein; or through the interaction with retinoblastoma protein (pRB), resulting in inhibition of E2F-mediated transcription, and expression of the majority of genes with E2F1- responsive elements. Recently, Limd1 was shown to interact with the p62/sequestosome protein and influence IL-1 and RANKL signaling by facilitating the assembly of a p62/TRAF6/a-PKC multi-protein complex. The Limd1-p62 interaction affects both NF-kappaB and AP-1 activity in epithelial cells and osteoclasts. Moreover, LIMD1 functions as tumor repressor to block lung tumor cell line in vitro and in vivo. Recent studies revealed that LIM proteins Wtip, LIMD1 and Ajuba interact with components of RNA induced silencing complexes (RISC) as well as eIF4E and the mRNA m7GTP cap-protein complex and are required for microRNA-mediated gene silencing. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188741 [Multi-domain] Cd Length: 53 Bit Score: 39.25 E-value: 2.08e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 122056614 500 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHME-DGEPYCEKDY 551
Cdd:cd09355    1 CAVCGHLIMEMILQALGKSYHPGCFRCCVCNECLDGVPFTVDvENNIYCVKDY 53

The first LIM domain of Four and a half LIM domains protein 1; The first LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188730 Cd Length: 54 Bit Score: 39.35 E-value: 2.12e-04

                         10        20        30
                 ....*....|....*....|....*....|....*
gi 122056614 457 GRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERC 491
Cdd:cd09344   19 NRYWHETCFRCAKCYKPLANEPFVAKDNKILCGKC 53

The second LIM domain of Zyxin; The second LIM domain of Zyxin: Zyxin exhibits three copies of the LIM domain, an extensive proline-rich domain and a nuclear export signal. Localized at sites of cellsubstratum adhesion in fibroblasts, Zyxin interacts with alpha-actinin, members of the cysteine-rich protein (CRP) family, proteins that display Src homology 3 (SH3) domains and Ena/VASP family members. Zyxin and its partners have been implicated in the spatial control of actin filament assembly as well as in pathways important for cell differentiation. In addition to its functions at focal adhesion plaques, recent work has shown that zyxin moves from the sites of cell contacts to the nucleus, where it directly participates in the regulation of gene expression. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors o r scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188739 [Multi-domain] Cd Length: 60 Bit Score: 39.53 E-value: 2.14e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 122056614 500 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDG-EPYCEKDY 551
Cdd:cd09353    1 CAVCDQKITDRMLKATGKSYHPQCFTCVVCKCPLEGESFIVDQAnQPHCVNDY 53

The third LIM domain of Prickle; The third LIM domain of Prickle: Prickle contains three C-terminal LIM domains and a N-terminal PET domain. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). PCP establishment requires the conserved Frizzled/Dishevelled PCP pathway. Prickle interacts with Dishevelled, thereby modulating Frizzled/Dishevelled activity and PCP signaling. Two forms of prickles have been identified; namely prickle 1 and prickle 2. Prickle 1 and prickle 2 are differentially expressed. While prickle 1 is expressed in fetal heart and hematological malignancies, prickle 2 is found in fetal brain, adult cartilage, pancreatic islet, and some types of timorous cells. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188804 Cd Length: 59 Bit Score: 39.34 E-value: 2.28e-04

                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 122056614 577 GHTWH--DTCFICAVCHVNLEGQPFYSKKDRPLCKK 610
Cdd:cd09420   21 GQHWHatEKCFCCAQCKKSLLGRPFLPKQGQIYCSR 56

The second LIM domain of Four and a half LIM domains protein (FHL); The second LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 int eracts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188731 [Multi-domain] Cd Length: 54 Bit Score: 39.20 E-value: 2.36e-04

                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 122056614 457 GRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERCY 492
Cdd:cd09345   19 GKFWHEKCFTCSECKKPIGTKSFIPKDDKIYCVPCY 54

The first LIM domain of protein LIMPETin; The first LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the Testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188798 [Multi-domain] Cd Length: 58 Bit Score: 39.30 E-value: 2.42e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 122056614 500 CAKCNTKI----MGEVMHALRQT--WHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 551
Cdd:cd09414    1 CGGCSEPLkygeLAVTAPKFGESllWHPACFRCSTCEELLVDLTYCVHDDQIYCERHY 58

multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine pyrophosphate-binding subunit/dihydrolipoyllysine-residue succinyltransferase subunit;

Pssm-ID: 237030 [Multi-domain] Cd Length: 1228 Bit Score: 44.50 E-value: 2.43e-04

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 122056614  303 ASTYSPSPGANYSPTPYTPSPAPAYTPSPAPAYTPSPVPTYTPSPAPAYTPSPAPnyNPAPSVAYSGGPAEPASRPP 379
Cdd:PRK12270   34 ADYGPGSTAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAA--AAAAAAAPAAPPAAAAAAAP 108

The first LIM domain of Lrg1p, a LIM and RhoGap domain containing protein; The first LIM domain of Lrg1p, a LIM and RhoGap domain containing protein: The members of this family contain three tandem repeats of LIM domains and a Rho-type GTPase activating protein (RhoGap) domain. Lrg1p is a Rho1 GTPase-activating protein required for efficient cell fusion in yeast. Lrg1p-GAP domain strongly and specifically stimulates the GTPase activity of Rho1p, a regulator of beta (1-3)-glucan synthase in vitro. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188777 Cd Length: 57 Bit Score: 39.21 E-value: 2.43e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 122056614 441 CGHCNNVIRGPFLVAMGRSWHPEEFTCAYCKTSLADVCFVEEQNNVY-----CERCY 492
Cdd:cd09391    1 CAKCGKPITGQFVRALGDVYHLDCFTCHDCGKPVASKFFPVDDPDTSeqvplCETDY 57

The first LIM domain of Testin-like family; The first LIM domain of Testin_like family: This family includes testin, prickle, dyxin and LIMPETin. Structurally, testin and prickle proteins contain three LIM domains at C-terminal; LIMPETin has six LIM domains; and dyxin presents only two LIM domains. However, all members of the family contain a PET protein-protein interaction domain. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). Dyxin involves in lung and heart development by interaction with GATA6 and blocking GATA6 activated target genes. LIMPETin might be the recombinant product of genes coding testin and four and half LIM proteins and its function is not well understood. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188726 Cd Length: 58 Bit Score: 39.12 E-value: 2.49e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 559 CHGCDFPVEAGDK--FIEALGH--TWHDTCFICAVCH---VNLegQPFYsKKDRPLCKKH 611
Cdd:cd09340    1 CEKCKEPINPGEVavFAERAGEdaCWHPGCFVCETCNellVDL--IYFY-HDGKIYCGRH 57

The LIM domain of LIM and SH3 Protein (LASP); The LIM domain of LIM and SH3 Protein (LASP): LASP family contains two highly homologous members, LASP-1 and LASP-2. LASP contains a LIM motif at its amino terminus, a src homology 3 (SH3) domains at its C-terminal part, and a nebulin-like region in the middle. LASP-1 and -2 are highly conserved in their LIM, nebulin-like, and SH3 domains ,but differ significantly at their linker regions. Both proteins are ubiquitously expressed and involved in cytoskeletal architecture, especially in the organization of focal adhesions. LASP-1 and LASP-2, are important during early embryo- and fetogenesis and are highly expressed in the central nervous system of the adult. However, only LASP-1 seems to participate significantly in neuronal differentiation and plays an important functional role in migration and proliferation of certain cancer cells while the role of LASP-2 is more structural. The expression of LASP-1 in breast tumors is increased significantly. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188831 Cd Length: 53 Bit Score: 39.28 E-value: 2.54e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 122056614 500 CAKCN-TKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 551
Cdd:cd09447    1 CARCGkTVYPTEKLNCLDKIWHKGCFKCEVCGMTLNMKNYKGYNKKPYCNAHY 53

PDZ domain 6 of PDZ domain containing 2 (PDZD2), PDZ domain 3 of human pro-interleukin-16 (isoform 1, 1332 AA), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 6 of PDZD2, also known as KIAA0300, PIN-1, activated in prostate cancer (AIPC) and PDZ domain-containing protein 3 (PDZK3). PDZD2 has seven PDZ domains. PDZD2 is expressed at exceptionally high levels in the pancreas and certain cancer tissues, such as prostate cancer. It promotes the proliferation of insulinoma cells and is upregulated during prostate tumorigenesis. In osteosarcoma (OS), the microRNA miR-363 acts as a tumor suppressor by inhibiting PDZD2. This family also includes the third PDZ domain (PDZ3) of human pro-interleukin-16 (isoform 1, also known as nPro-IL-16). Precursor IL-16 is cleaved to produce pro-IL-16 and C-terminal mature IL-16. Pro-IL-16 functions as a regulator of T cell growth; mature IL-16 is a CD4 ligand that induces chemotaxis and CD25 expression in CD4+ T cells. IL-16 bioactivity has been closely associated with the progression of several different cancers. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD2-like family PDZ6 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467243 [Multi-domain] Cd Length: 86 Bit Score: 39.94 E-value: 2.73e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 122056614  14 GFRLQGGKDF-NMPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSA 72
Cdd:cd06762   15 GFSLAGGSDLeNKSITVHRVFPSGLAAQEgTIQKGDRILSINGKSLKGVTHGDALSVLKQA 75

The first LIM domain of Lhx3 and Lhx4 family; The first LIM domain of Lhx3-Lhx4 family: Lhx3 and Lhx4 belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. The LHX3 and LHX4 LIM-homeodomain transcription factors play essential roles in pituitary gland and nervous system development. Although LHX3 and LHX4 share marked sequence homology, the genes have different expression patterns. They play overlapping, but distinct functions during the establishment of the specialized cells of the mammalian pituitary gland and the nervous system. Lhx3 proteins have been demonstrated the ability to directly bind to the promoters/enhancers of several pituitary hormone gene promoters to cause increased transcription. Lhx3a and Lhx3b, whose mRNAs have distinct temporal expression profiles during development, are two isoforms of Lhx3. LHX4 plays essential roles in pituitary gland and nervous system development. In mice, the lhx4 gene is expressed in the developing hindbrain, cerebral cortex, pituitary gland, and spinal cord. LHX4 shows significant sequence similarity to LHX3, particularly to isoforms Lhx3a. In gene regulation experiments, the LHX4 protein exhibits regulation roles towards pituitary genes, acting on their promoters/enhancers. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188754 Cd Length: 52 Bit Score: 38.94 E-value: 2.74e-04

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                 ....*....|....*....|....*....|....*....|....*....|
gi 122056614 441 CGHCNNVIRGPF-LVAMGRSWHPEEFTCAYCKTSLADVCFvEEQNNVYCE 489
Cdd:cd09368    1 CGGCQEHILDRFiLKVLDRTWHAKCLKCNDCGAQLTDKCF-ARNGHVYCK 49

large tegument protein UL36; Provisional

Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 44.16 E-value: 2.79e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  300 PVPASTYSPSPGANYSptpyTPSPAPAYTPSPAPAYTPSPVPTYTPSPAPAYTPSPAPNYNPAPSVAYSGGPAEPASRPP 379
Cdd:PHA03247 2552 PPPLPPAAPPAAPDRS----VPPPRPAPRPSEPAVTSRARRPDAPPQSARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPP 2627

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  380 wvtddSFSQKFAPGKSTTSISKQTLPRGGPAYTPAGPQVPPLARgtVQRAERFPASSRTP 439
Cdd:PHA03247 2628 -----PPSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPRR--ARRLGRAAQASSPP 2680

The LIM domain of LIM and SH3 Protein (LASP)-like proteins; The LIM domain of LIM and SH3 Protein (LASP) like proteins: This family contains two types of LIM containing proteins; LASP and N-RAP. LASP family contains two highly homologous members, LASP-1 and LASP-2. LASP contains a LIM motif at its amino terminus, a src homology 3 (SH3) domains at its C-terminal part, and a nebulin-like region in the middle. LASP-1 and -2 are highly conserved in their LIM, nebulin-like, and SH3 domains, but differ significantly at their linker regions. Both proteins are ubiquitously expressed and involved in cytoskeletal architecture, especially in the organization of focal adhesions. LASP-1 and LASP-2, are important during early embryo- and fetogenesis and are highly expressed in the central nervous system of the adult. However, only LASP-1 seems to participate significantly in neuronal differentiation and plays an important functional role in migration and proliferation of certain cancer cells while the role of LASP-2 is more structural. The expression of LASP-1 in breast tumors is increased significantly. N-RAP is a muscle-specific protein concentrated at myotendinous junctions in skeletal muscle and intercalated disks in cardiac muscle. LIM domain is found at the N-terminus of N-RAP and the C-terminal of N-RAP contains a region with multiple of nebulin repeats. N-RAP functions as a scaffolding protein that organizes alpha-actinin and actin into symmetrical I-Z-I structures in developing myofibrils. Nebulin repeat is known as actin binding domain. The N-RAP is hypothesized to form antiparallel dimerization via its LIM domain. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188745 Cd Length: 53 Bit Score: 39.17 E-value: 2.88e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 122056614 500 CAKCNTKIM-GEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 551
Cdd:cd09359    1 CARCGKIVYpTEKVNCLDKTWHKACFHCEVCKMTLNMNNYKGYQKKPYCNAHY 53

The second LIM domain of Lhx3-Lhx4 family; The second LIM domain of Lhx3-Lhx4 family: Lhx3 and Lhx4 belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. The LHX3 and LHX4 LIM-homeodomain transcription factors play essential roles in pituitary gland and nervous system development. Although LHX3 and LHX4 share marked sequence homology, the genes have different expression patterns. They play overlapping, but distinct functions during the establishment of the specialized cells of the mammalian pituitary gland and the nervous system. Lhx3 proteins have been demonstrated the ability to directly bind to the promoters/enhancers of several pituitary hormone gene promoters to cause increased transcription.Lhx3a and Lhx3b, whose mRNAs have distinct temporal expression profiles during development, are two isoforms of Lhx3. LHX4 plays essential roles in pituitary gland and nervous system development. In mice, the lhx4 gene is expressed in the developing hindbrain, cerebral cortex, pituitary gland, and spinal cord. LHX4 shows significant sequence similarity to LHX3, particularly to isoforms Lhx3a. In gene regulation experiments, the LHX4 protein exhibits regulation roles towards pituitary genes, acting on their promoters/enhancers. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188762 Cd Length: 56 Bit Score: 38.87 E-value: 2.96e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 122056614 500 CAKCNTKIMGE--VMHALRQTWHTTCFVCAACKKPF--GNSLFHMEDGEPYCEKDY 551
Cdd:cd09376    1 CAGCDEGIPPTqvVRRAQDNVYHLECFACFMCKRQLetGDEFYLMEDDRLVCKKDY 56

PDZ domain 1 of the full-length isoform of whirlin and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of the full-length isoform of whirlin and related domains. Whirlin is an essential protein for developmental pathways in photoreceptor cells of the retina and hair cells of the inner ear. The full-length whirlin isoform has two harmonin N-like domains, three PDZ domains, a proline-rich region, and a PDZ-binding motif. Whirlin isoforms may form different complexes at the periciliary membrane complex (PMC) in photoreceptors, and the stereociliary tip and base in inner ear hair cells. It interacts with ADGRV1 and usherin at the PMC; with SANS and RpgrORF15 at the connecting cilium in photoreceptors; with EPS8, MYO15A, p55, and CASK proteins at the stereociliary tip of inner ear hair cells; and with ADGRV1, usherin, and PDZD7 at the stereociliary base in inner ear hair cells. Mutations in the gene encoding whirlin (WHRN; also known as USH2D and DFNB31), have been found to cause either USH2 subtype (USH2D) or autosomal recessive non-syndromic deafness type 31 (DFNB31). Whirlin is the key protein in the USH2 complex (whirlin, usherin and GPR98) which recruits other USH2 causative proteins at the periciliary membrane in photoreceptors and the ankle link of the stereocilia in hair cells. Whirlin's interaction with espin, another stereociliary protein, may be important for the architecture of the USH2 complex. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This whirlin family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467222 [Multi-domain] Cd Length: 82 Bit Score: 39.65 E-value: 3.12e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  13 WGFRLQGGKDFNMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSA 72
Cdd:cd06740   15 LGFSIRGGAEHGVGIYVSLVEPGSLAEKEGLRVGDQILRVNDVSFEKVTHAEAVKILRVS 74

PDZ domain 2 of the full-length isoform of whirlin and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of the full-length isoform of whirlin and related domains. Whirlin is an essential protein for developmental pathways in photoreceptor cells of the retina and hair cells of the inner ear. The full-length whirlin isoform has two harmonin N-like domains, three PDZ domains, a proline-rich region, and a PDZ-binding motif. Whirlin isoforms may form different complexes at the periciliary membrane complex (PMC) in photoreceptors, and the stereociliary tip and base in inner ear hair cells. It interacts with ADGRV1 and usherin at the PMC; with SANS and RpgrORF15 at the connecting cilium in photoreceptors; with EPS8, MYO15A, p55, and CASK proteins at the stereociliary tip of inner ear hair cells; and with ADGRV1, usherin, and PDZD7 at the stereociliary base in inner ear hair cells. Mutations in the gene encoding whirlin (WHRN; also known as USH2D and DFNB31), have been found to cause either USH2 subtype (USH2D) or autosomal recessive non-syndromic deafness type 31 (DFNB31). Whirlin is the key protein in the USH2 complex (whirlin, usherin and GPR98) which recruits other USH2 causative proteins at the periciliary membrane in photoreceptors and the ankle link of the stereocilia in hair cells. Whirlin's interaction with espin, another stereociliary protein, may be important for the architecture of the USH2 complex. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This whirlin family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467223 [Multi-domain] Cd Length: 84 Bit Score: 39.94 E-value: 3.19e-04

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 122056614   4 SVTLTGPGPWGFRLQGGKDFNMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSaSYNLSLTL 80
Cdd:cd06741    5 NLVVEDGQSLGLMIRGGAEYGLGIYVTGVDPGSVAENAGLKVGDQILEVNGRSFLDITHDEAVKILKS-SKHLIMTV 80

PDZ domain 2 of Drosophila Scribble, human Scribble homolog, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of Drosophila Scribble (also known as LAP4), human Scribble homolog (also known as hScrib, LAP4, CriB1, ScrB1 and Vartul), and related domains. They belong to the LAP family, which describes proteins that contain either one or four PDZ domains and 16 LRRs (leucine-rich repeats) and function in controlling cell shape, size and subcellular protein localization. In Drosophila, the Scribble complex, comprising Scribble, discs large, and lethal giant larvae, plays a role in apico-basal cell polarity, in other forms of polarity, including regulation of the actin cytoskeleton, cell signaling and vesicular trafficking, and in tumor development. Mammalian Scribble is important in many aspects of cancer development. Scribble and its homologs can be downregulated or overexpressed in cancer; they have a role in cancer beyond their function in loss of cell polarity. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Scribble-like family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467187 [Multi-domain] Cd Length: 92 Bit Score: 39.94 E-value: 3.32e-04

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 122056614  14 GFRLQGGK------DFNMPLTISRITPGSKAA-QSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQK 82
Cdd:cd06703   15 GFSIAGGKgstpfrDGDEGIFISRITEGGAADrDGKLQVGDRVLSINGVDVTEARHDQAVALLTSSSPTITLVVER 90

The second LIM domain of the Enigma Homolog (ENH) family; The second LIM domain of the Enigma Homolog (ENH) family: ENH was initially identified in rat brain. Same as enigma, it contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ENH is implicated in signal transduction processes involving protein kinases. It has also been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ENH is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188841 [Multi-domain] Cd Length: 52 Bit Score: 38.86 E-value: 3.42e-04

                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 122056614 573 IEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCK 609
Cdd:cd09457   13 INALKQTWHVSCFVCVACHNPIRNNVFHLEDGEPYCE 49

The second LIM domain of protein LIMPETin and related proteins; The second LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188801 Cd Length: 56 Bit Score: 38.67 E-value: 3.68e-04

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                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 122056614 439 PLCGHCNNVIR-GPFLVAMGRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERCYE 493
Cdd:cd09417    1 DRSVQCDELIFsGEYTKAMNKDWHSGHFCCWQCDESLTGQRYVLRDEHPYCIKCYE 56

The LIM domain of Mical (molecule interacting with CasL) like family; The LIM domain of Mical (molecule interacting with CasL) like family: Known members of this family includes LIM domain containing proteins; Mical (molecule interacting with CasL), pollen specific protein SF3, Eplin, xin actin-binding repeat-containing protein 2 (XIRP2) and Ltd-1. The members of this family function mainly at the cytoskeleton and focal adhesions. They interact with transcription factors or other signaling molecules to play roles in muscle development, neuronal differentiation, cell growth and mobility. Eplin has also found to be tumor suppressor. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs.. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188744 [Multi-domain] Cd Length: 53 Bit Score: 38.79 E-value: 3.83e-04

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                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 122056614 559 CHGCD---FPVEagdkFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKKH 611
Cdd:cd09358    1 CAVCGktvYPME----RLVADGKLFHKSCFRCSHCNKTLRLGNYASLEGKLYCKPH 52

The second LIM domain of LMO4 (LIM domain only protein 4); The second LIM domain of LMO4 (LIM domain only protein 4): LMO4 is a nuclear protein that plays important roles in transcriptional regulation and development. LMO4 is involved in various functions in tumorigenesis and cellular differentiation. LMO4 proteins regulate gene expression by interacting with a wide variety of transcription factors and cofactors to form large transcription complexes. It can interact with Smad proteins, and associate with the promoter of the PAI-1 (plasminogen activator inhibitor-1) gene in a TGFbeta (transforming growth factor beta)-dependent manner. LMO4 can also form a complex with transcription regulator CREB (cAMP response element-binding protein) and interact with CLIM1 and CLIM2. In breast tissue, LMO4 interacts with multiple proteins, including the cofactor CtIP [CtBP (C-terminal binding protein)-interacting protein], the breast and ovarian tumor suppressor BRCA1 (breast-cancer susceptibility gene 1) and the LIM-domain-binding protein LDB1. Functionally, LMO4 is shown to repress BRCA1-mediated transcription activation, thus invoking a potential role for LMO4 as a negative regulator of BRCA1 in sporadic breast cancer. LMO4 also forms complex to both ERa (oestrogen receptor alpha), MTA1 (metastasis tumor antigen 1), and HDACs (histone deacetylases), implying that LMO4 is also a component of the MTA1 corepressor complex. Over-expressed LMO4 represses ERa transactivation functions in an HDAC-dependent manner, and contributes to the process of breast cancer progression by allowing the development of Era-negative phenotypes. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188773 Cd Length: 55 Bit Score: 38.62 E-value: 3.86e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 122056614 500 CAKCNTKIMGE--VMHALRQTWHTTCFVCAACkkpfGNSL-----FHMEDGEPYCEKD 550
Cdd:cd09387    1 CSACGQSIPASelVMRAQGNVYHLKCFTCSTC----HNQLvpgdrFHYVNGSLFCEHD 54

The second LIM domain on actin binding LIM (abLIM) proteins; The second LIM domain of actin binding LIM (abLIM) proteins: Three homologous members of the abLIM protein family have been identified; abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM consists of four tandem repeats of LIM domains and the C-terminal of acting binding LIM protein is a villin headpiece domain, which has strong actin binding activity. The abLIM-1, which is expressed in retina, brain, and muscle tissue, has been indicated to function as a tumor suppressor. AbLIM-2 and -3, mainly expressed in muscle and neuronal tissue, bind to F-actin strongly. They may serve as a scaffold for signaling modules of the actin cytoskeleton and thereby modulate transcription. It has shown that LIM domains of abLIMs interact with STARS (striated muscle activator of Rho signaling), which directly binds actin and stimulates serum-response factor (SRF)-dependent transcription. All LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188714 Cd Length: 56 Bit Score: 38.87 E-value: 3.87e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 122056614 441 CGHCNNVIRGPFLVAMGRSWHPEEFTCAYCKTSLAD---VCFVEeqNNVYCERC 491
Cdd:cd09328    4 CDSCQDFVEGEVVSALGKTYHPKCFVCSVCRQPFPPgdrVTFNG--KECLCQKC 55

The second LIM domain of Thyroid receptor-interacting protein 6 (TRIP6); The second LIM domain of Thyroid receptor-interacting protein 6 (TRIP6): TRIP6 is a member of the zyxin LIM protein family and contains three LIM zinc-binding domains at the C-terminal. TRIP6 protein localizes to focal adhesion sites and along actin stress fibers. Recruitment of this protein to the plasma membrane occurs in a lysophosphatidic acid (LPA)-dependent manner. TRIP6 recruits a number of molecules involved in actin assembly, cell motility, survival and transcriptional control. The function of TRIP6 in cell motility is regulated by Src-dependent phosphorylation at a Tyr residue. The phosphorylation activates the coupling to the Crk SH2 domain, which is required for the function of TRIP6 in promoting lysophosphatidic acid (LPA)-induced cell migration. TRIP6 can shuttle to the nucleus to serve as a coactivator of AP-1 and NF-kappaB transcriptional factors. Moreover, TRIP6 can form a ternary complex with the NHERF2 PDZ protein and LPA2 receptor to regulate LPA-induced activation of ERK and AKT, rendering cells resistant to chemotherapy. Recent evidence shows that TRIP6 antagonizes Fas-Induced apoptosis by enhancing the antiapoptotic effect of LPA in cells. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188742 Cd Length: 53 Bit Score: 38.70 E-value: 3.88e-04

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 122056614 559 CHGCDFPVEagDKFIEALGHTWHDTCFICAVCHVNLEGQPF 599
Cdd:cd09356    1 CSVCSKPIM--ERILRATGKAYHPHCFTCVVCHRSLDGIPF 39

The first LIM domain of protein PINCH; The first LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188717 Cd Length: 59 Bit Score: 38.85 E-value: 3.97e-04

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 122056614 457 GRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERCYEQFFA 497
Cdd:cd09331   19 GELYHEQCFVCAQCFQPFPDGLFYEFEGRKYCEHDFQVLFA 59

The first LIM domain of Thyroid receptor-interacting protein 6 (TRIP6); The first LIM domain of Thyroid receptor-interacting protein 6 (TRIP6): TRIP6 is a member of the zyxin LIM protein family and contains three LIM zinc-binding domains at the C-terminal. TRIP6 protein localizes to focal adhesion sites and along actin stress fibers. Recruitment of this protein to the plasma membrane occurs in a lysophosphatidic acid (LPA)-dependent manner. TRIP6 recruits a number of molecules involved in actin assembly, cell motility, survival and transcriptional control. The function of TRIP6 in cell motility is regulated by Src-dependent phosphorylation at a Tyr residue. The phosphorylation activates the coupling to the Crk SH2 domain, which is required for the function of TRIP6 in promoting lysophosphatidic acid (LPA)-induced cell migration. TRIP6 can shuttle to the nucleus to serve as a coactivator of AP-1 and NF-kappaB transcriptional factors. Moreover, TRIP6 can form a ternary complex with the NHERF2 PDZ protein and LPA2 receptor to regulate LPA-induced activation of ERK and AKT, rendering cells resistant to chemotherapy. Recent evidence shows that TRIP6 antagonizes Fas-Induced apoptosis by enhancing the antiapoptotic effect of LPA in cells. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188736 Cd Length: 54 Bit Score: 38.54 E-value: 4.18e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 122056614 441 CGHCNN--VIRGPFLVAMGRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERCY 492
Cdd:cd09350    1 CGRCGEnvVGEGTGCTAMDQVFHVDCFTCMTCNGKLRGQPFYAVEKKAYCEPCY 54

PDZ domain 4 of glutamate receptor-interacting protein 1 (GRIP1) and GRIP2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) binding proteins GRIP1 (ABP/GRIP2) and GRIP2, and related domains. GRIP1 and GRIP2 each have 7 PDZ domains. The interaction of GRIP1 and GRIP2 with GluA2/3 (AMPAR subunit) regulates AMPAR trafficking and synaptic targeting. GRIP1 has an essential role in regulating AMPAR trafficking during synaptic plasticity and learning and memory. GRIP1 and GRIP2 interact with a variety of other proteins associated with protein trafficking and internalization, for example GRIP1 also interacts with KIF5 (also known as kinesin 1), EphB receptors, scaffold protein liprin-alpha, and the rasGEF GRASP-1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This GRIP family PDZ4 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467174 [Multi-domain] Cd Length: 99 Bit Score: 40.02 E-value: 4.25e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614   5 VTLTGP--GPWGFRLQGGKDFNMPLT----ISRITPGSKAAQSQLSQ-GDLVVAIDGVNTDTMTHLEAQNKIKSASYNLS 77
Cdd:cd06686   10 VILRGDplKGFGIQLQGGVFATETLSspplISFIEPDSPAERCGVLQvGDRVLSINGIPTEDRTLEEANQLLRDSASKVT 89


                 ....
gi 122056614  78 LTLQ 81
Cdd:cd06686   90 LEIE 93

EBNA-3B; Provisional

Pssm-ID: 223065 [Multi-domain] Cd Length: 991 Bit Score: 43.52 E-value: 4.34e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 278 PAAPAP-KPRVVTTASIRPSVYQPVPASTYSPSPGANYSPTPY-TPSPAPAYTPS----PAPAYTPSPVPTYTPSpAPAY 351
Cdd:PHA03378 698 PRAPTPmRPPAAPPGRAQRPAAATGRARPPAAAPGRARPPAAApGRARPPAAAPGrarpPAAAPGRARPPAAAPG-APTP 776

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 352 TPSPA--------PNYNPAPSVAYSGGPAEPASRPPWVTDDSFSQKFAPGKSTTSISKQ-----TLPRGGPAYTPAGPQV 418
Cdd:PHA03378 777 QPPPQappapqqrPRGAPTPQPPPQAGPTSMQLMPRAAPGQQGPTKQILRQLLTGGVKRgrpslKKPAALERQAAAGPTP 856


                 ..
gi 122056614 419 PP 420
Cdd:PHA03378 857 SP 858

The third LIM domain of Four and a half LIM domains protein 1 (FHL1); The third LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188813 Cd Length: 53 Bit Score: 38.64 E-value: 4.36e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 122056614 441 CGHCNNVIRGPFLVAMGRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERCYE 493
Cdd:cd09429    1 CVKCNKPITSGGVTYQDQPWHSECFVCSSCSKKLAGQRFTAVEDQYYCVDCYK 53

The third LIM domain of protein LIMPETin; The third LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188805 Cd Length: 59 Bit Score: 38.71 E-value: 4.70e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 122056614 441 CGHCNNVI--RGPFLVAMGRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERCYE 493
Cdd:cd09421    5 CEECSKIIgiDSKDLSYKDKHWHEACFLCSKCKISLVDKPFGSKADRIYCGNCYD 59

PDZ domain of Golgi-associated PDZ and coiled-coil motif-containing protein (GOPC), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of GOPC and related domains. GOPC, also known as PIST (PDZ domain protein interacting specifically with TC10), FIG (fused in glioblastoma), and CAL (CFTR-associated ligand), regulates the trafficking of a wide array of proteins, including small GTPases, receptors, and cell surface molecules such as cadherin 23 and CFTR. It may regulate CFTR chloride currents and acid-sensing ASIC3 currents by modulating cell surface expression of both channels, and may play a role in autophagy. Interaction partners of the GOPC PDZ domains include: FZD5, FZD8, ASIC3, CFTR, MUC3, ARFRP1, Ggamma13, neuroligin, and Stargazin. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This GOPC-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467261 [Multi-domain] Cd Length: 83 Bit Score: 39.28 E-value: 4.90e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 122056614  14 GFRLQGGKDFNMPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEA 65
Cdd:cd06800   14 GISITGGKEHGVPILISEIHEGQPADRCgGLYVGDAILSVNGIDLRDAKHKEA 66

The first LIM domain of Lmx1b; The first LIM domain of Lmx1b: Lmx1b belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. In mouse, Lmx1b functions in the developing limbs and eyes, the kidneys, the brain, and in cranial mesenchyme. The disruption of Lmx1b gene results kidney and limb defects. In the brain, Lmx1b is important for generation of mesencephalic dopamine neurons and the differentiation of serotonergic neurons. In the mouse eye, Lmx1b regulates anterior segment (cornea, iris, ciliary body, trabecular meshwork, and lens) development. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188757 [Multi-domain] Cd Length: 53 Bit Score: 38.13 E-value: 5.11e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 122056614 500 CAKCNTKIMGE-VMHALRQTWHTTCFVCAACKKPFGNSLFhMEDGEPYCEKDYI 552
Cdd:cd09371    1 CAGCQRPISDRyLLRVNERSWHEECLQCSVCQQPLTTSCY-FRDRKLYCKQDYQ 53

DNA polymerase III subunit gamma/tau;

Pssm-ID: 235906 [Multi-domain] Cd Length: 830 Bit Score: 43.30 E-value: 5.16e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 279 AAPAPKPRVVTTASIRPSVYQPVPASTYSPSPGAnySPTPYTPSPAPAYTPSPAPAYTPSPVPTYTPSPAPAYTPSPAPn 358
Cdd:PRK07003 396 VPAVTAVTGAAGAALAPKAAAAAAATRAEAPPAA--PAPPATADRGDDAADGDAPVPAKANARASADSRCDERDAQPPA- 472

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 359 yNPAPSVAySGGPAEPASRppwvtddsfsqkFAPGKSTTSISKQTLPRGGPAYTPAGPQ----VPPLARGTVQRAERFPA 434
Cdd:PRK07003 473 -DSGSASA-PASDAPPDAA------------FEPAPRAAAPSAATPAAVPDARAPAAASredaPAAAAPPAPEARPPTPA 538


                 ....*
gi 122056614 435 SSRTP 439
Cdd:PRK07003 539 AAAPA 543

PDZ domain 3 of membrane-associated guanylate kinase inverted 1 (MAGI-1), MAGI-2, and MAGI-3, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of MAGI1, 2, 3 (MAGI is also known as Membrane-associated guanylate kinase, WW and PDZ domain-containing protein) and related domains. MAGI proteins have been implicated in the control of cell migration and invasion through altering the activity of phosphatase and tensin homolog (PTEN) and modulating Akt signaling. Four MAGI proteins have been identified (MAGI1-3 and MAGIX). MAGI1-3 have 6 PDZ domains and bind to the C-terminus of PTEN via their PDZ2 domain. MAGIX has a single PDZ domain that is related to MAGI1-3 PDZ domain 5. Other binding partners for MAGI1 include JAM4, C-terminal tail of high risk HPV-18 E6, megalin, TRAF6, Kir4.1 (basolateral K+ channel subunit), and cadherin 23; for MAGI2, include DASM1, dendrin, axin, beta- and delta-catenin, neuroligin, hyperpolarization-activated cation channels, beta1-adrenergic receptors, NMDA receptor, and TARPs; and for MAGI3 includes LPA2. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MAGI family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as beta-strands A, -B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467215 [Multi-domain] Cd Length: 85 Bit Score: 39.13 E-value: 5.25e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 122056614  14 GFRLQGGKDFNMPLTISRITPGSKAAQSQ-LSQGDLVVAIDGVNTDTMTH 62
Cdd:cd06733   14 GFRILGGTEEGSQVSIGAIVPGGAADLDGrLRTGDELLSVDGVNVVGASH 63

Chitinase [Carbohydrate transport and metabolism];

Pssm-ID: 442692 [Multi-domain] Cd Length: 534 Bit Score: 42.82 E-value: 5.36e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 277 GPAAPAPKPRVVTTASIRPSVYQPVPASTYSPSPGANYSPTPYTPSPAPAYTPSPAPAYTPSPVPTYTPSPAPAYTPSPA 356
Cdd:COG3469  127 SSTAGSTTTSGASATSSAGSTTTTTTVSGTETATGGTTTTSTTTTTTSASTTPSATTTATATTASGATTPSATTTATTTG 206


                 ....*...
gi 122056614 357 PNYNPAPS 364
Cdd:COG3469  207 PPTPGLPK 214

The second LIM domain of Prickle; The second LIM domain of Prickle: Prickle contains three C-terminal LIM domains and a N-terminal PET domain. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). PCP establishment requires the conserved Frizzled/Dishevelled PCP pathway. Prickle interacts with Dishevelled, thereby modulating Frizzled/Dishevelled activity and PCP signaling. Two forms of prickles have been identified; namely prickle 1 and prickle 2. Prickle 1 and prickle 2 are differentially expressed. While prickle 1 is expressed in fetal heart and hematological malignancies, prickle 2 is found in fetal brain, adult cartilage, pancreatic islet, and some types of timorous cells. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188802 Cd Length: 56 Bit Score: 38.18 E-value: 5.42e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 122056614 558 KCHGCDFPVEAgDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLC 608
Cdd:cd09418    2 RCSACDEIIFA-DECTEAEGRHWHMKHFCCFECECQLGGQRYIMREGRPYC 51

cytoskeleton protein RodZ;

Pssm-ID: 236776 [Multi-domain] Cd Length: 331 Bit Score: 42.32 E-value: 5.55e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 299 QPVPASTYS-------PSPGANYSPTPyTPSPAPAYTPSPAPAYTPSPVPTYTPSPA---PAYTPSPAPNYNP---APSV 365
Cdd:PRK10856 160 QSVPLDTSTttdpattPAPAAPVDTTP-TNSQTPAVATAPAPAVDPQQNAVVAPSQAnvdTAATPAPAAPATPdgaAPLP 238

                         90
                 ....*....|...
gi 122056614 366 AYSGGPAEPASRP 378
Cdd:PRK10856 239 TDQAGVSTPAADP 251

K+-dependent Na+/Ca+ exchanger; [Transport and binding proteins, Cations and iron carrying compounds]

Pssm-ID: 273344 [Multi-domain] Cd Length: 1096 Bit Score: 43.06 E-value: 5.65e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614   275 SEGPAAPAPKprvVTTASIRPSVYQPVPASTYSPSPGANYSPTP-----YTPSPAPAYTPSPAPAYTPSPVPTyTPSPAP 349
Cdd:TIGR00927  351 LSRTSAPAVR---IASATFRGLEKNPSTAPSTPATPRVRAVLTTqvhhcVVVKPAPAVPTTPSPSLTTALFPE-APSPSP 426

                           90
                   ....*....|..
gi 122056614   350 AYTPSPAPNYNP 361
Cdd:TIGR00927  427 SALPPGQPDLHP 438

transcriptional regulator ICP4; Provisional

Pssm-ID: 223039 [Multi-domain] Cd Length: 1352 Bit Score: 43.24 E-value: 5.88e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  278 PAAPAPKPRVVTTASIRPSVYQPVPASTYSPSPGANYSPTPytPSPAPAytPSPAPAYTPSPVPTYTPSPAPAYTPSPAP 357
Cdd:PHA03307  139 RPVGSPGPPPAASPPAAGASPAAVASDAASSRQAALPLSSP--EETARA--PSSPPAEPPPSTPPAAASPRPPRRSSPIS 214

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  358 NYNPAPSVAYSGGPAEPASRPPWVTDDSFSQKFA-------PGKSTTSISKQTLPRGGPAYTPAGPQVPPLARGTVQRAE 430
Cdd:PHA03307  215 ASASSPAPAPGRSAADDAGASSSDSSSSESSGCGwgpenecPLPRPAPITLPTRIWEASGWNGPSSRPGPASSSSSPRER 294

                         170
                  ....*....|....*....
gi 122056614  431 RFPASSRTPLCGHCNNVIR 449
Cdd:PHA03307  295 SPSPSPSSPGSGPAPSSPR 313

PDZ domain of regulator of G-protein signaling 3 (RGS3), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of RGS3, and related domains. RGS3 down-regulates GPCR signal transduction by increasing the GTPase activity of G-protein alpha subunits, thereby driving G-proteins into their inactive GDP-bound form. It downregulates G-protein-mediated release of inositol phosphates and activation of MAP kinases. In Eph/ephrin signaling, RGS3 binds via its PDZ domain to the cytoplasmic C terminus of Eph receptor tyrosine kinase EphB. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This RGS3-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467195 [Multi-domain] Cd Length: 77 Bit Score: 38.91 E-value: 6.19e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 122056614  24 NMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTL 80
Cdd:cd06711   19 DSPVRVQAVDPGGPAEQAGLQQGDTVLQINGQPVERSKCVELAHAIRNCPSEIILLV 75

The second LIM domain of Cysteine Rich Protein 3 (CRP3/MLP); The second LIM domain of Cysteine Rich Protein 3 (CRP3/MLP): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network.CRP3 also called Muscle LIM Protein (MLP), which is a striated muscle-specific factor that enhances myogenic differentiation. The second LIM domain of CRP3/MLP interacts with cytoskeletal protein beta-spectrin. CRP3/MLP also interacts with the basic helix-loop-helix myogenic transcription factors MyoD, myogenin, and MRF4 thereby increasing their affinity for specific DNA regulatory elements. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188866 [Multi-domain] Cd Length: 54 Bit Score: 38.07 E-value: 6.31e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 122056614 439 PLCGhcNNVIRGPFLVAMGRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERCY 492
Cdd:cd09482    2 PRCG--KSVYAAEKVMGGGKPWHKTCFRCAICGKSLESTTVTDKDGELYCKVCY 53

The LIM domains of thymus LIM protein (TLP); The LIM domain of thymus LIM protein (TLP) like proteins: This family includes the LIM domains of TLP and CRIP (Cysteine-Rich Intestinal Protein). TLP is the distant member of the CRP family of proteins. TLP has two isomers (TLP-A and TLP-B) and sharing approximately 30% with each of the three other CRPs. Like CRP1, CRP2 and CRP3/MLP, TLP has two LIM domains, connected by a flexible linker region. Unlike the CRPs, TLP lacks the nuclear targeting signal (K/R-K/R-Y-G-P-K) and is localized solely in the cytoplasm. TLP is specifically expressed in the thymus in a subset of cortical epithelial cells. TLP has a role in development of normal thymus and in controlling the development and differentiation of thymic epithelial cells. CRIP is a short LIM protein with only one LIM domain. CRIP gene is developmentally regulated and can be induced by glucocorticoid hormones during the first three postnatal weeks. The domain shows close sequence homology to LIM domain of thymus LIM protein. However, unlike the TLP proteins which have two LIM domains, the members of this family have only one LIM domain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188785 [Multi-domain] Cd Length: 53 Bit Score: 38.09 E-value: 6.38e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 559 CHGCDFPVEAGDKfIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKK 610
Cdd:cd09401    1 CPKCGKPVYFAEK-KTSLGRDWHKPCLRCEKCKKTLTPGQHSEHEGKPYCNK 51

Chitinase [Carbohydrate transport and metabolism];

Pssm-ID: 442692 [Multi-domain] Cd Length: 534 Bit Score: 42.82 E-value: 6.42e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 270 THTSYSEGPAAPAPKPRVVTTASIRPSVYQPVPASTYSPSPGANYSPTPYTPSPAPAYTPSP------APAYTPSPVPTY 343
Cdd:COG3469   90 TSTSATLVATSTASGANTGTSTVTTTSTGAGSVTSTTSSTAGSTTTSGASATSSAGSTTTTTtvsgteTATGGTTTTSTT 169

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 122056614 344 TPSPAPAYTPSPAPNYNPAPSVAYSGGPAEPASRPPWVTDDSFSQK 389
Cdd:COG3469  170 TTTTSASTTPSATTTATATTASGATTPSATTTATTTGPPTPGLPKH 215

The second LIM domain of Cysteine Rich Protein 2 (CRP2); The second LIM domain of Cysteine Rich Protein 2 (CRP2): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network.CRP3 also called Muscle LIM Protein (MLP), which is a striated muscle-specific factor that enhances myogenic differentiation. The second LIM domain of CRP3/MLP interacts with cytoskeletal protein beta-spectrin. CRP3/MLP also interacts with the basic helix-loop-helix myogenic transcription factors MyoD, myogenin, and MRF4 thereby increasing their affinity for specific DNA regulatory elements. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188871 [Multi-domain] Cd Length: 54 Bit Score: 38.17 E-value: 6.52e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 122056614 559 CHGCDFPVEAGDKFIEAlGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCK 609
Cdd:cd09840    1 CSRCGDSVYAAEKIMGA-GKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCK 50

The second LIM domain of Ajuba-like proteins; The second LIM domain of Ajuba-like proteins: Ajuba like LIM protein family includes three highly homologous proteins Ajuba, Limd1, and WTIP. Members of the family contain three tandem C-terminal LIM domains and a proline-rich N-terminal region. This family of proteins functions as scaffolds, participating in the assembly of numerous protein complexes. In the cytoplasm, Ajuba binds Grb2 to modulate serum-stimulated ERK activation. Ajuba also recruits the TNF receptor-associated factor 6 (TRAF6) to p62 and activates PKCKappa activity. Ajuba interacts with alpha-catenin and F-actin to contribute to the formation or stabilization of adheren junctions by linking adhesive receptors to the actin cytoskeleton. Although Ajuba is a cytoplasmic protein, it can shuttle into the nucleus. In nucleus, Ajuba functions as a corepressor for the zinc finger-protein Snail. It binds to the SNAG repression domain of Snail through its LIM region. Arginine methyltransferase-5 (Prmt5), a protein in the complex, is recruited to Snai l through an interaction with Ajuba. This ternary complex functions to repress E-cadherin, a Snail target gene. In addition, Ajuba contains functional nuclear-receptor interacting motifs and selectively interacts with retinoic acid receptors (RARs) and rexinoid receptor (RXRs) to negatively regulate retinoic acid signaling. Wtip, the Wt1-interacting protein, was originally identified as an interaction partner of the Wilms tumour protein 1 (WT1). Wtip is involved in kidney and neural crest development. Wtip interacts with the receptor tyrosine kinase Ror2 and inhibits canonical Wnt signaling. LIMD1 was reported to inhibit cell growth and metastases. The inhibition may be mediated through an interaction with the protein barrier-to-autointegration (BAF), a component of SWI/SNF chromatin-remodeling protein; or through the interaction with retinoblastoma protein (pRB), resulting in inhibition of E2F-mediated transcription, and expression of the majority of genes with E2F1- responsive elements. Recently, Limd1 was shown to interact with the p62/sequestosome protein and influence IL-1 and RANKL signaling by facilitating the assembly of a p62/TRAF6/a-PKC multi-protein complex. The Limd1-p62 interaction affects both NF-kappaB and AP-1 activity in epithelial cells and osteoclasts. Moreover, LIMD1 functions as tumor repressor to block lung tumor cell line in vitro and in vivo. Recent studies revealed that LIM proteins Wtip, LIMD1 and Ajuba interact with components of RNA induced silencing complexes (RISC) as well as eIF4E and the mRNA m7GTP cap-protein complex and are required for microRNA-mediated gene silencing. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188741 [Multi-domain] Cd Length: 53 Bit Score: 38.09 E-value: 6.63e-04

                         10        20        30
                 ....*....|....*....|....*....|.
gi 122056614 569 GDKFIEALGHTWHDTCFICAVCHVNLEGQPF 599
Cdd:cd09355    9 MEMILQALGKSYHPGCFRCCVCNECLDGVPF 39

The fourth LIM domain of the Paxillin-like protein family; The fourth LIM domain of the Paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188725 [Multi-domain] Cd Length: 52 Bit Score: 38.09 E-value: 6.68e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 500 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 551
Cdd:cd09339    1 CAGCGKPITGRCITAMGRKFHPEHFVCAFCLKQLSKGTFKEQDDKPYCHPCF 52

cell division protein DedD; Provisional

Pssm-ID: 236940 [Multi-domain] Cd Length: 226 Bit Score: 41.53 E-value: 6.81e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 295 PSVYQPVPAStysPSPGAN---YSPTPYTPSPAPAYTPSPAPAYTPSPVPTYTPSPAPAYTPSPAPNYNPAPSVAysgGP 371
Cdd:PRK11633  57 PAATQALPTQ---PPEGAAeavRAGDAAAPSLDPATVAPPNTPVEPEPAPVEPPKPKPVEKPKPKPKPQQKVEAP---PA 130


                 ....*...
gi 122056614 372 AEPASRPP 379
Cdd:PRK11633 131 PKPEPKPV 138

AIDA-I family autotransporter YfaL;

Pssm-ID: 182059 [Multi-domain] Cd Length: 1250 Bit Score: 42.74 E-value: 6.83e-04

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 122056614  317 TPYTPsPAPAYTPSPAPayTPSPVPTYTPSPAPAYTP 353
Cdd:PRK09752  919 TPPSP-PDPDPTPDPDP--TPDPDPTPDPEPTPAYQP 952

The second LIM domain of Thyroid receptor-interacting protein 6 (TRIP6); The second LIM domain of Thyroid receptor-interacting protein 6 (TRIP6): TRIP6 is a member of the zyxin LIM protein family and contains three LIM zinc-binding domains at the C-terminal. TRIP6 protein localizes to focal adhesion sites and along actin stress fibers. Recruitment of this protein to the plasma membrane occurs in a lysophosphatidic acid (LPA)-dependent manner. TRIP6 recruits a number of molecules involved in actin assembly, cell motility, survival and transcriptional control. The function of TRIP6 in cell motility is regulated by Src-dependent phosphorylation at a Tyr residue. The phosphorylation activates the coupling to the Crk SH2 domain, which is required for the function of TRIP6 in promoting lysophosphatidic acid (LPA)-induced cell migration. TRIP6 can shuttle to the nucleus to serve as a coactivator of AP-1 and NF-kappaB transcriptional factors. Moreover, TRIP6 can form a ternary complex with the NHERF2 PDZ protein and LPA2 receptor to regulate LPA-induced activation of ERK and AKT, rendering cells resistant to chemotherapy. Recent evidence shows that TRIP6 antagonizes Fas-Induced apoptosis by enhancing the antiapoptotic effect of LPA in cells. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188742 Cd Length: 53 Bit Score: 37.92 E-value: 7.01e-04

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 122056614 441 CGHCNNVIRGPFLVAMGRSWHPEEFTCAYCKTSLADVCF-VEEQNNVYC 488
Cdd:cd09356    1 CSVCSKPIMERILRATGKAYHPHCFTCVVCHRSLDGIPFtVDATGQIHC 49

The third LIM domain of paxillin; The third LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188793 [Multi-domain] Cd Length: 53 Bit Score: 37.90 E-value: 7.14e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 441 CGHCNNVIRGPFLVAMGRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERCY 492
Cdd:cd09409    1 CGGCARAILENYISALNTLWHPECFVCRECFTPFVNGSFFEHDGQPYCEAHY 52

envelope glycoprotein C; Provisional

Pssm-ID: 165527 [Multi-domain] Cd Length: 566 Bit Score: 42.41 E-value: 7.48e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 273 SYSEGPAAPAPKPRVVTTASIRPSVYQ-PVPASTYSPSPG-ANYSPTPYTPSPAPAYTPSPAPAYTPSPVPTYTPS--PA 348
Cdd:PHA03269  46 PHQAASRAPDPAVAPTSAASRKPDLAQaPTPAASEKFDPApAPHQAASRAPDPAVAPQLAAAPKPDAAEAFTSAAQahEA 125

                         90
                 ....*....|....*.
gi 122056614 349 PAYTPSPAPNYNPAPS 364
Cdd:PHA03269 126 PADAGTSAASKKPDPA 141

The first LIM domain of Prickle 1; The first LIM domain of Prickle 1. Prickle contains three C-terminal LIM domains and a N-terminal PET domain Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). PCP establishment requires the conserved Frizzled/Dishevelled PCP pathway. Prickle interacts with Dishevelled, thereby modulating Frizzled/Dishevelled activity and PCP signaling. Four forms of prickles have been identified: prickle 1-4. The best characterized is prickle 1 and prickle 2 which are differentially expressed. While prickle 1 is expressed in fetal heart and hematological malignancies, prickle 2 is found in mainly expressed in fetal brain, adult cartilage, pancreatic islet, and some types of timorous cells. In addition, Prickle 1 regulates cell movements during gastrulation and neuronal migration through interaction with the noncanonical Wnt11/Wnt5 pathway in zebrafish. Mutations in prickle 1 have been linked to progressive myoclonus epilepsy. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188867 Cd Length: 59 Bit Score: 37.98 E-value: 7.92e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 122056614 500 CAKCNTKI-MGEV-MHALRQ----TWHTTCFVCAACKKPFGNSLFHMEDGEPYC 547
Cdd:cd09483    1 CEQCGIKInGGEVaVFASRAgpgvCWHPSCFVCFTCNELLVDLIYFYQDGKIHC 54

The second LIM domain of Cysteine Rich Protein (CRP); The second LIM domain of Cysteine Rich Protein (CRP): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to a short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription control, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. It is evident that CRP1, CRP2, and CRP3/MLP are involved in promoting protein assembly along the actin-based cytoskeleton. Although members of the CRP family share common binding partners, they are also capable of recognizing different and specific targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residu es, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188787 Cd Length: 54 Bit Score: 37.94 E-value: 8.00e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 122056614 488 CERCYEQFFAPlcakcnTKIMGEvmhalRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 551
Cdd:cd09403    1 CPRCGKSVYAA------EKIIGA-----GKPWHKNCFRCAKCGKSLESTTLADKDGEIYCKGCY 53

chromosomal replication initiator protein DnaA;

Pssm-ID: 237605 [Multi-domain] Cd Length: 617 Bit Score: 42.51 E-value: 8.06e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 271 HTSYSEGPAAPAPKPRVVTTASIRPSVYQPVPASTYSPSPGANYSPTPYTPSPAPAYTPSPAPAYTPSPVPTYTPSPAPA 350
Cdd:PRK14086 101 HARRTSEPELPRPGRRPYEGYGGPRADDRPPGLPRQDQLPTARPAYPAYQQRPEPGAWPRAADDYGWQQQRLGFPPRAPY 180

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 351 YTPS---PAPNYNPAPSVAysGGPAEPASRPPWVTDDSFSQKfaPGKSTTsisKQTLPRGGPAYTPAGPQVPPLARGTVQ 427
Cdd:PRK14086 181 ASPAsyaPEQERDREPYDA--GRPEYDQRRRDYDHPRPDWDR--PRRDRT---DRPEPPPGAGHVHRGGPGPPERDDAPV 253


                 ....*..
gi 122056614 428 RAERFPA 434
Cdd:PRK14086 254 VPIRPSA 260

transcriptional regulator ICP4; Provisional

Pssm-ID: 223039 [Multi-domain] Cd Length: 1352 Bit Score: 42.47 E-value: 8.27e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  275 SEGPAAPAPKPRVVTTASIRPSVYQPVPA-------------STYSPSPGANYSPTPYTP--SPAPAYTPSPAPAYTPSP 339
Cdd:PHA03307  197 TPPAAASPRPPRRSSPISASASSPAPAPGrsaaddagasssdSSSSESSGCGWGPENECPlpRPAPITLPTRIWEASGWN 276

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  340 VPTYTPSPAPAYTPSPAPNYNPAPSVAYSGGPAEPASRPPWVTDDSFSQKFAPGKSTTSISKQTLPRGGPAYTPAGPQVP 419
Cdd:PHA03307  277 GPSSRPGPASSSSSPRERSPSPSPSSPGSGPAPSSPRASSSSSSSRESSSSSTSSSSESSRGAAVSPGPSPSRSPSPSRP 356

                         170       180
                  ....*....|....*....|
gi 122056614  420 PLARGTVQRAERFPASSRTP 439
Cdd:PHA03307  357 PPPADPSSPRKRPRPSRAPS 376

The fourth LIM domain of Four and a half LIM domains protein 3 (FHL3); The fourth LIM domain of Four and a half LIM domains protein 3 (FHL3): FHL3 is highly expressed in the skeleton and cardiac muscles and possesses the transactivation and repression activities. FHL3 interacts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. Moreover, FHL3 interacts with alpha- and beta-subunits of the muscle alpha7beta1 integrin receptor. FHL3 was also proved to possess the auto-activation ability and was confirmed that the second zinc finger motif in fourth LIM domain was responsible for the auto-activation of FHL3. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188818 Cd Length: 56 Bit Score: 37.82 E-value: 8.46e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 122056614 441 CGHCNNVIRG----PFLVAMGRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERC 491
Cdd:cd09434    1 CAACNKPITGfgggKYVSFEDRQWHQPCFKCSRCSVSLVGAGFFPDGDQILCRDC 55

DNA polymerase III subunits gamma and tau; Provisional

Pssm-ID: 237864 [Multi-domain] Cd Length: 585 Bit Score: 42.49 E-value: 8.50e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 287 VVTTASIRPSVYQPVPASTYSPSPGANYSPTPYTPSPAPAYTPSPAPAYTPSPVPTyTPSPAPAYTPSPAPNyNPAPSVA 366
Cdd:PRK14950 355 VIEALLVPVPAPQPAKPTAAAPSPVRPTPAPSTRPKAAAAANIPPKEPVRETATPP-PVPPRPVAPPVPHTP-ESAPKLT 432

                         90
                 ....*....|....*
gi 122056614 367 YSGGPAE--PASRPP 379
Cdd:PRK14950 433 RAAIPVDekPKYTPP 447

DNA polymerase III subunits gamma and tau; Provisional

Pssm-ID: 237871 [Multi-domain] Cd Length: 576 Bit Score: 42.42 E-value: 8.79e-04

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 122056614 308 PSPGANYSPTPYTPSPAPAYTPSPAPAYTPSPVPTYTPSPAPAYTPSPAPnynPAPSVAysggPAEPASRPP-W 380
Cdd:PRK14965 384 PPSAAWGAPTPAAPAAPPPAAAPPVPPAAPARPAAARPAPAPAPPAAAAP---PARSAD----PAAAASAGDrW 450

The second LIM domain of paxillin; The second LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188791 [Multi-domain] Cd Length: 52 Bit Score: 37.63 E-value: 9.53e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 559 CHGCDFPVEagDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKK 610
Cdd:cd09407    1 CYYCNGPIL--DKVVTALDRTWHPEHFFCAQCGAFFGPEGFHEKDGKAYCRK 50

The third LIM domain of Four and a half LIM domains protein 2 (FHL2); The third LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung to a lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to s upport the assembly of multimeric protein complexes.

Pssm-ID: 188815 Cd Length: 57 Bit Score: 37.66 E-value: 1.00e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 122056614 559 CHGCDFPVEAGDkfIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLC 608
Cdd:cd09431    1 CVQCKKPITTGG--VTYRDQPWHKECFVCTGCKKQLSGQRFTSRDDFAYC 48

PDZ domain 5 of protein tyrosine phosphatase non-receptor type 13 (PTPN13), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 5 of PTPN13 [also known as Fas-associated protein-tyrosine phosphatase 1 (FAP-1), Protein-tyrosine phosphatase 1E (PTP-E1), and Protein-tyrosine phosphatase (PTPL1)] and related domains. PTPN13 regulates negative apoptotic signaling and mediates phosphoinositide 3-kinase (PI3K) signaling. PTPN13 has five PDZ domains. Proteins known to interact with PTPN13 PDZ domains include: PLEKHA1 and PLEKHA2 via PTPN13-PDZ domain 1, Fas receptor and thyroid receptor-interacting protein 6 via PTPN13-PDZ domain 2, nerve growth factor receptor and protein kinase N2 via PTPN13-PDZ domain 3, PDZ and LIM domain 4 (PDLIM4) via PTPN13-PDZ domains 2 and 4, and brain calpain-2 via PTPN13-PDZ domains 3, 4 and 5. Calpain-2-mediated PTPN13 fragments may be involved in abnormal tau aggregation and increased risk for Alzheimer's disease. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PTPN13 family PDZ5 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467183 [Multi-domain] Cd Length: 87 Bit Score: 38.48 E-value: 1.02e-03

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 122056614   5 VTLT-GPGPWGFRLQGGKDFNMP-LTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSL 78
Cdd:cd06697    6 ITLTcHPGQLGLKLTGGSDSKYQvIYVLEIVPGSAAAEEgSLQPLDIIHYINGVSTQGMTLEDAVRALEASLPTVVL 82

envelope glycoprotein I; Provisional

Pssm-ID: 223033 [Multi-domain] Cd Length: 401 Bit Score: 41.86 E-value: 1.08e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 278 PAAPAPKPRVVTTASIRPSVYQPVPASTYSPspgaNYSPTPYTPSPAPAYTPSPAPAYTPSPVPTYTP-SPAPAYTPSPA 356
Cdd:PHA03291 188 PALPLSAPRLGPADVFVPATPRPTPRTTASP----ETTPTPSTTTSPPSTTIPAPSTTIAAPQAGTTPeAEGTPAPPTPG 263

                         90       100
                 ....*....|....*....|.
gi 122056614 357 PNYNPAPsvaySGGPAEPASR 377
Cdd:PHA03291 264 GGEAPPA----NATPAPEASR 280

The second LIM domain of Four and a half LIM domains protein 1 (FHL1); The second LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188808 Cd Length: 58 Bit Score: 37.43 E-value: 1.08e-03

                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 122056614 519 WHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDYINLF 555
Cdd:cd09424   22 WHKDCFTCSNCKQPIGTKSFFPKGEDFYCVPCHEKKF 58

The second LIM domain of Four and a half LIM domains protein 5 (FHL5); The second LIM domain of Four and a half LIM domains protein 5 (FHL5): FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors , which are highly expressed in male germ cells and is required for post-meiotic gene expression. FHL5 associates with CREM and confers a powerful transcriptional activation function. Activation by CREB has known to occur upon phosphorylation at an essential regulatory site and the subsequent interaction with the ubiquitous coactivator CREB-binding protein (CBP). However, the activation by FHL5 is independent of phosphorylation and CBP association. It represents a new route for transcriptional activation by CREM and CREB. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188812 Cd Length: 54 Bit Score: 37.51 E-value: 1.09e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 122056614 500 CAKCNTKIM--GEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYC 547
Cdd:cd09428    1 CFHCKKTIMpgSRKLEFEGNEWHETCFVCQSCQQPIGTKPLITKENKNYC 50

This family represents the LIM domain of CLP36; This family represents the LIM domain of CLP36. CLP36 has also been named as CLIM1, Elfin, or PDLIM1. CLP36 contains a C-terminal LIM domain and an N-terminal PDZ domain. CLP36 is highly expressed in heart and is present in many other tissues including lung, liver, spleen, and blood. CLP36 has been implicated in many processes including hypoxia and regulation of actin stress fibers. CLP36 co-localizes with alpha-actinin-2 at the Z-lines in myocardium. In addition, CLP36 binds to alpha-actinin-1 and alpha-actinin-4, and associates with F-actin filaments and stress fibers. CLP36 might be involved in not only the function of sarcomeres in muscle cells, but also in actin stress fiber-mediated cellular processes, such as cell shape, migration, polarit, and cytokinesis in non-muscle cells. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188832 Cd Length: 52 Bit Score: 37.20 E-value: 1.09e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 441 CGHCNNVIRGPFLVAMGRSWHPEEFTCAYCKTSLADV--CFVEEQnnVYCER 490
Cdd:cd09448    1 CDKCGSGIVGVFVKIRDKPRHPECYVCTDCGTNLKQKghFFVEDQ--IYCEK 50

DNA polymerase III subunits gamma and tau; Provisional

Pssm-ID: 184927 [Multi-domain] Cd Length: 504 Bit Score: 41.75 E-value: 1.15e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 271 HTSYSEGPAAPAPKPRVVTTASIRPSVYQPVPASTyspsPGANYSPTPYTPSPAPAYTPSPAPAytPSPVPTYTPSPAPA 350
Cdd:PRK14963 343 GGAPSEGVAAVAPPAPAPADLTQRLNRLEKEVRSL----RSAPTAAATAAGAPLPDFDPRPRGP--PAPEPARSAEAPPL 416


                 ....*..
gi 122056614 351 YTPSPAP 357
Cdd:PRK14963 417 VAPAAAP 423

The second LIM domain of Cysteine Rich Protein 3 (CRP3/MLP); The second LIM domain of Cysteine Rich Protein 3 (CRP3/MLP): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network.CRP3 also called Muscle LIM Protein (MLP), which is a striated muscle-specific factor that enhances myogenic differentiation. The second LIM domain of CRP3/MLP interacts with cytoskeletal protein beta-spectrin. CRP3/MLP also interacts with the basic helix-loop-helix myogenic transcription factors MyoD, myogenin, and MRF4 thereby increasing their affinity for specific DNA regulatory elements. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188866 [Multi-domain] Cd Length: 54 Bit Score: 37.30 E-value: 1.15e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 122056614 559 CHGCDFPVEAGDKFIEAlGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCK 609
Cdd:cd09482    1 CPRCGKSVYAAEKVMGG-GKPWHKTCFRCAICGKSLESTTVTDKDGELYCK 50

LIM domain in proteins of unknown function; The first Lim domain of a LIM domain containing protein: The functions of the proteins are unknown. The members of this family contain two copies of LIM domain. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188783 [Multi-domain] Cd Length: 58 Bit Score: 37.24 E-value: 1.16e-03

                         10        20        30
                 ....*....|....*....|....*....|....*
gi 122056614 580 WHDTCFICAVCHVNLEGQ-PFYSKKDRPLCKKHAH 613
Cdd:cd09397   24 WHRECFVCTTCGCPFQFSvPCYVLDDKPYCQQHYH 58

DNA polymerase III subunits gamma and tau; Provisional

Pssm-ID: 237864 [Multi-domain] Cd Length: 585 Bit Score: 41.72 E-value: 1.18e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 323 PAPAYTPSPAPAYTPSPVptyTPSPAPAYTPSPAPNYN--PAPSVAYSGGPAEPASRPPwvtddsfsqkfAPGKSTTSIS 400
Cdd:PRK14950 362 PVPAPQPAKPTAAAPSPV---RPTPAPSTRPKAAAAANipPKEPVRETATPPPVPPRPV-----------APPVPHTPES 427

                         90       100
                 ....*....|....*....|...
gi 122056614 401 KQTLPRG------GPAYTPAGPQ 417
Cdd:PRK14950 428 APKLTRAaipvdeKPKYTPPAPP 450

PDZ domain 6 of glutamate receptor-interacting protein 1 (GRIP1) and GRIP2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) binding proteins GRIP1 (ABP/GRIP2) and GRIP2, and related domains. GRIP1 and GRIP2 each have 7 PDZ domains. The interaction of GRIP1 and GRIP2 with GluA2/3 (AMPAR subunit) regulates AMPAR trafficking and synaptic targeting. GRIP1 has an essential role in regulating AMPAR trafficking during synaptic plasticity and learning and memory. GRIP1 and GRIP2 interact with a variety of other proteins associated with protein trafficking and internalization, for example GRIP1 also interacts with KIF5 (also known as kinesin 1), EphB receptors, scaffold protein liprin-alpha, and the rasGEF GRASP-1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This GRIP family PDZ6 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467171 [Multi-domain] Cd Length: 85 Bit Score: 38.05 E-value: 1.20e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614   3 YSVTLT--GpGPWGFRLQGGKDFNMPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLT 79
Cdd:cd06683    4 YTVELKryG-GPLGITISGTEEPFDPIVISGLTEGGLAERTgAIHVGDRILAINGESLRGKPLSEAIHLLQNAGDTVTLK 82


                 ...
gi 122056614  80 LQK 82
Cdd:cd06683   83 ISR 85

multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine pyrophosphate-binding subunit/dihydrolipoyllysine-residue succinyltransferase subunit;

Pssm-ID: 237030 [Multi-domain] Cd Length: 1228 Bit Score: 41.80 E-value: 1.29e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  298 YQPvPASTYSPSPGANYSPTPYTPSPAPAYTPSPAPAYTPSPVPTYTPSPAPAYTPSPAPNYNPAPSVAYSGGPAEPASR 377
Cdd:PRK12270   36 YGP-GSTAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAAAAAAAAAPAAPPAAAAAAAPAAAAVE 114


                  .
gi 122056614  378 P 378
Cdd:PRK12270  115 D 115

The second LIM domain of Four and a half LIM domains protein 2 (FHL2); The second LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung to a lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to s upport the assembly of multimeric protein complexes.

Pssm-ID: 188810 Cd Length: 57 Bit Score: 37.34 E-value: 1.29e-03

                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 122056614 457 GRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERCYEQ 494
Cdd:cd09426   19 GNSWHETCFICQRCQQPIGTKSFIPKDNQNFCVPCYEK 56

multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine pyrophosphate-binding subunit/dihydrolipoyllysine-residue succinyltransferase subunit;

Pssm-ID: 237030 [Multi-domain] Cd Length: 1228 Bit Score: 41.80 E-value: 1.30e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  302 PASTYSPSPGANYSPTPYTPSPAPAYTPSPAPAYTPSPVPTyTPSPAPAYTPSPAPnynPAPSVAYSGGPAEPASRPPWV 381
Cdd:PRK12270   38 PGSTAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAA-APAAPPKPAAAAAA---AAAPAAPPAAAAAAAPAAAAV 113


                  ....
gi 122056614  382 TDDS 385
Cdd:PRK12270  114 EDEV 117

putative acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated

Pssm-ID: 235540 [Multi-domain] Cd Length: 153 Bit Score: 39.85 E-value: 1.32e-03

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 122056614 318 PYTPSPAPAYTPSPAPAytpsPVPTYTPSPAPAYTPSPAP 357
Cdd:PRK05641  44 DLSAVQEQVPTPAPAPA----PAVPSAPTPVAPAAPAPAP 79

The second LIM domain of Cysteine Rich Protein (CRP); The second LIM domain of Cysteine Rich Protein (CRP): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to a short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription control, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. It is evident that CRP1, CRP2, and CRP3/MLP are involved in promoting protein assembly along the actin-based cytoskeleton. Although members of the CRP family share common binding partners, they are also capable of recognizing different and specific targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residu es, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188787 Cd Length: 54 Bit Score: 37.17 E-value: 1.34e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 122056614 441 CGHCNN-VIRGPFLVAMGRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERCY 492
Cdd:cd09403    1 CPRCGKsVYAAEKIIGAGKPWHKNCFRCAKCGKSLESTTLADKDGEIYCKGCY 53

The fourth LIM domain of Four and a half LIM domains protein 2 (FHL2); The fourth LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung to a lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to s upport the assembly of multimeric protein complexes.

Pssm-ID: 188817 Cd Length: 58 Bit Score: 37.28 E-value: 1.36e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 122056614 441 CGHCNNVIRG----PFLVAMGRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERC 491
Cdd:cd09433    1 CAGCTNPISGlggtKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPEC 55

The fifth LIM domain of protein PINCH; The fifth LIM domain of protein PINCH: PINCH plays pivotal roles in the assembly of focal adhesions (FAs), regulating diverse functions in cell adhesion, growth, and differentiation through LIM-mediated protein-protein interactions. PINCH comprises an array of five LIM domains that interact with integrin-linked kinase (ILK), Nck2 (also called Nckbeta or Grb4) and other interaction partners. These interactions are essential for triggering the FA assembly and for relaying diverse mechanical and biochemical signals between Cell-extracellular matrix and the actin cytoskeleton. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188721 [Multi-domain] Cd Length: 54 Bit Score: 36.94 E-value: 1.36e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 122056614 559 CHGCDFPVEaGDkFIEALGHTWHDTCFICAVCHVNLEGQ-PFYSKKDRPLCKK 610
Cdd:cd09335    1 CYHCNQVIE-GD-VVSALNKTWCVDHFSCSFCDTKLTLKsKFYEFDMKPVCKK 51

The second LIM domain of Testin; The second LIM domain of Testin: Testin contains three C-terminal LIM domains and a PET protein-protein interaction domain at the N-terminal. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Knockout mice experiments reveal that tumor repressor function of testin. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188800 Cd Length: 56 Bit Score: 37.14 E-value: 1.40e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 558 KCHGCDFPVEAgDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCK 609
Cdd:cd09416    2 RCAGCDELIFS-NEYTQAENQNWHLKHFCCFDCDNILAGEIYVMVNDKPVCK 52

The first LIM domain of Lmx1a; The first LIM domain of Lmx1a: Lmx1a belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Mouse Lmx1a is expressed in multiple tissues, including the roof plate of the neural tube, the developing brain, the otic vesicles, the notochord, and the pancreas. Human Lmx1a can be found in pancreas, skeletal muscle, adipose tissue, developing brain, mammary glands, and pituitary. The functions of Lmx1a in the developing nervous system were revealed by studies of mutant mouse. In mouse, mutations in Lmx1a result in failure of the roof plate to develop. Lmx1a may act upstream of other roof plate markers such as MafB, Gdf7, Bmp 6, and Bmp7. Further characterization of these mice reveals numerous defects including disorganized cerebellum, hippocampus, and cortex; altered pigmentation; female sterility; skeletal defects; and behavioral abnormalities. Within pancreatic cells, the Lmx1a protein interacts synergistically with the bHLH transcription factor E47 to activate the insulin gene enhancer/promoter. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188756 [Multi-domain] Cd Length: 52 Bit Score: 37.06 E-value: 1.42e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 122056614 500 CAKCNTKIMGEVMHALRQT-WHTTCFVCAACKKPFGNSLFhMEDGEPYCEKDY 551
Cdd:cd09370    1 CEGCNRVIQDRFLLRVNDSlWHERCLQCASCKEPLETTCF-YRDKKLYCKEDY 52

The first LIM domain of protein LIMPETin; The first LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the Testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188798 [Multi-domain] Cd Length: 58 Bit Score: 36.99 E-value: 1.42e-03

                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 122056614 559 CHGCDFPVEAGD------KFIEALGhtWHDTCFICAVC 590
Cdd:cd09414    1 CGGCSEPLKYGElavtapKFGESLL--WHPACFRCSTC 36

The third LIM domain of Four and a half LIM domains protein 1 (FHL1); The third LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188813 Cd Length: 53 Bit Score: 37.10 E-value: 1.45e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 122056614 559 CHGCDFPVEAGDkfIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLC 608
Cdd:cd09429    1 CVKCNKPITSGG--VTYQDQPWHSECFVCSSCSKKLAGQRFTAVEDQYYC 48

The first LIM domain of LIMK2 (LIM domain Kinase 2); The first LIM domain of LIMK2 (LIM domain Kinase 2): LIMK2 is a member of the LIMK protein family, which comprises LIMK1 and LIMK2. LIMK contains two LIM domains, a PDZ domain, and a kinase domain. LIMK is involved in the regulation of actin polymerization and microtubule disassembly. LIMK influences architecture of the actin cytoskeleton by regulating the activity of the cofilin family proteins cofilin1, cofilin2, and destrin. The mechanism of the activation is to phosphorylates cofilin on serine 3 and inactivates its actin-severing activity, altering the rate of actin depolymerization. LIMK activity is activated by phosphorylation of a threonine residue within the activation loop of the kinase by p21-activated kinases 1 and 4 and by Rho kinase. LIMKs can function in both cytoplasm and nucleus. Both LIMK1 and LIMK2 can act in the nucleus to suppress Rac/Cdc42-dependent cyclin D1 expression. LIMK2 is expressed in all tissues. While LIMK1 localizes mainly at focal adhesions, LIMK2 is found in cytoplasmic punctae, suggesting that they may have different cellular functions. The activity of LIM kinase 2 to regulate cofilin phosphorylation is inhibited by the direct binding of Par-3. LIMK2 activation promotes cell cycle progression. The phenotype of Limk2 knockout mice shows a defect in spermatogenesis. The LIM domains have been shown to play an important role in regulating kinase activity and likely also contribute to LIMK function by acting as sites of protein-to-protein interactions. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188847 [Multi-domain] Cd Length: 53 Bit Score: 37.16 E-value: 1.48e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 122056614 559 CHGCDFPVEAGdKFIEALGHTWHDTCFICAVCHVNLEGQpFYSKKDRPLCKKH 611
Cdd:cd09463    1 CTGCGGRIQDS-FHYRVVQEAWHNSCFQCSVCQDLLTNW-YYEKDGKLYCHKH 51

The first LIM domain of Testin-like family; The first LIM domain of Testin_like family: This family includes testin, prickle, dyxin and LIMPETin. Structurally, testin and prickle proteins contain three LIM domains at C-terminal; LIMPETin has six LIM domains; and dyxin presents only two LIM domains. However, all members of the family contain a PET protein-protein interaction domain. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). Dyxin involves in lung and heart development by interaction with GATA6 and blocking GATA6 activated target genes. LIMPETin might be the recombinant product of genes coding testin and four and half LIM proteins and its function is not well understood. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188726 Cd Length: 58 Bit Score: 37.20 E-value: 1.48e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 122056614 441 CGHCNNVIRG--PFLVAM----GRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERCY 492
Cdd:cd09340    1 CEKCKEPINPgeVAVFAErageDACWHPGCFVCETCNELLVDLIYFYHDGKIYCGRHY 58

biotin carboxyl carrier protein of acetyl-CoA carboxylase

Pssm-ID: 215533 [Multi-domain] Cd Length: 274 Bit Score: 40.98 E-value: 1.54e-03

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 122056614 299 QPVPASTYSPSPGANYSPTPYTPSPAPAYTPSPAPAyTPSPVPTyTPSPAPAYTPSPAPNYNPAPSVAY-SGGPAEP 374
Cdd:PLN02983 143 QPPPPAPVVMMQPPPPHAMPPASPPAAQPAPSAPAS-SPPPTPA-SPPPAKAPKSSHPPLKSPMAGTFYrSPAPGEP 217

The second LIM domain of Four and a half LIM domains protein 5 (FHL5); The second LIM domain of Four and a half LIM domains protein 5 (FHL5): FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors , which are highly expressed in male germ cells and is required for post-meiotic gene expression. FHL5 associates with CREM and confers a powerful transcriptional activation function. Activation by CREB has known to occur upon phosphorylation at an essential regulatory site and the subsequent interaction with the ubiquitous coactivator CREB-binding protein (CBP). However, the activation by FHL5 is independent of phosphorylation and CBP association. It represents a new route for transcriptional activation by CREM and CREB. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188812 Cd Length: 54 Bit Score: 37.13 E-value: 1.59e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 122056614 559 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLC 608
Cdd:cd09428    1 CFHCKKTIMPGSRKLEFEGNEWHETCFVCQSCQQPIGTKPLITKENKNYC 50

Neisseria meningitidis TspB protein; This family consists of several Neisseria meningitidis TspB virulence factor proteins.

Pssm-ID: 283306 [Multi-domain] Cd Length: 517 Bit Score: 41.23 E-value: 1.63e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 122056614  323 PAPAYTPSPAPAYTPSPVPTYTPSPAPAYTPSP------APNYNPAPSVAYSGGP---AEPASRP--PWVTD 383
Cdd:pfam05616 326 PRPDLTPASAEAPHAQPLPEVSPAENPANNPDPdenpgtRPNPEPDPDLNPDANPdtdGQPGTRPdsPAVPD 397

transcriptional regulator ICP4; Provisional

Pssm-ID: 223039 [Multi-domain] Cd Length: 1352 Bit Score: 41.70 E-value: 1.65e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  275 SEGPAAPAPKPRVVTTASIRPSVYQPVPASTYSPSPGANYSPTPYTPSPAPAYTPSPAPAYTPSPVPTYTPSPAPAYTPS 354
Cdd:PHA03307   46 DSAELAAVTVVAGAAACDRFEPPTGPPPGPGTEAPANESRSTPTWSLSTLAPASPAREGSPTPPGPSSPDPPPPTPPPAS 125

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  355 PAPNYNPAPS----VAYSGGPAEPASRPPwvTDDSFSQKFAPGKST------TSISKQTLPRGGPAYTPAGPQVPPLARG 424
Cdd:PHA03307  126 PPPSPAPDLSemlrPVGSPGPPPAASPPA--AGASPAAVASDAASSrqaalpLSSPEETARAPSSPPAEPPPSTPPAAAS 203

                         170
                  ....*....|....*
gi 122056614  425 TVQRAERFPASSRTP 439
Cdd:PHA03307  204 PRPPRRSSPISASAS 218

The first LIM domain of Lhx2 and Lhx9 family; The first LIM domain of Lhx2 and Lhx9 family: Lhx2 and Lhx9 are highly homologous LHX regulatory proteins. They belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Although Lhx2 and Lhx9 are highly homologous, they seems to play regulatory roles in different organs. In animals, Lhx2 plays important roles in eye, cerebral cortex, limb, the olfactory organs, and erythrocyte development. Lhx2 gene knockout mice exhibit impaired patterning of the cortical hem and the telencephalon of the developing brain, and a lack of development in olfactory structures. Lhx9 is expressed in several regions of the developing mouse brain , the spinal cord, the pancreas, in limb mesenchyme, and in the urogenital region. Lhx9 plays critical roles in gonad development. Homozygous mice lacking functional Lhx9 alleles exhibit numerous urogenital defects, such as gonadal agenesis, infertility, and undetectable levels of testosterone and estradiol coupled with high FSH levels. Lhx9 null mice are phenotypically female, even those that are genotypically male. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188755 [Multi-domain] Cd Length: 54 Bit Score: 36.93 E-value: 1.69e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 122056614 559 CHGCDFPVEagDKF-IEALGHTWHDTCFICAVCHVNLEGQ-PFYSKKDRPLCKK 610
Cdd:cd09369    1 CAGCGEKIQ--DRFyLLAVDRQWHASCLKCCECRLPLDSElSCFSRDGNIYCKE 52

DNA polymerase III subunits gamma and tau; Provisional

Pssm-ID: 184923 [Multi-domain] Cd Length: 624 Bit Score: 41.59 E-value: 1.69e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 285 PRVVTTASIRPSVYQPVPAS-TYSPSPGANYSPTpyTPSPAPAYTPSPAPAytpspvPTYTPSPAPAYTPSPAPnyNPAP 363
Cdd:PRK14959 363 PRLMPVESLRPSGGGASAPSgSAAEGPASGGAAT--IPTPGTQGPQGTAPA------AGMTPSSAAPATPAPSA--APSP 432

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 122056614 364 SVAYSGGPaePAsrPPWVTDDSFSQKFAPGKSTTSiskqtlprGGPAYTPAGPQVPPLARGTVQRAERFPASSRT 438
Cdd:PRK14959 433 RVPWDDAP--PA--PPRSGIPPRPAPRMPEASPVP--------GAPDSVASASDAPPTLGDPSDTAEHTPSGPRT 495

PDZ domain 5 of glutamate receptor-interacting protein 1 (GRIP1) and GRIP2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) binding proteins GRIP1 (ABP/GRIP2) and GRIP2, and related domains. GRIP1 and GRIP2 each have 7 PDZ domains. The interaction of GRIP1 and GRIP2 with GluA2/3 (AMPAR subunit) regulates AMPAR trafficking and synaptic targeting. GRIP1 has an essential role in regulating AMPAR trafficking during synaptic plasticity and learning and memory. GRIP1 and GRIP2 interact with a variety of other proteins associated with protein trafficking and internalization, for example GRIP1 also interacts with KIF5 (also known as kinesin 1), EphB receptors, scaffold protein liprin-alpha, and the rasGEF GRASP-1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This GRIP family domain PDZ5 is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467170 [Multi-domain] Cd Length: 85 Bit Score: 37.71 E-value: 1.73e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 122056614  26 PLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQK 82
Cdd:cd06682   28 PLIISDVKKGSVAHRTgTLEPGDKLLAIDNIRLDNCSMEDAAQILQQAEDIVKLKIRK 85

putative scaffolding protein

Pssm-ID: 177328 Cd Length: 306 Bit Score: 40.81 E-value: 1.79e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 279 AAPAPKPRVVTTASIRPSVYQPV-PASTYSPSPGANYSPT-PYTP--------SPAPAYTPSPAPA----YTPSPVPTYT 344
Cdd:PHA01929  23 AAPTPQPNPVIQPQAPVQPGQPGaPQQLAIPTQQPQPVPTsAMTPhvvqqapaQPAPAAPPAAGAAlpeaLEVPPPPAFT 102

                         90       100
                 ....*....|....*....|....*
gi 122056614 345 PSPAPAYTPSPAPNYNP--APSVAY 367
Cdd:PHA01929 103 PNGEIVGTLAGNLEGDPqlAPSVSY 127

The first LIM domain of Isl, a member of LHX protein family; The first LIM domain of Isl: Isl is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Isl1 and Isl2 are the two conserved members of this family. Proteins in this group are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Isl-1 is one of the LHX proteins isolated originally by virtue of its ability to bind DNA sequences from the 5'-flanking region of the rat insulin gene in pancreatic insulin-producing cells. Mice deficient in Isl-1 fail to form the dorsal exocrine pancreas and islet cells fail to differentiate. On the other hand, Isl-1 takes part in the pituitary development by activating the gonadotropin-releasing hormone receptor gene together with LHX3 and steroidogenic factor 1. Mouse Is l2 is expressed in the retinal ganglion cells and the developing spinal cord where it plays a role in motor neuron development. Same as Isl1, Isl2 may also be able to bind to the insulin gene enhancer to promote gene activation. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188752 [Multi-domain] Cd Length: 55 Bit Score: 36.94 E-value: 1.83e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 122056614 500 CAKCNTKIMGEVMhaLR----QTWHTTCFVCAACKKPFGNS--LFhMEDGEPYCEKDY 551
Cdd:cd09366    1 CVGCGGKIHDQYI--LRvapdLEWHAACLKCAECGQYLDETctCF-VRDGKTYCKRDY 55

PDZ domain 1 of the canonical isoform 1 of PDZ domain containing 7 (PDZD7), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of the long isoform 1 of PDZD7, and related domains. PDZD7 is critical for the organization of Usher syndrome type 2 (USH2) complex. Usher syndrome is the leading cause of hereditary sensory deaf-blindness in humans; USH2 is the most common sub-type. Formation of the USH2 complex is based upon heterodimerization between PDZD7 and whirlin (another PDZ domain-containing protein) and a subsequent dynamic interplay between USH2 proteins via their multiple PDZ domains. The PDZD7 PDZ2 domain binds GPR98 (also known as VLGR1) and usherin (USH2A). PDZD7 and whirlin form heterodimers through their multiple PDZ domains; whirlin and PDZD7 interact with usherin and GPR98 to form an interdependent ankle link complex. PDZD7 also interacts with myosin VIIa. PDZD7 also forms homodimers through its PDZ2 domain. Various isoforms of PDZD7 produced by alternative splicing have been identified; this subgroup includes the first PDZ domain of the canonical isoform of PDZD7- isoform 1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD7-like family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467269 [Multi-domain] Cd Length: 84 Bit Score: 37.41 E-value: 1.91e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 122056614  11 GPWGFRLQGGKDFNMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMT 61
Cdd:cd10833   12 GSLGFSVRGGSEHGLGIFVSKVEEGSAAERAGLCVGDKITEVNGVSLENIT 62

PDZ domain 3 of human Ligand of Numb protein X 1 (LNX1) and LNX2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of LNX1 (also known as PDZ domain-containing RING finger protein 2, PDZRN2) and LNX2 (also known as PDZ domain-containing RING finger protein 1, PDZRN1), and related domains. LNX1 and LNX2 are Ring (Really Interesting New Gene) finger and PDZ domain-containing E3 ubiquitin ligases that bind to the cell fate determinant protein NUMB and mediate its ubiquitination. LNX1 can ubiquitinate a number of other ligands including PPFIA1, KLHL11, KIF7 and ERC2. LNX1 and LNX2 each have four PDZ domains. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This LNX family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467167 [Multi-domain] Cd Length: 88 Bit Score: 37.62 E-value: 1.92e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 122056614  19 GGKDFNMPLTISRITP-GSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQ 81
Cdd:cd06679   22 GSRRGDLPIYVTNVQPdGCLGRDGRIKKGDVLLSINGISLTNLSHSEAVAVLKASAASSSIVLK 85

The first LIM domain of Testin; The first LIM domain of Testin: Testin contains three C-terminal LIM domains and a PET protein-protein interaction domain at the N-terminal. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Knockout mice experiments reveal that tumor repressor function of Testin. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188797 Cd Length: 58 Bit Score: 36.67 E-value: 1.95e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 122056614 559 CHGCDFPVEAGDK--FIEALGHT--WHDTCFICAVCHVNLEGQPFYSKKDRPLCKKH 611
Cdd:cd09413    1 CYCCKQPMKEGDPavYAERAGYDklWHPACFVCSTCGELLVDMIYFWKNGKLYCGRH 57

The first LIM domain of Lhx1 (also known as Lim1) and Lhx5; The first LIM domain of Lhx1 (also known as Lim1) and Lhx5. Lhx1 and Lhx5 are closely related members of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx1 is required for regulating the vertebrate head organizer, the nervous system, and female reproductive tract development. During embryogenesis in the mouse, Lhx1 is expressed early in mesodermal tissue, then later during urogenital, kidney, liver, and nervous system development. In the adult, expression is restricted to the kidney and brain. A mouse embryos with Lhx1 gene knockout cannot grow normal anterior head structures, kidneys, and gonads, but with normally developed trunk and tail morphology. In the developing nervous system, Lhx1 is required to direct the trajectories of motor axons in the limb. Lhx1 null female mice lack the oviducts and uterus. Lhx5 protein may play complementary or overlapping roles with Lhx1. The expression of Lhx5 in the anterior portion of the mouse neural tube suggests a role in patterning of the forebrain. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188753 [Multi-domain] Cd Length: 52 Bit Score: 36.64 E-value: 1.97e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 122056614 500 CAKCNTKIMGE-VMHALRQTWHTTCFVCAACKKPFGNSLFHmEDGEPYCEKDY 551
Cdd:cd09367    1 CAGCDRPILDKfLLNVLDRAWHAKCVQCCDCKCPLTEKCFS-REGKLYCRNDF 52

transcriptional regulator ICP4; Provisional

Pssm-ID: 223039 [Multi-domain] Cd Length: 1352 Bit Score: 41.31 E-value: 2.01e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  279 AAPAPKPRVVTTASIRPSVYQPVPASTYSPSPGANYSPTPYTPSPAPAYTPSPAPAYTPSPVPTYTPSPaPAYTPSPAPN 358
Cdd:PHA03307  254 ECPLPRPAPITLPTRIWEASGWNGPSSRPGPASSSSSPRERSPSPSPSSPGSGPAPSSPRASSSSSSSR-ESSSSSTSSS 332

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  359 YNPAPSVAYSGGPAEPASRPPWVTDDSfsqkfAPGKSTtsiskqtlPRGGPAYTPAGPQVPPLARGTVQRAERFPASSRT 438
Cdd:PHA03307  333 SESSRGAAVSPGPSPSRSPSPSRPPPP-----ADPSSP--------RKRPRPSRAPSSPAASAGRPTRRRARAAVAGRAR 399


                  .
gi 122056614  439 P 439
Cdd:PHA03307  400 R 400

biotin carboxyl carrier protein of acetyl-CoA carboxylase

Pssm-ID: 215533 [Multi-domain] Cd Length: 274 Bit Score: 40.59 E-value: 2.05e-03

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 122056614 278 PAAPAPKPRVVTTASIRPSV--YQPVPASTYSPSPGANYSPTPYTPSPAPAYTPSPAPAYTPSpVPTYTPSPAPAYTP 353
Cdd:PLN02983 142 PQPPPPAPVVMMQPPPPHAMppASPPAAQPAPSAPASSPPPTPASPPPAKAPKSSHPPLKSPM-AGTFYRSPAPGEPP 218

DNA polymerase III subunits gamma and tau; Validated

Pssm-ID: 236090 [Multi-domain] Cd Length: 824 Bit Score: 41.12 E-value: 2.06e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 271 HTSYSEGPAAPAPKPRVVTTA--SIRPSVYQPVPASTYSPSP--GANYSPTPYTPSPAPAYTPSPAPAYTPSPVPTYTPS 346
Cdd:PRK07764 691 AAPAGAAPAQPAPAPAATPPAgqADDPAAQPPQAAQGASAPSpaADDPVPLPPEPDDPPDPAGAPAQPPPPPAPAPAAAP 770

                         90       100
                 ....*....|....*....|....*
gi 122056614 347 PAPAYTPSPAPNYNPAPSVAYSGGP 371
Cdd:PRK07764 771 AAAPPPSPPSEEEEMAEDDAPSMDD 795

flagellar motor protein MotB; Reviewed

Pssm-ID: 183756 [Multi-domain] Cd Length: 421 Bit Score: 40.85 E-value: 2.10e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 300 PVPASTYSPSPGANYSPTPYTPS-PAPAYTPSPAPayTPSPVPTYTPSPA-PAYTPSPAPNYNPAPSVAYSggpAEPASR 377
Cdd:PRK12799 300 PVAAVTPSSAVTQSSAITPSSAAiPSPAVIPSSVT--TQSATTTQASAVAlSSAGVLPSDVTLPGTVALPA---AEPVNM 374

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 122056614 378 PPWVTDDSFSQKFAPGKSTTSiskqtlpRGGPAYT-PAGP--QVPP 420
Cdd:PRK12799 375 QPQPMSTTETQQSSTGNITST-------ANGPTTSlPAAPasNIPV 413

transcriptional regulator ICP4; Provisional

Pssm-ID: 223039 [Multi-domain] Cd Length: 1352 Bit Score: 41.31 E-value: 2.11e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  275 SEGPAAPAPKPRVVTTASIRPSVYQPVPASTYSPSPGANYSPTPYTPSPAPAYTPSPAPAYTPSPVPTYTPSPAPAYTPS 354
Cdd:PHA03307  293 ERSPSPSPSSPGSGPAPSSPRASSSSSSSRESSSSSTSSSSESSRGAAVSPGPSPSRSPSPSRPPPPADPSSPRKRPRPS 372

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  355 PAPNYNPAPsvaySGGPAEPASRppWVTDDSFSQKFAPGKSTTSISKQTLPRG----------GPAYTPAG---PQVPPL 421
Cdd:PHA03307  373 RAPSSPAAS----AGRPTRRRAR--AAVAGRARRRDATGRFPAGRPRPSPLDAgaasgafyarYPLLTPSGepwPGSPPP 446


                  ....*
gi 122056614  422 ARGTV 426
Cdd:PHA03307  447 PPGRV 451

multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine pyrophosphate-binding subunit/dihydrolipoyllysine-residue succinyltransferase subunit;

Pssm-ID: 237030 [Multi-domain] Cd Length: 1228 Bit Score: 41.41 E-value: 2.21e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  272 TSYSEGPAAPAPKPrvvTTASIRPSVYQPVPASTYSPSPganySPTPYTPSPAPAYTPSPAPAYTPSPVPTYTPSPAPAY 351
Cdd:PRK12270   34 ADYGPGSTAAPTAA---AAAAAAAASAPAAAPAAKAPAA----PAPAPPAAAAPAAPPKPAAAAAAAAAPAAPPAAAAAA 106


                  ....*.
gi 122056614  352 TPSPAP 357
Cdd:PRK12270  107 APAAAA 112

PDZ domain 1 of protein tyrosine phosphatase non-receptor type 13 (PTPN13), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of PTPN13 [also known as Fas-associated protein-tyrosine phosphatase 1 (FAP-1), protein-tyrosine phosphatase 1E (PTP-E1), and protein-tyrosine phosphatase (PTPL1)], and related domains. PTPN13 regulates negative apoptotic signaling and mediates phosphoinositide 3-kinase (PI3K) signaling. PTPN13 has five PDZ domains. Proteins known to interact with PTPN13 PDZ domains include: PLEKHA1 and PLEKHA2 via PTPN13-PDZ domain 1, Fas receptor and thyroid receptor-interacting protein 6 via PTPN13-PDZ domain 2, nerve growth factor receptor and protein kinase N2 via PTPN13-PDZ domain 3, PDZ and LIM domain 4 (PDLIM4) via PTPN13-PDZ domains 2 and 4, and brain calpain-2 via PTPN13-PDZ domains 3, 4 and 5. Calpain-2-mediated PTPN13 fragments may be involved in abnormal tau aggregation and increased risk for Alzheimer's disease. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PTPN13 family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467285 [Multi-domain] Cd Length: 92 Bit Score: 37.47 E-value: 2.23e-03

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 122056614  14 GFRLQGGKD---FNMPLTISRITPGSKA-AQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQKSK 84
Cdd:cd23072   16 GFQIVGGEKsgrLDLGIFISSITPGGPAdLDGRLKPGDRLISVNDVSLEGLSHDAAVEILQNAPEDVTLVVSQPK 90

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.

Pssm-ID: 460830 [Multi-domain] Cd Length: 991 Bit Score: 41.29 E-value: 2.26e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  278 PAAPAPKPRVVTTASIRPSVYQP----VPASTYSPSPGANysPTPYTPSPA-PAYTPSPAPAYTPSPVPTYTPSPAPAYT 352
Cdd:pfam03154 391 PPPPALKPLSSLSTHHPPSAHPPplqlMPQSQQLPPPPAQ--PPVLTQSQSlPPPAASHPPTSGLHQVPSQSPFPQHPFV 468

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 122056614  353 PSPAPNYNPAPSVAYSGGPAEPASRPPWVTDDSFSQKFAPGKSTT----SISKQTLPRGGPAYTPAGPQVPPLARGTV 426
Cdd:pfam03154 469 PGGPPPITPPSGPPTSTSSAMPGIQPPSSASVSSSGPVPAAVSCPlppvQIKEEALDEAEEPESPPPPPRSPSPEPTV 546

60S ribosomal protein L19-like protein; Provisional

Pssm-ID: 185616 [Multi-domain] Cd Length: 357 Bit Score: 40.70 E-value: 2.31e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 279 AAPAPKPRVVTTAsirPSVYQPVPASTYSPSPGANYSPTPYTPSPAPAYTPspaPAYTPSPVPTYTPSPAPAYTPspaPN 358
Cdd:PTZ00436 209 AAPSGKKSAKAAA---PAKAAAAPAKAAAPPAKAAAAPAKAAAAPAKAAAP---PAKAAAPPAKAAAPPAKAAAP---PA 279

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 122056614 359 YNPAPSVAYSGGPAEPASRPPWVTDDSFSQKFAPGKSTTSISKQTLPRGGPAYTPAGPQVPP 420
Cdd:PTZ00436 280 KAAAPPAKAAAPPAKAAAAPAKAAAAPAKAAAAPAKAAAPPAKAAAPPAKAATPPAKAAAPP 341

The LIM domains of Cysteine Rich Protein (CRP) family; The LIM domains of Cysteine Rich Protein (CRP) family: Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to a short glycine-rich repeats (GRRs). The known CRP family members include CRP1, CRP2, and CRP3/MLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription control, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. CRP1, CRP2, and CRP3/MLP are involved in promoting protein assembly along the actin-based cytoskeleton. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188712 Cd Length: 53 Bit Score: 36.42 E-value: 2.35e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 122056614 559 CHGCDFPVEAGDKFIeALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCK 609
Cdd:cd09326    1 CPRCGKSVYAAEEVI-AAGKSWHKSCFTCAVCNKRLDSTTLAEHDGEIYCK 50

The second LIM domain of Cysteine Rich Protein (CRP); The second LIM domain of Cysteine Rich Protein (CRP): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to a short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription control, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. It is evident that CRP1, CRP2, and CRP3/MLP are involved in promoting protein assembly along the actin-based cytoskeleton. Although members of the CRP family share common binding partners, they are also capable of recognizing different and specific targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residu es, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188787 Cd Length: 54 Bit Score: 36.40 E-value: 2.51e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 122056614 559 CHGCDFPVEAGDKFIEAlGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCK 609
Cdd:cd09403    1 CPRCGKSVYAAEKIIGA-GKPWHKNCFRCAKCGKSLESTTLADKDGEIYCK 50

flagellar biosynthesis protein FlhF;

Pssm-ID: 237182 [Multi-domain] Cd Length: 559 Bit Score: 40.74 E-value: 2.55e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 280 APAPKPrVVTTASIRPSVYQPVPASTYSPSPGANYSpTPYTPSPAPAYTPSPAPAytpsPVPTYTPSPAPAYTPSPAPNY 359
Cdd:PRK12727 124 APAAAP-VRAASIPSPAAQALAHAAAVRTAPRQEHA-LSAVPEQLFADFLTTAPV----PRAPVQAPVVAAPAPVPAIAA 197

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 122056614 360 NPAPSVAYSGGPAEPASRPPWVTDDSFSQKFAPGKSTTSISKQTLPRGGPAYTPAGP 416
Cdd:PRK12727 198 ALAAHAAYAQDDDEQLDDDGFDLDDALPQILPPAALPPIVVAPAAPAALAAVAAAAP 254

large tegument protein UL36; Provisional

Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 41.08 E-value: 2.58e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  278 PAAPAPKPRVvTTASIRPSVYQPVPASTysPSPGANYSPTPYTPSPAPAyTPSPAPAYTPSPVPTYTPSPAPAYTPSPAP 357
Cdd:PHA03247  389 RHAATPFARG-PGGDDQTRPAAPVPASV--PTPAPTPVPASAPPPPATP-LPSAEPGSDDGPAPPPERQPPAPATEPAPD 464

                          90       100
                  ....*....|....*....|..
gi 122056614  358 NYNPAPSVAYSggpAEPASRPP 379
Cdd:PHA03247  465 DPDDATRKALD---ALRERRPP 483

The first LIM domain of Prickle; The first LIM domain of Prickle: Prickle contains three C-terminal LIM domains and a N-terminal PET domain. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). PCP establishment requires the conserved Frizzled/Dishevelled PCP pathway. Prickle interacts with Dishevelled, thereby modulating Frizzled/Dishevelled activity and PCP signaling. Four forms of prickles have been identified: prickle 1-4. The best characterized is prickle 1 and prickle 2 which are differentially expressed. While prickle 1 is expressed in fetal heart and hematological malignancies, prickle 2 is found in fetal brain, adult cartilage, pancreatic islet, and some types of timorous cells. Mutations in prickle 1 have been linked to progressive myoclonus epilepsy. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188799 Cd Length: 59 Bit Score: 36.47 E-value: 2.69e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 122056614 441 CGHCNNVIRGPFLV------AMGRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCER 490
Cdd:cd09415    1 CEQCGEQISGGDIAvfasraGPGACWHPACFVCSTCKELLVDLIYFYQDGKVYCGR 56

PDZ domain 5 of Danio rerio tyrosine-protein phosphatase non-receptor type 13 (Ptpn13) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 5 of Danio rerio Ptpn13, and related domains. Protein-tyrosine phosphatases (PTPs) dephosphorylate phosphotyrosyl residues in proteins that are phosphorylated by protein tyrosine kinases (PTKs). Danio rerio Ptpn13 is a classical non-receptor-like PTP. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PTPN13-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467273 [Multi-domain] Cd Length: 80 Bit Score: 36.94 E-value: 2.70e-03

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 122056614   5 VTLTGP--GPWGFRLQGGKDFNmPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTL 80
Cdd:cd23060    2 IELEKPanGGLGFSLVGGEGGS-GIFVKSISPGGVADRDgRLQVGDRLLQVNGESVIGLSHSKAVNILRKAKGTVQLTV 79

Domain of unknown function (DUF3432); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is about 100 amino acids in length. This domain is found associated with pfam00096. This domain has two conserved sequence motifs: YPSPV and PSP.

Pssm-ID: 403204 [Multi-domain] Cd Length: 98 Bit Score: 37.78 E-value: 2.75e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 122056614  295 PSVYQPVPASTYSPSPGANYsPTPYT---PSPAPAYTPSPAPAYTPSPVPTYTPSPAPAYTPSPAPNYNPA 362
Cdd:pfam11914   4 APASAVSSISSYSSSVTTSY-PSPITtsyPSPVSTSYSSPVPSSYPSPVHTSFPSPSIATTYPSVTTTFQT 73

The LIM domain of Mlp84B and Mlp60A; The LIM domain of Mlp84B and Mlp60A: Mlp84B and Mlp60A belong to the CRP LIM domain protein family. The Mlp84B protein contains five copies of the LIM domains, each followed by a Glycin Rich Region (GRR). However, only the first LIM domain of Mlp84B is in this family. Mlp60A exhibits only one LIM domain linked to a glycin-rich region. Mlp84B and Mlp60A are muscle specific proteins and have been implicated in muscle differentiation. While Mlp84B transcripts are enriched at the terminal ends of muscle fibers, Mlp60A transcripts are found throughout the muscle fibers. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188788 Cd Length: 54 Bit Score: 36.31 E-value: 2.80e-03

                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 122056614 558 KCHGCDFPVEAGDKFIeALGHTWHDTCFICAVCHVNLE 595
Cdd:cd09404    1 KCPKCGKSVYAAEERL-AGGYKWHKMCFKCGMCNKLLD 37

The first LIM domain of Prickle 3; The first LIM domain of Prickle 3/LIM domain only 6 (LM06): Prickle contains three C-terminal LIM domains and a N-terminal PET domain. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). PCP establishment requires the conserved Frizzled/Dishevelled PCP pathway. Prickle interacts with Dishevelled, thereby modulating Frizzled/Dishevelled activity and PCP signaling. Four forms of prickles have been identified: prickle 1-4. The best characterized is prickle 1 and prickle 2 which are differentially expressed. While prickle 1 is expressed in fetal heart and hematological malignancies, prickle 2 is found in fetal brain, adult cartilage, pancreatic islet, and some types of timorous cells. Mutations in prickle 1 have been linked to progressive myoclonus epilepsy. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188872 Cd Length: 59 Bit Score: 36.39 E-value: 2.83e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 122056614 441 CGHCNNVIRGPFLV------AMGRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCER 490
Cdd:cd09841    1 CQQCGRQICGGDIAvfasraGLGACWHPQCFQCASCQELLVDLIYFYQDGKIYCGR 56

DNA polymerase III subunits gamma and tau; Provisional

Pssm-ID: 184923 [Multi-domain] Cd Length: 624 Bit Score: 40.82 E-value: 2.85e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 277 GPAAPAPKPRVVTT------ASIRPSVYQP-VPASTYSPSPGANYSPTPYTPsPAPAYTPSPAPAytpspVPTYTPSPAP 349
Cdd:PRK14959 392 GGAATIPTPGTQGPqgtapaAGMTPSSAAPaTPAPSAAPSPRVPWDDAPPAP-PRSGIPPRPAPR-----MPEASPVPGA 465

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 350 AYTPSPAPNYNPAPSVAYSGGPAEPASRPPWVTDDSFSQ-KFAPGKSTTSISKQTLPRGG 408
Cdd:PRK14959 466 PDSVASASDAPPTLGDPSDTAEHTPSGPRTWDGFLEFCQgRNGQGGRLATVLRQATPEHA 525

Hedgehog signalling target; TALPID3 is a family of eukaryotic proteins that are targets for Hedgehog signalling. Mutations in this gene noticed first in chickens lead to multiple abnormalities of development.

Pssm-ID: 434634 [Multi-domain] Cd Length: 1288 Bit Score: 41.03 E-value: 2.94e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614   321 PSPAPAYTPSPAP---AYTPSPVPTytPSPAPAYTPSPAPNynpAPSvaysggpaePASRPPWVTDDSFSQKFAPGKSTT 397
Cdd:pfam15324  966 EPPVAASVPGDLPtkeTLLPTPVPT--PQPTPPCSPPSPLK---EPS---------PVKTPDSSPCVSEHDFFPVKEIPP 1031

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 122056614   398 SISKQTLPRGGPAYTPAG---PQVPPLARGTVQRAERFPASSRTP 439
Cdd:pfam15324 1032 EKGADTGPAVSLVITPTVtpiATPPPAATPTPPLSENSIDKLKSP 1076

The first LIM domain of Cysteine Rich Protein 3 (CRP3/MLP); The first LIM domain of Cysteine Rich Protein 3 (CRP3/MLP): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network.CRP3 also called Muscle LIM Protein (MLP), which is a striated muscle-specific factor that enhances myogenic differentiation. CRP3/MLP interacts with cytoskeletal protein beta-spectrin. CRP3/MLP also interacts with the basic helix-loop-helix myogenic transcriptio n factors MyoD, myogenin, and MRF4 thereby increasing their affinity for specific DNA regulatory elements. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188865 Cd Length: 54 Bit Score: 36.27 E-value: 2.96e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 122056614 500 CAKCNTKIM-GEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 551
Cdd:cd09481    2 CGACEKTVYhAEEIQCNGRSFHKTCFICMACRKALDSTTVAAHESEIYCKTCY 54

DNA translocase FtsK; Provisional

Pssm-ID: 236669 [Multi-domain] Cd Length: 1355 Bit Score: 40.84 E-value: 3.14e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  280 APAPKPRVVTTASIRPSVY------QPVPASTYSPSPGAN-------YSPTPYTPSPAPAYTPSPA------------PA 334
Cdd:PRK10263  374 APAPEGYPQQSQYAQPAVQyneplqQPVQPQQPYYAPAAEqpaqqpyYAPAPEQPAQQPYYAPAPEqpvagnawqaeeQQ 453

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  335 YTPSPVPTYTP-----SPAPAYTPSPAPNYNPAPSVAYSGGPAEPA--SRPPWVTDDSFSQKFAPGKSTTSISKQTLPRG 407
Cdd:PRK10263  454 STFAPQSTYQTeqtyqQPAAQEPLYQQPQPVEQQPVVEPEPVVEETkpARPPLYYFEEVEEKRAREREQLAAWYQPIPEP 533

                         170       180
                  ....*....|....*....|....*....
gi 122056614  408 GPAYTPAGPQVPPLARGTVQRAERFPASS 436
Cdd:PRK10263  534 VKEPEPIKSSLKAPSVAAVPPVEAAAAVS 562

conjugal transfer pilus assembly protein TraB; Provisional

Pssm-ID: 184281 [Multi-domain] Cd Length: 475 Bit Score: 40.19 E-value: 3.24e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 279 AAPAPKPRVVTTASirpsvyQPVPaSTYSPSPGANYSPTPYTPSPA--PAYTPSPAP--------AYTPSPVPTYTPSPA 348
Cdd:PRK13729 119 QVKALGANPVTATG------EPVP-QMPASPPGPEGEPQPGNTPVSfpPQGSVAVPPptafypgnGVTPPPQVTYQSVPV 191

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 122056614 349 PaytpspapnyNPAPSVAYSGGPAEPASRPPWVTDDSFS 387
Cdd:PRK13729 192 P----------NRIQRKTFTYNEGKKGPSLPYIPSGSFA 220

The first LIM domain of Cysteine Rich Protein 2 (CRP2); The first LIM domain of Cysteine Rich Protein 2 (CRP2): The CRP family members include CRP1, CRP2, CRP3/MLP and TLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. CRP2 specifically binds to protein inhibitor of activated STAT-1 (PIAS1) and a novel human protein designed CRP2BP (for CRP2 binding partner). PIAS1 specifically inhibits the STAT-1 pathway and CRP2BP is homologous to members of the histone acetyltransferase family raising the possibility that CRP2 is a modulator of cytokine-controlled pathways or is functionally active in the transcriptional regulatory network. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188864 Cd Length: 55 Bit Score: 36.12 E-value: 3.24e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 122056614 500 CAKCNTKIM-GEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 551
Cdd:cd09480    2 CGACGRTVYhAEEVQCDGRSFHKCCFLCMVCRKNLDSTTVAIHDQEIYCKSCY 54

Yeast cortical protein KAR9; The KAR9 protein in Saccharomyces cerevisiae is a cytoskeletal protein required for karyogamy, correct positioning of the mitotic spindle and for orientation of cytoplasmic microtubules. KAR9 localizes at the shmoo tip in mating cells and at the tip of the growing bud in anaphase.

Pssm-ID: 430088 [Multi-domain] Cd Length: 684 Bit Score: 40.58 E-value: 3.25e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  272 TSYSEGPAAPAPKPRVVTTASIRPSVYQPVPASTYSPSPgaNYSPTPYTPSPAPAYTPSPAPAYTPSP---VPTYTPSPA 348
Cdd:pfam08580 506 STPSNTATSETPTPALRPPSRPQPPPPGNRPRWNASTNT--NDLDVGHNFKPLTLTTPSPTPSRSSRSsstLPPVSPLSR 583

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  349 PAyTPSPAPNYNPAPSVAY---SGGPAE---PASRPPWVTDDSFSqkfapgKSTTSISKQTLPRGGPAYTPAGPQVPPLA 422
Cdd:pfam08580 584 DK-SRSPAPTCRSVSRASRrraSRKPTRigsPNSRTSLLDEPPYP------KLTLSKGLPRTPRNRQSYAGTSPSRSVSV 656

                         170
                  ....*....|....
gi 122056614  423 RGTVQRAERfPASS 436
Cdd:pfam08580 657 SSGLGPQTR-PGTS 669

The second LIM domain of Lmx1a and Lmx1b; The second LIM domain of Lmx1a and Lmx1b: Lmx1a and Lmx1b belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs such as the pituitary gland and the pancreas. Mouse Lmx1a is expressed in multiple tissues, including the roof plate of the neural tube, the developing brain, the otic vesicles, the notochord, and the pancreas. In mouse, mutations in Lmx1a result in failure of the roof plate to develop. Lmx1a may act upstream of other roof plate markers such as MafB, Gdf7, Bmp6, and Bmp7. Further characterization of these mice reveals numerous defects including disorganized cerebellum, hippocampus, and cortex; altered pigmentation; female sterility, skeletal defects, and behavioral abnormalities. In the mouse, Lmx1b functions in the developing limbs and eyes, the kidneys, the brain, and in cranial mesenchyme. The disruption of Lmx1b gene results kidney and limb defects. In the brain, Lmx1b is important for generation of mesencephalic dopamine neurons and the differentiation of serotonergic neurons. In the mouse eye, Lmx1b regulates anterior segment (cornea, iris, ciliary body, trabecular meshwork, and lens) development. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188764 Cd Length: 55 Bit Score: 35.89 E-value: 3.36e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 122056614 500 CAKCNTKIMGE--VMHALRQTWHTTCFVCAACKKPF--GNSlFHMEDGEPYCEKDY 551
Cdd:cd09378    1 CSGCLEKIAPSelVMRALENVYHLRCFCCCVCERQLqkGDE-FVLKEGQLLCKSDY 55

pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; This model describes a subset of pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase specifically close by both phylogenetic and per cent identity (UPGMA) trees. Members of this set include two or three copies of the lipoyl-binding domain. E. coli AceF is a member of this model, while mitochondrial and some other bacterial forms belong to a separate model. [Energy metabolism, Pyruvate dehydrogenase]

Pssm-ID: 273566 [Multi-domain] Cd Length: 546 Bit Score: 40.24 E-value: 3.36e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  281 PAPKPRVVTTASIRPSVYQPVPASTYSPSPGANYSPTPYTPSPAPAYTPSPA-----PAYTPSPVPTYTPSPAPAYTPSP 355
Cdd:TIGR01348 162 PAPASGVVKSVKVKVGDSVPTGDLILTLSVAGSTPATAPAPASAQPAAQSPAatqpePAAAPAAAKAQAPAPQQAGTQNP 241

                          90
                  ....*....|
gi 122056614  356 APNYNPAPSV 365
Cdd:TIGR01348 242 AKVDHAAPAV 251

The first LIM domain of Zyxin; The first LIM domain of Zyxin: Zyxin exhibits three copies of the LIM domain, an extensive proline-rich domain and a nuclear export signal. Localized at sites of cell substratum adhesion in fibroblasts, Zyxin interacts with alpha-actinin, members of the cysteine-rich protein (CRP) family, proteins that display Src homology 3 (SH3) domains and Ena/VASP family members. Zyxin and its partners have been implicated in the spatial control of actin filament assembly as well as in pathways important for cell differentiation. In addition to its functions at focal adhesion plaques, recent work has shown that zyxin moves from the sites of cell contacts to the nucleus, where it directly participates in the regulation of gene expression. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188735 [Multi-domain] Cd Length: 87 Bit Score: 36.76 E-value: 3.68e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 122056614 440 LCGHCNNVI--RGPFLVAMGRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERCY 492
Cdd:cd09349   33 LCGICGQPLsrTQPAVRALGHLFHVTCFTCHQCEQQLQGQQFYSLEGKPYCEECY 87

The third LIM domain of Lrg1p, a LIM and RhoGap domain containing protein; The third LIM domain of Lrg1p, a LIM and RhoGap domain containing protein: The members of this family contain three tandem repeats of LIM domains and a Rho-type GTPase activating protein (RhoGap) domain. Lrg1p is a Rho1 GTPase-activating protein required for efficient cell fusion in yeast. Lrg1p-GAP domain strongly and specifically stimulates the GTPase activity of Rho1p, a regulator of beta (1-3)-glucan synthase in vitro. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188779 Cd Length: 56 Bit Score: 35.76 E-value: 3.84e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 500 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSL----FHMEDGEPYC 547
Cdd:cd09393    1 CASCGKSIEDECIKFEDKRWHLKCFTCSRCHREISSELsdaaFNNKDQRILC 52

PDZ domain; This entry represents the PDZ domain from a wide variety of proteins.

Pssm-ID: 436067 [Multi-domain] Cd Length: 54 Bit Score: 35.97 E-value: 3.85e-03

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 122056614   28 TISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHL 63
Cdd:pfam17820   1 VVTAVVPGSPAERAGLRVGDVILAVNGKPVRSLEDV 36

putative scaffolding protein

Pssm-ID: 177328 Cd Length: 306 Bit Score: 39.65 E-value: 4.14e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 322 SPAPAYTPSPAPAYTPSPVPTYTPSPAPAYTPSPAPNYNPAPSVAYSG-----GPAEPA-SRPPwvtddsfsqkfAPGKS 395
Cdd:PHA01929  20 PPAAAPTPQPNPVIQPQAPVQPGQPGAPQQLAIPTQQPQPVPTSAMTPhvvqqAPAQPApAAPP-----------AAGAA 88

                         90       100
                 ....*....|....*....|....*...
gi 122056614 396 TtsisKQTLPRGG-PAYTPAGPQVPPLA 422
Cdd:PHA01929  89 L----PEALEVPPpPAFTPNGEIVGTLA 112

biotin carboxyl carrier protein of acetyl-CoA carboxylase

Pssm-ID: 215533 [Multi-domain] Cd Length: 274 Bit Score: 39.44 E-value: 4.22e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 122056614 318 PYTPSPAPAYT---PSPAPAYTPSPVPTYTPSPAPAYTPSPAPNYNPAPSVAYSGGPA 372
Cdd:PLN02983 142 PQPPPPAPVVMmqpPPPHAMPPASPPAAQPAPSAPASSPPPTPASPPPAKAPKSSHPP 199

The first LIM domain of Rga GTPase-Activating Proteins; The first LIM domain of Rga GTPase-Activating Proteins: The members of this family contain two tandem repeats of LIM domains and a Rho-type GTPase activating protein (RhoGap) domain. Rga activates GTPases during polarized morphogenesis. In yeast, a known regulating target of Rga is CDC42p, a small GTPase. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188780 Cd Length: 55 Bit Score: 35.80 E-value: 4.52e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 122056614 500 CAKCNTKIMGEVMHALRQT-WHTTCFVCAACKKPFG-NSLF-HMEDGEPYC 547
Cdd:cd09394    1 CVGCKESITEGHAYELGGDrWHIHCFKCYKCDKKLScDSNFlVLGDGSLIC 51

large tegument protein UL36; Provisional

Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 40.31 E-value: 4.52e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  290 TASIRPSVYQPVPASTYSPSPGANyspTPYTPSPAPAYTPSPAPaytPSPVPTYTPSPAPAYTPSPAPNYNPAPSV--AY 367
Cdd:PHA03247  369 SAGRHHPKRASLPTRKRRSARHAA---TPFARGPGGDDQTRPAA---PVPASVPTPAPTPVPASAPPPPATPLPSAepGS 442

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  368 SGGPAEPASRPPwVTDDSFSQKFAPGKSTTSISKQTLPRGGPAYTPAGP-----QVPPLARGTVQRAERFPASSR-TPLC 441
Cdd:PHA03247  443 DDGPAPPPERQP-PAPATEPAPDDPDDATRKALDALRERRPPEPPGADLaellgRHPDTAGTVVRLAAREAAIAReVAEC 521

                         170
                  ....*....|....*..
gi 122056614  442 GHCN-NVIRGPFLVAMG 457
Cdd:PHA03247  522 SRLTiNALRSPFPASPG 538

The first LIM domain of Four and a half LIM domains protein 2 (FHL2); The first LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung at lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188806 Cd Length: 62 Bit Score: 36.04 E-value: 4.55e-03

                         10        20        30
                 ....*....|....*....|....*....|....*
gi 122056614 458 RSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERCY 492
Cdd:cd09422   24 RHWHESCFHCFQCKNSLVDKPFAAKEEHLLCTECY 58

cell division protein FtsN; Provisional

Pssm-ID: 237191 [Multi-domain] Cd Length: 256 Bit Score: 39.26 E-value: 4.55e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 122056614 299 QPVPASTYSPSPGANYS---PTPYTPSPAPAYTPSPAPAYTPSPVPTYTPSPAPAYTPSPAP 357
Cdd:PRK12757 112 PQVPRSTVQIQQQAQQQqppATTAQPQPVTPPRQTTAPVQPQTPAPVRTQPAAPVTQAVEAP 173

The first LIM domain of Lhx3b; The first LIM domain of Lhx3b. Lhx3b is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx3b is one of the two isoforms of Lhx3. The Lhx3 gene is expressed in the ventral spinal cord, the pons, the medulla oblongata, and the pineal gland of the developing nervous system during mouse embryogenesis, and transcripts are found in the emergent pituitary gland. Lhx3 functions in concert with other transcription factors to specify interneuron and motor neuron fates during development. Lhx3 proteins have been demonstrated to directly bind to the promoters of several pituitary hormone gene promoters. The Lhx3 gene encodes two isoforms, LHX3a and LHX3b that differ in their amino-terminal sequences, where Lhx3a has longer N-terminal. They show differential activation of pituitary hormone genes and distinct DNA binding properties. In human, Lhx3a trans-activated the alpha-glycoprotein subunit promoter and genes containing a high-affinity Lhx3 binding site more effectively than the hLhx3b isoform. In addition, hLhx3a induce transcription of the TSHbeta-subunit gene by acting on pituitary POU domain factor, Pit-1, while hLhx3b does not. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188851 [Multi-domain] Cd Length: 55 Bit Score: 35.68 E-value: 4.85e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 559 CHGCDFPVEagDKFI-EALGHTWHDTCFICAVCHVNLEGQPFySKKDRPLCK 609
Cdd:cd09467    4 CAGCNQHIV--DRFIlKVLDRHWHSKCLKCSDCQTQLAEKCF-SRGDSVYCK 52

PDZ domain 1 of human discs large homolog 1 (Dlg1), Dlg2, and Dlg4, Drosophila disc large (Dlg), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of Drosophila Dlg1, human Dlg1,2, and 4 and related domains. Dlg1 (also known as synapse-associated protein Dlg197 or SAP-97), Dlg2 (also known as channel-associated protein of synapse-110, postsynaptic density protein 93, or PSD-93), Dlg4 (also known as postsynaptic density protein 95, PSD-95, synapse-associated protein 90, or SAP-90) each have 3 PDZ domains and belong to the membrane-associated guanylate kinase family. Dlg1 regulates antigen receptor signaling and cell polarity in lymphocytes, B-cell proliferation and antibody production, and TGFalpha bioavailability; its PDZ3 domain binds pro-TGFalpha, and its PDZ2 domain binds the TACE metalloprotease responsible for cleaving pro-TGFalpha to a soluble form. Dlg2 is involved in N-methyl-D-aspartate (NMDA) receptor signaling. It regulates surface expression of NMDA receptors in dorsal horn neurons of the spinal cord, and it also interacts with NMDA receptor subunits and with Shaker-type K+ channel subunits to cluster into a channel complex. Dlg4 PDZ1 domain binds NMDA receptors, and its PDZ2 domain binds neuronal nitric oxide synthase (nNOS), forming a complex in neurons. The Drosophila Scribble complex (Scribble, Dlg, and lethal giant larvae) plays a role in apico-basal cell polarity, and in other forms of polarity, including regulation of the actin cytoskeleton, cell signaling and vesicular trafficking, and in tumor development. Postsynaptic targeting of Drosophila DLG requires interactions mediated by the first two PDZ domains. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Dlg-like family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467206 [Multi-domain] Cd Length: 89 Bit Score: 36.52 E-value: 4.95e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 122056614  14 GFRLQGGKDF----NMP-LTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSA 72
Cdd:cd06723   14 GFSIAGGTDNphigDDPsIYITKIIPGGAAAADgRLRVNDIILRVNDVDVRNVTHSVAVEALKEA 78

The first LIM domain of Lhx2 and Lhx9 family; The first LIM domain of Lhx2 and Lhx9 family: Lhx2 and Lhx9 are highly homologous LHX regulatory proteins. They belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Although Lhx2 and Lhx9 are highly homologous, they seems to play regulatory roles in different organs. In animals, Lhx2 plays important roles in eye, cerebral cortex, limb, the olfactory organs, and erythrocyte development. Lhx2 gene knockout mice exhibit impaired patterning of the cortical hem and the telencephalon of the developing brain, and a lack of development in olfactory structures. Lhx9 is expressed in several regions of the developing mouse brain , the spinal cord, the pancreas, in limb mesenchyme, and in the urogenital region. Lhx9 plays critical roles in gonad development. Homozygous mice lacking functional Lhx9 alleles exhibit numerous urogenital defects, such as gonadal agenesis, infertility, and undetectable levels of testosterone and estradiol coupled with high FSH levels. Lhx9 null mice are phenotypically female, even those that are genotypically male. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188755 [Multi-domain] Cd Length: 54 Bit Score: 35.39 E-value: 4.99e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 122056614 441 CGHCNNVIRGPF-LVAMGRSWHPEEFTCAYCKTSLAD--VCFVEEqNNVYCERCY 492
Cdd:cd09369    1 CAGCGEKIQDRFyLLAVDRQWHASCLKCCECRLPLDSelSCFSRD-GNIYCKEDY 54

DNA polymerase III subunits gamma and tau; Provisional

Pssm-ID: 237871 [Multi-domain] Cd Length: 576 Bit Score: 39.72 E-value: 5.12e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 122056614 289 TTASIRPSVYQPVPASTYSPSPGANYSPTPYTPSPAPAYTPSPAPAYTPSPVPtytpsPAPAYTPSPAP 357
Cdd:PRK14965 381 APAPPSAAWGAPTPAAPAAPPPAAAPPVPPAAPARPAAARPAPAPAPPAAAAP-----PARSADPAAAA 444

The third LIM domain of an Enigma subfamily with unknown function; The third LIM domain of an Enigma subfamily with unknown function: The Enigma LIM domain family is comprised of three characterized members: Enigma, ENH, and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. They serve as adaptor proteins, where the PDZ domain tethers the protein to the cytoskeleton and the LIM domains, recruit signaling proteins to implement corresponding functions. The members of the enigma family have been implicated in regulating or organizing cytoskeletal structure, as well as involving multiple signaling pathways. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188845 Cd Length: 54 Bit Score: 35.60 E-value: 5.24e-03

                         10        20        30
                 ....*....|....*....|....*....|....*
gi 122056614 514 ALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCE 548
Cdd:cd09461   17 ALNNNYHSQCFNCTRCNVNLEGQSFYAKGGRPFCK 51

The first LIM domain of LIMK1 (LIM domain Kinase 1); The first LIM domain of LIMK1 (LIM domain Kinase 1): LIMK1 belongs to the LIMK protein family, which comprises LIMK1 and LIMK2. LIMK contains two LIM domains, a PDZ domain, and a kinase domain. LIMK is involved in the regulation of actin polymerization and microtubule disassembly. LIMK influences architecture of the actin cytoskeleton by regulating the activity of the cofilin family proteins cofilin1, cofilin2, and destrin. The mechanism of the activation is to phosphorylates cofilin on serine 3 and inactivates its actin-severing activity, and altering the rate of actin depolymerization. LIMKs can function in both cytoplasm and nucleus. Both LIMK1 and LIMK2 can act in the nucleus to suppress Rac/Cdc42-dependent cyclin D1 expression. LIMK1 is expressed in all tissues and is localized to focal adhesions in the cell. LIMK1 can form homodimers upon binding of HSP90 and is activated by Rho effector Rho kinase and MAPKAPK2. LIMK1 is important for normal central nervous system development, and its deletion has been implicated in the development of the human genetic disorder Williams syndrome. Moreover, LIMK1 up-regulates the promoter activity of urokinase type plasminogen activator and induces its mRNA and protein expression in breast cancer cells. The LIM domains have been shown to play an important role in regulating kinase activity and likely also contribute to LIMK function by acting as sites of protein-to-protein interactions. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188846 [Multi-domain] Cd Length: 74 Bit Score: 36.02 E-value: 5.34e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 122056614 439 PLCGHCNNVI-RGPFLVAMGRSWHPEEFTCAYCKTSLADVcFVEEQNNVYCERCY 492
Cdd:cd09462   20 PVCASCGQSIyDGQYLQALNSDWHADCFRCCECGASLSHW-YYEKDGRLFCKKDY 73

The fourth LIM domain of actin binding LIM (abLIM) proteins; The fourth LIM domain of actin binding LIM (abLIM) proteins: Three homologous members of the abLIM protein family have been identified; abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM consists of four tandem repeats of LIM domains and the C-terminal of acting binding LIM protein is a villin headpiece domain, which has strong actin binding activity. The abLIM-1, which is expressed in retina, brain, and muscle tissue, has been indicated to function as a tumor suppressor. AbLIM-2 and -3, mainly expressed in muscle and neuronal tissue, bind to F-actin strongly. They may serve as a scaffold for signaling modules of the actin cytoskeleton and thereby modulate transcription. It has shown that LIM domains of abLIMs interact with STARS (striated muscle activator of Rho signaling), which directly binds actin and stimulates serum-response factor (SRF)-dependent transcription. All LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188716 Cd Length: 56 Bit Score: 35.41 E-value: 5.48e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 122056614 500 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPF---------GNSLFHmedgePYCEK 549
Cdd:cd09330    1 CEACDKFITGKVLEAGGKHYHPTCARCSRCGQMFgegeemylqGSEIWH-----PDCRQ 54

60S ribosomal protein L19-like protein; Provisional

Pssm-ID: 185616 [Multi-domain] Cd Length: 357 Bit Score: 39.55 E-value: 5.73e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 275 SEGPAAPAPKPRVVTTASIRPSVYQPVPASTYSPSPGANYSPTPYTPSPAPAYTPspaPAYTPSPVPTYTPSPAPAYTPS 354
Cdd:PTZ00436 216 SAKAAAPAKAAAAPAKAAAPPAKAAAAPAKAAAAPAKAAAPPAKAAAPPAKAAAP---PAKAAAPPAKAAAPPAKAAAPP 292

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 122056614 355 PAPNYNPAPSVAysgGPAEPASRPPWVTDDSFSQKFAPGKSTTSISKQTLPRGGPAYTPAGPQ 417
Cdd:PTZ00436 293 AKAAAAPAKAAA---APAKAAAAPAKAAAPPAKAAAPPAKAATPPAKAAAPPAKAAAAPVGKK 352

The first LIM domain of Lhx7 and Lhx8; The first LIM domain of Lhx7 and Lhx8: Lhx7 and Lhx8 belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs such as the pituitary gland and the pancreas. Studies using mutant mice have revealed roles for Lhx7 and Lhx8 in the development of cholinergic neurons in the telencephalon and in basal forebrain development. Mice lacking alleles of the LIM-homeobox gene Lhx7 or Lhx8 display dramatically reduced number of forebrain cholinergic neurons. In addition, Lhx7 mutation affects male and female mice differently, with females appearing more affected than males. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188767 [Multi-domain] Cd Length: 56 Bit Score: 35.34 E-value: 5.77e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 122056614 499 LCAKCNTKIMGEVMHALRQ-TWHTTCFVCAACKKPFGNSLF-HMEDGEPYCEKDY 551
Cdd:cd09381    1 VCSSCGLEIVDKYLLKVNDlCWHVRCLSCSVCRTSLGRHTScYIKDKDIFCKLDY 55

The LIM domain of N-RAP; The LIM domain of N-RAP: N-RAP is a muscle-specific protein concentrated at myotendinous junctions in skeletal muscle and intercalated disks in cardiac muscle. LIM domain is found at the N-terminus of N-RAP and the C-terminal of N-RAP contains a region with multiple of nebulin repeats. N-RAP functions as a scaffolding protein that organizes alpha-actinin and actin into symmetrical I-Z-I structures in developing myofibrils. Nebulin repeat is known as actin binding domain. The N-RAP is hypothesized to form antiparallel dimerization via its LIM domain. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188830 Cd Length: 53 Bit Score: 35.28 E-value: 5.86e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 122056614 500 CAKCNTKIM-GEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCE 548
Cdd:cd09446    1 CARCGYGVYpAEKINCIDQTWHKACFHCEVCKMMLTVNNFVSHQKKPYCQ 50

The first LIM domain of Lhx2; The first LIM domain of Lhx2: Lhx2 belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. In animals, Lhx2 plays important roles in eye, cerebral cortex, limb, the olfactory organs, and erythrocyte development. Lhx2 gene knockout mice exhibit impaired patterning of the cortical hem and the telencephalon of the developing brain, and a lack of development in olfactory structures. The Lhx2 protein has been shown to bind to the mouse M71 olfactory receptor promoter. Similar to other LIM domains, this domain family is 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188853 Cd Length: 64 Bit Score: 35.75 E-value: 5.94e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 122056614 499 LCAKCNTKIMGEV-MHALRQTWHTTCFVCAACKKPFGNSLF-HMEDGEPYCEKDY 551
Cdd:cd09469   10 LCAGCGGKISDRYyLLAVDKQWHMRCLKCCECKLNLESELTcFSKDGSIYCKEDY 64

Periplasmic serine protease, S1-C subfamily, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones];

Pssm-ID: 440035 [Multi-domain] Cd Length: 274 Bit Score: 38.98 E-value: 5.96e-03

                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 122056614  29 ISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQ 66
Cdd:COG0265  205 VARVEPGSPAAKAGLRPGDVILAVDGKPVTSARDLQRL 242

The first LIM domain of Lhx4; The first LIM domain of Lhx4. Lhx4 belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. LHX4 plays essential roles in pituitary gland and nervous system development. In mice, the lhx4 gene is expressed in the developing hindbrain, cerebral cortex, pituitary gland, and spinal cord. LHX4 shows significant sequence similarity to LHX3, particularly to isoforms Lhx3a. In gene regulation experiments, the LHX4 protein exhibits regulation roles towards pituitary genes, acting on their promoters/enhancers. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188852 Cd Length: 52 Bit Score: 35.33 E-value: 5.97e-03

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 122056614 559 CHGCDFPVEagDKFI-EALGHTWHDTCFICAVCHVNLEGQPFY 600
Cdd:cd09468    1 CAGCNQHIL--DKFIlKVLDRHWHSSCLKCADCQMQLAERCFS 41

The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3); The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3): LMO1 and LMO3 are highly homologous and belong to the LMO protein family. LMO1 and LMO3 are nuclear protein that plays important roles in transcriptional regulation and development. As LIM domains lack intrinsic DNA-binding activity, nuclear LMOs are involved in transcriptional regulation by forming complexes with other transcription factors or cofactors. For example, LMO1 interacts with the the bHLH domain of bHLH transcription factor, TAL1 (T-cell acute leukemia1)/SCL (stem cell leukemia) . LMO1 inhibits the expression of TAL1/SCL target genes. LMO3 facilitates p53 binding to its response elements, which suggests that LMO3 acts as a co-repressor of p53, suppressing p53-dependent transcriptional regulation. In addition, LMO3 interacts with neuronal transcription factor, HEN2, and acts as an oncogene in neuroblastoma. Another binding partner of LMO3 is calcium- and integrin-binding protein CIB, which binds via the second LIM domain (LIM2) of LMO3. One role of the CIB/LMO3 complex is to inhibit cell proliferation. Although LMO1 and LMO3 are highly homologous proteins, they play different roles in the regulation of the pituitary glycoprotein hormone alpha-subunit (alpha GSU) gene. Alpha GSU promoter activity was markedly repressed by LMO1 but activated by LMO3. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188774 Cd Length: 55 Bit Score: 35.22 E-value: 6.11e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 122056614 559 CHGCDFPVEagDKF-IEALGHTWHDTCFICAVCHVNLE--GQPFYSKKDRPLCKK 610
Cdd:cd09388    1 CAGCNRKIK--DRYlLKALDQYWHEDCLKCACCDCRLGevGSTLYTKANLILCRR 53

capsid maturational protease; Provisional

Pssm-ID: 223061 [Multi-domain] Cd Length: 663 Bit Score: 39.60 E-value: 6.14e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 308 PSPGANYSPTPYTPSPA-PAYTPSPAPAYTPSPVPTYTPSPAPAYTPSPAP-------------NYNPAPSVAYSG---- 369
Cdd:PHA03369 354 TAPSRVLAAAAKVAVIAaPQTHTGPADRQRPQRPDGIPYSVPARSPMTAYPpvpqfcgdpglvsPYNPQSPGTSYGpepv 433

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 122056614 370 GPAEPASRPPWVTDDSFSQKFAPGKSTTSISKQTLPRGG 408
Cdd:PHA03369 434 GPVPPQPTNPYVMPISMANMVYPGHPQEHGHERKRKRGG 472

This domain belongs to the LIM domain family which are found on Mical (molecule interacting with CasL) like proteins; The LIM domain on proteins of unknown function: This domain belongs to the LIM domain family which are found on Mical (molecule interacting with CasL)-like proteins. Known members of the Mical-like family includes single LIM domain containing proteins, Mical (molecule interacting with CasL), pollen specific protein SF3, Eplin, xin actin-binding repeat-containing protein 2 (XIRP2), and Ltd-1. The members of this family function mainly at the cytoskeleton and focal adhesions. They interact with transcription factors or other signaling molecules to play roles in muscle development, neuronal differentiation, cell growth, and mobility. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188829 [Multi-domain] Cd Length: 53 Bit Score: 35.13 E-value: 6.18e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 122056614 500 CAKCNTKI--MGEVMhALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYC 547
Cdd:cd09445    1 CRSCGKPVykMEEII-AEKHIYHKNCFRCKDCNKQLKVDNYQSHEGNLYC 49

The first LIM domain of Cysteine Rich Protein 1 (CRP1); The first LIM domain of Cysteine Rich Protein 1 (CRP1): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to a short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP and TLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. CRP1 can associate with the actin cytoskeleton and are capable of interacting with alpha-actinin and zyxin. CRP1 was shown to regulate actin filament bundling by interaction with alpha-actinin and direct binding to actin filaments. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188863 Cd Length: 56 Bit Score: 35.38 E-value: 6.25e-03

                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 122056614 457 GRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERCY 492
Cdd:cd09479   20 GRSFHKSCFLCMVCKKNLDSTTVAVHGEEIYCKSCY 55

UV excision repair protein Rad23; All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]

Pssm-ID: 273167 [Multi-domain] Cd Length: 378 Bit Score: 39.11 E-value: 6.36e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 122056614  320 TPSPAPAYTPSPAPAYTPSPVPTYTPSPAPAyTPSPAPNYNPAPSVAYSGGPAEPASRPPWVTDDSFS 387
Cdd:TIGR00601  82 GKVAPPAATPTSAPTPTPSPPASPASGMSAA-PASAVEEKSPSEESATATAPESPSTSVPSSGSDAAS 148

sec-independent translocase; Provisional

Pssm-ID: 135173 [Multi-domain] Cd Length: 214 Bit Score: 38.64 E-value: 6.47e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 278 PAAPAPKPRVVTtASIRPsvYQPVPASTYSPSPGANYSPTPYTPSPAPAytpsPAPAYTPSPVPTYTPSPAPAYTPSPAP 357
Cdd:PRK04654 138 AHTPVPAPAPVI-AQAQP--IAPAPHQTLVPAPHDTIVPAPHAAHLPSA----PATPVSVAPVDAGTSASPTPSEPTKIQ 210


                 ....
gi 122056614 358 NYNP 361
Cdd:PRK04654 211 EKQP 214

bifunctional uroporphyrinogen-III synthetase/uroporphyrin-III C-methyltransferase; Reviewed

Pssm-ID: 235899 [Multi-domain] Cd Length: 656 Bit Score: 39.70 E-value: 6.60e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 122056614 321 PSPAPAYTPSPAPAYTPSPVPTYTPSPAPAyTPSPAPNYNPAPSVAYSGGPAEPASRPPWV 381
Cdd:PRK06975 267 DAAAQPATAAPAPSRMTDTNDSKSVTSQPA-AAAAAPAPPPNPPATPPEPPARRGRGSAAL 326

The LIM domain of Mical (molecule interacting with CasL); The LIM domain of Mical (molecule interacting with CasL): MICAL is a large, multidomain, cytosolic protein with a single LIM domain, a calponin homology (CH) domain and a flavoprotein monooxygenase domain. In Drosophila, MICAL is expressed in axons, interacts with the neuronal A (PlexA) receptor and is required for Semapho-rin 1a (Sema-1a)-PlexA-mediated repulsive axon guidance. The LIM domain and calporin homology domain are known for interactions with the cytoskeleton, cytoskeletal adaptor proteins, and other signaling proteins. The flavoprotein monooxygenase (MO) is required for semaphorin-plexin repulsive axon guidance during axonal pathfinding in the Drosophila neuromuscular system. In addition, MICAL was characterized to interact with Rab13 and Rab8 to coordinate the assembly of tight junctions and adherens junctions in epithelial cells. Thus, MICAL was also named junctional Rab13-binding protein (JRAB). As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188823 [Multi-domain] Cd Length: 55 Bit Score: 35.35 E-value: 6.67e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 122056614 559 CHGCDFPVEAGDKfIEALGHTWHDTCFICAVCHVNLE--GQPFYSKKDRPLCKKH 611
Cdd:cd09439    1 CYFCKKRVYVMER-LSAEGLFFHRSCFKCSYCGTTLRlgAYAFDRDDGKFYCKPH 54

septation protein SepH; Septation protein H (SepH) was firstly characterized in Streptomyces venezuelae, and homologs were identified in Mycobacterium smegmatis. SepH contains a N-terminal DUF3071 domain and a conserved C-terminal region. It binds directly to cell division protein FtsZ to stimulate the assembly of FtsZ protofilaments.

Pssm-ID: 468676 [Multi-domain] Cd Length: 346 Bit Score: 38.98 E-value: 6.74e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614 278 PAAPAPKPRVVTTASIR---PSVYQPV---PASTYSPSPGANYSPTPYTPSPAPAYTPSPAPAYTPSPVPTytpSPAPAY 351
Cdd:NF040712 230 DSDPAEAGTPDDLASARrrrAGVEQPEdepVGPGAAPAAEPDEATRDAGEPPAPGAAETPEAAEPPAPAPA---APAAPA 306

                         90       100
                 ....*....|....*....|....*...
gi 122056614 352 TPSPAPNYNPAPSVAysGGPAEPASRPP 379
Cdd:NF040712 307 APEAEEPARPEPPPA--PKPKRRRRRAS 332

The first LIM domain of Lhx1 (also known as Lim1) and Lhx5; The first LIM domain of Lhx1 (also known as Lim1) and Lhx5. Lhx1 and Lhx5 are closely related members of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx1 is required for regulating the vertebrate head organizer, the nervous system, and female reproductive tract development. During embryogenesis in the mouse, Lhx1 is expressed early in mesodermal tissue, then later during urogenital, kidney, liver, and nervous system development. In the adult, expression is restricted to the kidney and brain. A mouse embryos with Lhx1 gene knockout cannot grow normal anterior head structures, kidneys, and gonads, but with normally developed trunk and tail morphology. In the developing nervous system, Lhx1 is required to direct the trajectories of motor axons in the limb. Lhx1 null female mice lack the oviducts and uterus. Lhx5 protein may play complementary or overlapping roles with Lhx1. The expression of Lhx5 in the anterior portion of the mouse neural tube suggests a role in patterning of the forebrain. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188753 [Multi-domain] Cd Length: 52 Bit Score: 35.10 E-value: 6.89e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 559 CHGCDFPVEagDKFI-EALGHTWHDTCFICAVCHVNLEGQPFySKKDRPLCK 609
Cdd:cd09367    1 CAGCDRPIL--DKFLlNVLDRAWHAKCVQCCDCKCPLTEKCF-SREGKLYCR 49

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.

Pssm-ID: 460830 [Multi-domain] Cd Length: 991 Bit Score: 39.75 E-value: 6.96e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  279 AAPAPKPRVVTTASirpsvyQPVPASTYSP----SPGANYSPTPYTPSPAPAYTPSPAPAYTPSPVPTYTPSPAPAYTPS 354
Cdd:pfam03154 195 ATAGPTPSAPSVPP------QGSPATSQPPnqtqSTAAPHTLIQQTPTLHPQRLPSPHPPLQPMTQPPPPSQVSPQPLPQ 268

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 122056614  355 PAPN--YNPAPSVAYSGGPAEPASRPP----WVTDDSFSQKFAPGKSTTSISKQTLPRGGPAYTPAGPQVPP 420
Cdd:pfam03154 269 PSLHgqMPPMPHSLQTGPSHMQHPVPPqpfpLTPQSSQSQVPPGPSPAAPGQSQQRIHTPPSQSQLQSQQPP 340

The first LIM domain of LMO4 (LIM domain only protein 4); The first LIM domain of LMO4 (LIM domain only protein 4): LMO4 is a nuclear protein that plays important roles in transcriptional regulation and development. LMO4 is involved in various functions in tumorigenesis and cellular differentiation. LMO4 proteins regulate gene expression by interacting with a wide variety of transcription factors and cofactors to form large transcription complexes. It can interact with Smad proteins, and associate with the promoter of the PAI-1 (plasminogen activator inhibitor-1) gene in a TGFbeta (transforming growth factor beta)-dependent manner. LMO4 can also form a complex with transcription regulator CREB (cAMP response element-binding protein) and interact with CLIM1 and CLIM2. In breast tissue, LMO4 interacts with multiple proteins, including the cofactor CtIP [CtBP (C-terminal binding protein)-interacting protein], the breast and ovarian tumor suppressor BRCA1 (breast-cancer susceptibility gene 1) and the LIM-domain-binding protein LDB1. Functionally, LMO4 is shown to repress BRCA1-mediated transcription activation, thus invoking a potential role for LMO4 as a negative regulator of BRCA1 in sporadic breast cancer. LMO4 also forms complex to both ERa (oestrogen receptor alpha), MTA1 (metastasis tumor antigen 1), and HDACs (histone deacetylases), implying that LMO4 is also a component of the MTA1 corepressor complex. Over-expressed LMO4 represses ERa transactivation functions in an HDAC-dependent manner, and contributes to the process of breast cancer progression by allowing the development of Era-negative phenotypes. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188772 [Multi-domain] Cd Length: 55 Bit Score: 35.09 E-value: 7.15e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 122056614 500 CAKCNTKIMGE-VMHALRQTWHTTCFVCAACKKPF---GNSLFhMEDGEPYCEKDY 551
Cdd:cd09386    1 CAGCGGKIVDRfLLHALDRYWHNGCLKCSCCQAQLgeiGSSCY-TKGGMILCKNDY 55

Cornifin (SPRR) family; SPRR genes (formerly SPR) encode a novel class of polypeptides (small proline rich proteins) that are strongly induced during differentiation of human epidermal keratinocytes in vitro and in vivo. The most characteriztic feature of the SPRR gene family resides in the structure of the central segments of the encoded polypeptides that are built up from tandemly repeated units of either eight (SPRR1 and SPRR3) or nine (SPRR2) amino acids with the general consensus XKXPEPXX where X is any amino acid. In order to avoid bacterial contamination due to the high polar-nature of the HMM the threshold has been set very high.

Pssm-ID: 280537 [Multi-domain] Cd Length: 135 Bit Score: 37.34 E-value: 7.34e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  278 PAAPAPKPRVVTTASIRPSVYQPVPASTYSPSPGANYSPTPYTPS-PAPAYTPSPAPAYTPSPVPTYTPSPAPAYTPSPA 356
Cdd:pfam02389   8 PCQPPPQEPCVPTTKEPCHSKVPEPCNPKVPEPCCPKVPEPCCPKvPEPCCPKVPEPCCPKVPEPCYPKVPEPCSPKVPE 87


                  ....*..
gi 122056614  357 PNYNPAP 363
Cdd:pfam02389  88 PCHPKAP 94

The first LIM domain of Cysteine Rich Protein 3 (CRP3/MLP); The first LIM domain of Cysteine Rich Protein 3 (CRP3/MLP): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network.CRP3 also called Muscle LIM Protein (MLP), which is a striated muscle-specific factor that enhances myogenic differentiation. CRP3/MLP interacts with cytoskeletal protein beta-spectrin. CRP3/MLP also interacts with the basic helix-loop-helix myogenic transcriptio n factors MyoD, myogenin, and MRF4 thereby increasing their affinity for specific DNA regulatory elements. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188865 Cd Length: 54 Bit Score: 35.12 E-value: 7.49e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 122056614 441 CGHC-NNVIRGPFLVAMGRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCERCY 492
Cdd:cd09481    2 CGACeKTVYHAEEIQCNGRSFHKTCFICMACRKALDSTTVAAHESEIYCKTCY 54

Domain of unknwon function (DUF3824); This is a repeating domain found in fungal proteins. It is proline-rich, and the function is not known.

Pssm-ID: 372351 [Multi-domain] Cd Length: 145 Bit Score: 37.41 E-value: 7.53e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 122056614  306 YSPSPGANYSPTPYTPSPAPAYTPS----PAPAYTPSPVPTYTPSPAPAYTPSPAPNYNPAPsvaYSGGPA 372
Cdd:pfam12868  48 YRDYYEDPYSPSPYPPSPAGPYASQgqyyPETNYFPPPPGSTPQPPVDPQPNAPPPPYNPAD---YPPPPG 115

The fourth LIM domain of Paxillin; The fourth LIM domain of Paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188795 [Multi-domain] Cd Length: 52 Bit Score: 34.93 E-value: 7.60e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 122056614 559 CHGCDFPVEAgdKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLC 608
Cdd:cd09411    1 CSGCQKPITG--RCITAMGKKFHPEHFVCAFCLKQLNKGTFKEQNDKPYC 48

The first LIM domain of Lhx3a; The first LIM domain of Lhx3a: Lhx3a is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx3a is one of the two isoforms of Lhx3. The Lhx3 gene is expressed in the ventral spinal cord, the pons, the medulla oblongata, and the pineal gland of the developing nervous system during mouse embryogenesis, and transcripts are found in the emergent pituitary gland. Lhx3 functions in concert with other transcription factors to specify interneuron and motor neuron fates during development. Lhx3 proteins have been demonstrated to directly bind to the promoters of several pituitary hormone gene promoters. The Lhx3 gene encodes two isoforms, LHX3a and LHX3b that differ in their amino-terminal sequences, where Lhx3a has longer N-terminal. They show differential activation of pituitary hormone genes and distinct DNA binding properties. In human, Lhx3a trans-activated the alpha-glycoprotein subunit promoter and genes containing a high-affinity Lhx3 binding site more effectively than the hLhx3b isoform. In addition, hLhx3a induce transcription of the TSHbeta-subunit gene by acting on pituitary POU domain factor, Pit-1, while hLhx3b does not. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188850 [Multi-domain] Cd Length: 56 Bit Score: 35.14 E-value: 7.75e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 122056614 439 PLCGHCNNVIRGPF-LVAMGRSWHPEEFTCAYCKTSLADVCFvEEQNNVYCErcyEQFF 496
Cdd:cd09466    2 PKCAGCDHPIFDRFiLKVQDKPWHSKCLKCVDCQAQLTDKCF-SRGGQVYCK---EDFF 56

The first LIM domain of thymus LIM protein (TLP); The first LIM domain of thymus LIM protein (TLP): TLP is the distant member of the CRP family of proteins. TLP has two isomers (TLP-A and TLP-B) and sharing approximately 30% with each of the three other CRPs. Like CRP1, CRP2 and CRP3/MLP, TLP has two LIM domains, connected by a flexible linker region. Unlike the CRPs, TLP lacks the nuclear targeting signal (K/R-K/R-Y-G-P-K) and is localized solely in the cytoplasm. TLP is specifically expressed in the thymus in a subset of cortical epithelial cells. TLP has a role in development of normal thymus and in controlling the development and differentiation of thymic epithelial cells. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188860 Cd Length: 54 Bit Score: 34.94 E-value: 7.82e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 122056614 500 CAKCNTKI-MGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEK 549
Cdd:cd09476    1 CPRCDKTVyFAEKVSSLGKNWHRFCLKCERCSKILSPGGHAEHDGKPYCHK 51

multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine pyrophosphate-binding subunit/dihydrolipoyllysine-residue succinyltransferase subunit;

Pssm-ID: 237030 [Multi-domain] Cd Length: 1228 Bit Score: 39.49 E-value: 8.07e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122056614  312 ANYSPTPyTPSPAPAYTPSPAPAytpspvPTYTPSPAPAYTPSPAPNYNPAPSVAYSGGPAEPASRPPWVTDDSFSQKFA 391
Cdd:PRK12270   34 ADYGPGS-TAAPTAAAAAAAAAA------SAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAAAAAAAAAPAAPPAAAAAA 106

                          90
                  ....*....|....*....
gi 122056614  392 PGKSTTSISKQTLPRGGPA 410
Cdd:PRK12270  107 APAAAAVEDEVTPLRGAAA 125

The fourth LIM domain of the Paxillin-like protein family; The fourth LIM domain of the Paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188725 [Multi-domain] Cd Length: 52 Bit Score: 35.01 E-value: 8.25e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 122056614 559 CHGCDFPVEAGdkFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKK 610
Cdd:cd09339    1 CAGCGKPITGR--CITAMGRKFHPEHFVCAFCLKQLSKGTFKEQDDKPYCHP 50

Membrane-associated protease RseP, regulator of RpoE activity [Posttranslational modification, protein turnover, chaperones, Transcription];

Pssm-ID: 440513 [Multi-domain] Cd Length: 349 Bit Score: 38.91 E-value: 8.57e-03

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 122056614  20 GKDFNMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHL 63
Cdd:COG0750  123 GVPVLTPPVVGEVVPGSPAAKAGLQPGDRIVAINGQPVTSWDDL 166

UV excision repair protein Rad23; All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]

Pssm-ID: 273167 [Multi-domain] Cd Length: 378 Bit Score: 38.72 E-value: 8.70e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 122056614  316 PTPYTPSPAPAYTPSPAPAYTPSPVPTyTPSPAPAYTPSPAPNYNPAPSVAYSGGPAE 373
Cdd:TIGR00601  86 PPAATPTSAPTPTPSPPASPASGMSAA-PASAVEEKSPSEESATATAPESPSTSVPSS 142

circularly permuted PDZ domains of Escherichia coli Regulator of sigma-E protease (RseP) and related domains; Permuted PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of ResP (also known as Site-2 protease RseP, and YaeL), and related domains. RseP is involved in the regulation of an extracytoplasmic stress response through the cleavage of membrane-spanning anti-stress-response transcription factor (anti-sigmE) protein RseA; it cleaves the peptide bond between the critical alanine and cysteine in the transmembrane region of RseA, releasing the cytoplasmic domain of RseA with its associated sigmaE. RseP contains two tandem-arranged periplasmic PDZ domains (PDZ-N/PDZ1 and PDZ-C/PDZ2) which act to negatively regulate protease action on intact RseA; they serve as a size-exclusion filter which prevents the access of an intact RseA into the active site of RseP. PDZ domains usually bind in sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This RseP family PDZ domain is a circularly permuted PDZ domain which places both beta-strands A and B at the C-terminus. Another permutation exists in the PDZ superfamily which places beta-strand A at the C-terminus.

Pssm-ID: 467638 [Multi-domain] Cd Length: 83 Bit Score: 35.63 E-value: 8.79e-03

                         10        20        30
                 ....*....|....*....|....*....|..
gi 122056614  28 TISRITPGSKAAQSQLSQGDLVVAIDGVNTDT 59
Cdd:cd23081    2 VVGEVVANSPAAEAGLKPGDRILKIDGQKVRT 33

PDZ domain of regulator of G-protein signaling 12 (RGS12), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of RGS12, and related domains. RGS12 downregulates GPCR signal transduction by increasing the GTPase activity of G-protein alpha subunits, thereby driving G-proteins into their inactive GDP-bound form. The RGS12 PDZ domain can bind selectively to C-terminal (A/S)-T-X-(L/V) motifs as found within both the CXCR2 IL-8 receptor, and the alternative 3' exon form of RGS12. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This RGS12-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467194 [Multi-domain] Cd Length: 76 Bit Score: 35.30 E-value: 8.91e-03

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gi 122056614   9 GPGPWGFRLQGgkdfNMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTH 62
Cdd:cd06710    8 GRAGYGFTISG----QAPCVLSCVVRGSPADVAGLKAGDQILAVNGINVSKASH 57

DNA polymerase III subunit gamma/tau;

Pssm-ID: 237862 [Multi-domain] Cd Length: 620 Bit Score: 39.18 E-value: 9.03e-03

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gi 122056614 282 APKPRVVTTASIRPSVYQPVPASTYSPSPGANYSPTPYTPSPAPAYTPSPAPAYTPSPVPTYTPSPAPAYTPSPAPNY 359
Cdd:PRK14948 363 AFISEIANASAPANPTPAPNPSPPPAPIQPSAPKTKQAATTPSPPPAKASPPIPVPAEPTEPSPTPPANAANAPPSLN 440

PDZ domain 1 of membrane-associated guanylate kinase inverted 1 (MAGI-1), MAGI-2, and MAGI-3, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of MAGI1, 2, 3 (MAGI is also known as Membrane-associated guanylate kinase, WW and PDZ domain-containing protein) and related domains. MAGI proteins have been implicated in the control of cell migration and invasion through altering the activity of phosphatase and tensin homolog (PTEN) and modulating Akt signaling. Four MAGI proteins have been identified (MAGI1-3 and MAGIX). MAGI1-3 have 6 PDZ domains and bind to the C-terminus of PTEN via their PDZ2 domain. MAGIX has a single PDZ domain that is related to MAGI1-3 PDZ domain 5. Other binding partners for MAGI1 include JAM4, C-terminal tail of high risk HPV-18 E6, megalin, TRAF6, Kir4.1 (basolateral K+ channel subunit), and cadherin 23; for MAGI2, include DASM1, dendrin, axin, beta- and delta-catenin, neuroligin, hyperpolarization-activated cation channels, beta1-adrenergic receptors, NMDA receptor, and TARPs; and for MAGI3 includes LPA2. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MAGI family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as beta-strands A, -B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467213 [Multi-domain] Cd Length: 85 Bit Score: 35.65 E-value: 9.17e-03

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gi 122056614   2 SYSVTLT-GPGPWGFRLQGGKDFNMPLTISRITPGSKAAQ-SQLSQGDLVVAIDGVNTDTMTHLEA 65
Cdd:cd06731    1 LIRTSLKkSARGFGFTIIGGDEPDEFLQIKSVVPDGPAALdGKLRTGDVLVSVNDTCVLGYTHADV 66

The second LIM domain of Isl, a member of LHX protein family; The second LIM domain of Isl: Isl is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Isl1 and Isl2 are the two conserved members of this family. Proteins in this group are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Isl-1 is one of the LHX proteins isolated originally by virtue of its ability to bind DNA sequences from the 5'-flanking region of the rat insulin gene in pancreatic insulin-producing cells. Mice deficient in Isl-1 fail to form the dorsal exocrine pancreas and islet cells fail to differentiate. On the other hand, Isl-1 takes part in the pituitary development by activating the gonadotropin-releasing hormone receptor gene together with LHX3 and steroidogenic factor 1. Mouse Isl2 is expressed in the retinal ganglion cells and the developing spinal cord where it plays a role in motor neuron development. Same as Isl1, Isl2 may also be able to bind to the insulin gene enhancer to promote gene activation. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188760 Cd Length: 55 Bit Score: 34.72 E-value: 9.64e-03

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gi 122056614 500 CAKCNTKIMGE--VMHALRQTWHTTCFVCAACKKPF--GNSlFHMEDGEPYCEKDY 551
Cdd:cd09374    1 CAKCQQSFSKNdfVMRARTKIYHIECFRCSACSRQLipGDE-FALRDDGLFCKADH 55