NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1720399825|ref|XP_030107702|]
View 

bromodomain adjacent to zinc finger domain protein 2B isoform X13 [Mus musculus]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

Name Accession Description Interval E-value
Bromo_BAZ2A_B_like cd05503
Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B ...
2035-2131 2.43e-64

Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B (BAZ2B) were identified as a novel human bromodomain gene by cDNA library screening. BAZ2A is also known as Tip5 (Transcription termination factor I-interacting protein 5) and hWALp3. The proteins may play roles in transcriptional regulation. Human Tip5 is part of a complex termed NoRC (nucleolar remodeling complex), which induces nucleosome sliding and may play a role in the regulation of the rDNA locus. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


:

Pssm-ID: 99935  Cd Length: 97  Bit Score: 213.39  E-value: 2.43e-64
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825 2035 DLALCSMILTEMETHEDSWPFLLPVNLKLVPGYKKVIKKPMDFSTIREKLNNGQYPNFETFALDVRLVFDNCETFNEDDS 2114
Cdd:cd05503      1 DLALCETILDEMEAHEDAWPFLEPVNTKLVPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDS 80
                           90
                   ....*....|....*..
gi 1720399825 2115 DIGRAGHSMRKYFEKKW 2131
Cdd:cd05503     81 EVGRAGHNMRKFFEKRW 97
PHD_BAZ2B cd15630
PHD finger found in bromodomain adjacent to zinc finger domain protein 2B (BAZ2B); BAZ2B, also ...
1902-1950 4.29e-32

PHD finger found in bromodomain adjacent to zinc finger domain protein 2B (BAZ2B); BAZ2B, also termed WALp4, is a bromodomain-containing protein whose biological role is still elusive. It shows high sequence similarly with BAZ2A, which is the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP-and histone H4 tail-dependent fashion. BAZ2B contains a TAM (TIP5/ARBP/MBD) domain, an Apolipophorin-III like domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


:

Pssm-ID: 277100  Cd Length: 49  Bit Score: 119.31  E-value: 4.29e-32
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1720399825 1902 VYCQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIPDGDWFCPACIS 1950
Cdd:cd15630      1 VYCQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIPEGDWFCPACIA 49
MBD super family cl00110
MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of ...
758-827 1.97e-25

MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1. The MBDs present in putative chromatin remodelling subunit, BAZ2A, and putative histone methyltransferase, CLLD8, represent two phylogenetically distinct groups within the MBD protein family.


The actual alignment was detected with superfamily member cd01397:

Pssm-ID: 469618 [Multi-domain]  Cd Length: 73  Bit Score: 101.33  E-value: 1.97e-25
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1720399825  758 ELRIPLDYGWQRETRVRNFGGRLPGEVAYYAPCGKKLRQCPDMVKGMQW---CLLKEEDVIPRIRAMDGRRGR 827
Cdd:cd01397      1 ELRVPLELGWRRETRIRGLGGRIQGEVAYYAPCGKKLRQYPEVIKYLSKngiSLLSRENFSFSARAPVGDFYE 73
TPH pfam13868
Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of ...
877-1028 2.79e-16

Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain.


:

Pssm-ID: 464007 [Multi-domain]  Cd Length: 341  Bit Score: 82.66  E-value: 2.79e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  877 QAAQIKLLRKLQKQEQARVAKEAKKQQAIMAAEEKRKQKEQMKIIKQQEKIKRIQQIRMEKELRAQqiLEEKELRRQQAV 956
Cdd:pfam13868   16 LAAKCNKERDAQIAEKKRIKAEEKEEERRLDEMMEEERERALEEEEEKEEERKEERKRYRQELEEQ--IEEREQKRQEEY 93
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  957 LLKHQE------------LERHRLDMERERRRQHVM--LMKAMEARKKAEEKERLKQEKRDEKRLNKERKLEQRRLELEM 1022
Cdd:pfam13868   94 EEKLQEreqmdeiveriqEEDQAEAEEKLEKQRQLReeIDEFNEEQAEWKELEKEEEREEDERILEYLKEKAEREEEREA 173

                   ....*.
gi 1720399825 1023 AKELKK 1028
Cdd:pfam13868  174 EREEIE 179
DDT smart00571
domain in different transcription and chromosome remodeling factors;
1055-1118 3.02e-14

domain in different transcription and chromosome remodeling factors;


:

Pssm-ID: 214726  Cd Length: 63  Bit Score: 69.20  E-value: 3.02e-14
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1720399825  1055 TTFSDCLMVVQFLRNFGKVLGFDVNIDVpnLSVLQEGLLNIgDSMGEVQDLLVRLLSAAVCDPG 1118
Cdd:smart00571    2 EAFGDLLMVYEFLRSFGKVLGLSPFRAT--LEDFIAALKCR-DQNGLLTEVHVVLLRAILKDEG 62
WSD super family cl21412
Williams-Beuren syndrome DDT (WSD), D-TOX E motif; This family represents the combined ...
1339-1371 6.17e-06

Williams-Beuren syndrome DDT (WSD), D-TOX E motif; This family represents the combined alpha-helical module found in diverse eukaryotic chromatin proteins. Based on the Ioc3 structure, the N-terminus of this module is inferred to interact with nucleosomal linker DNA and the SLIDE domain of ISWI proteins. The resulting complex forms a protein ruler that measures out the spacing between two adjacent nucleosomes. The acidic residue from the GxD signature at the N-terminus is a major determinant of the interaction between the ISWI and WHIM motifs. The N-terminal portion also contacts the inter-nucleosomal linker DNA. The module shows a great domain architectural diversity and is often combined with other modified histone peptide recognizing and DNA binding domains, some of which discriminate methylated DNA. The WSD module constitutes the inter-nucleosomal linker DNA binding site in the major groove of DNA, and was first identified as WSD, the D-TOX E motif of plant homeodomains homologous with the mutant transcription factor causing Williams-Beuren syndrome in association with the DDT-domain.


The actual alignment was detected with superfamily member pfam15613:

Pssm-ID: 464775 [Multi-domain]  Cd Length: 69  Bit Score: 45.60  E-value: 6.17e-06
                           10        20        30
                   ....*....|....*....|....*....|....
gi 1720399825 1339 LRSMMFGQDRYRRRYWIL-PQCGGIFVEGMESGE 1371
Cdd:pfam15613    1 IRSLPLGRDRRYNRYWWFdPGTGRLFVESPSDGE 34
WSD super family cl21412
Williams-Beuren syndrome DDT (WSD), D-TOX E motif; This family represents the combined ...
1682-1721 3.08e-05

Williams-Beuren syndrome DDT (WSD), D-TOX E motif; This family represents the combined alpha-helical module found in diverse eukaryotic chromatin proteins. Based on the Ioc3 structure, the N-terminus of this module is inferred to interact with nucleosomal linker DNA and the SLIDE domain of ISWI proteins. The resulting complex forms a protein ruler that measures out the spacing between two adjacent nucleosomes. The acidic residue from the GxD signature at the N-terminus is a major determinant of the interaction between the ISWI and WHIM motifs. The N-terminal portion also contacts the inter-nucleosomal linker DNA. The module shows a great domain architectural diversity and is often combined with other modified histone peptide recognizing and DNA binding domains, some of which discriminate methylated DNA. The WSD module constitutes the inter-nucleosomal linker DNA binding site in the major groove of DNA, and was first identified as WSD, the D-TOX E motif of plant homeodomains homologous with the mutant transcription factor causing Williams-Beuren syndrome in association with the DDT-domain.


The actual alignment was detected with superfamily member pfam15613:

Pssm-ID: 464775 [Multi-domain]  Cd Length: 69  Bit Score: 43.68  E-value: 3.08e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 1720399825 1682 EEMQFGWWRIID-PEDLKTLLKVLHLRGIREKALQKQIQKH 1721
Cdd:pfam15613   28 ESPSDGEWGVYSsKEQLDALIASLNPRGVRESALKEALEKI 68
WHIM1 pfam15612
WSTF, HB1, Itc1p, MBD9 motif 1; A conserved alpha helical motif that along with the WHIM2 and ...
1159-1199 2.65e-03

WSTF, HB1, Itc1p, MBD9 motif 1; A conserved alpha helical motif that along with the WHIM2 and WHIM3 motifs, and the DDT domain comprise an alpha helical module found in diverse eukaryotic chromatin proteins.Based on the Ioc3 structure, this module is inferred to interact with nucleosomal linker DNA and the SLIDE domain of ISWI proteins. The resulting complex forms a protein ruler that measures out the spacing between two adjacent nucleosomes. The conserved basic residue in WHIM1 is involved in packing with the DDT motif. The module shows a great domain architectural diversity and is often combined with other modified histone peptide recognising and DNA binding domains, some of which discriminate methylated DNA.


:

Pssm-ID: 464774 [Multi-domain]  Cd Length: 46  Bit Score: 37.48  E-value: 2.65e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 1720399825 1159 ELTESLKTKAFQAHTPAQKASILAFLVNELACSKSVVSEID 1199
Cdd:pfam15612    6 GLLETLKKGGYYELSPEEKLKILKALCDLLLSSSAIRDEIE 46
 
Name Accession Description Interval E-value
Bromo_BAZ2A_B_like cd05503
Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B ...
2035-2131 2.43e-64

Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B (BAZ2B) were identified as a novel human bromodomain gene by cDNA library screening. BAZ2A is also known as Tip5 (Transcription termination factor I-interacting protein 5) and hWALp3. The proteins may play roles in transcriptional regulation. Human Tip5 is part of a complex termed NoRC (nucleolar remodeling complex), which induces nucleosome sliding and may play a role in the regulation of the rDNA locus. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99935  Cd Length: 97  Bit Score: 213.39  E-value: 2.43e-64
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825 2035 DLALCSMILTEMETHEDSWPFLLPVNLKLVPGYKKVIKKPMDFSTIREKLNNGQYPNFETFALDVRLVFDNCETFNEDDS 2114
Cdd:cd05503      1 DLALCETILDEMEAHEDAWPFLEPVNTKLVPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDS 80
                           90
                   ....*....|....*..
gi 1720399825 2115 DIGRAGHSMRKYFEKKW 2131
Cdd:cd05503     81 EVGRAGHNMRKFFEKRW 97
BROMO smart00297
bromo domain;
2029-2133 4.76e-35

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 130.09  E-value: 4.76e-35
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  2029 KKDESRDLALCSMILTEMETHEDSWPFLLPVNLKLVPGYKKVIKKPMDFSTIREKLNNGQYPNFETFALDVRLVFDNCET 2108
Cdd:smart00297    2 PKLQKKLQELLKAVLDKLDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNART 81
                            90       100
                    ....*....|....*....|....*
gi 1720399825  2109 FNEDDSDIGRAGHSMRKYFEKKWTD 2133
Cdd:smart00297   82 YNGPDSEVYKDAKKLEKFFEKKLRE 106
PHD_BAZ2B cd15630
PHD finger found in bromodomain adjacent to zinc finger domain protein 2B (BAZ2B); BAZ2B, also ...
1902-1950 4.29e-32

PHD finger found in bromodomain adjacent to zinc finger domain protein 2B (BAZ2B); BAZ2B, also termed WALp4, is a bromodomain-containing protein whose biological role is still elusive. It shows high sequence similarly with BAZ2A, which is the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP-and histone H4 tail-dependent fashion. BAZ2B contains a TAM (TIP5/ARBP/MBD) domain, an Apolipophorin-III like domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277100  Cd Length: 49  Bit Score: 119.31  E-value: 4.29e-32
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1720399825 1902 VYCQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIPDGDWFCPACIS 1950
Cdd:cd15630      1 VYCQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIPEGDWFCPACIA 49
HAT_MBD cd01397
Methyl-CpG binding domains (MBD) present in putative chromatin remodelling factor such as ...
758-827 1.97e-25

Methyl-CpG binding domains (MBD) present in putative chromatin remodelling factor such as BAZ2A; BAZ2A contains a MBD, DDT, PHD-type zinc finger and Bromo domain suggesting that BAZ2A might be associated with histone acetyltransferase (HAT) activity. The Drosophila melanogaster toutatis protein, a putative subunit of the chromatin-remodeling complex, and other such proteins in this group share a similar domain architecture with BAZ2A, as does the Caenorhabditis elegans flectin homolog.


Pssm-ID: 238691 [Multi-domain]  Cd Length: 73  Bit Score: 101.33  E-value: 1.97e-25
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1720399825  758 ELRIPLDYGWQRETRVRNFGGRLPGEVAYYAPCGKKLRQCPDMVKGMQW---CLLKEEDVIPRIRAMDGRRGR 827
Cdd:cd01397      1 ELRVPLELGWRRETRIRGLGGRIQGEVAYYAPCGKKLRQYPEVIKYLSKngiSLLSRENFSFSARAPVGDFYE 73
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
2039-2121 4.80e-22

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 91.99  E-value: 4.80e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825 2039 CSMILTEMETHEDSWPFLLPVNLKLVPGYKKVIKKPMDFSTIREKLNNGQYPNFETFALDVRLVFDNCETFNEDDSDIGR 2118
Cdd:pfam00439    1 CLEILDKLMEHPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYK 80

                   ...
gi 1720399825 2119 AGH 2121
Cdd:pfam00439   81 AAE 83
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
1903-1951 8.29e-18

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 78.69  E-value: 8.29e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1720399825 1903 YCQICRKGDNEELLLLCDGCDKGCHTYCHRPKITT--IPDGDWFCPACISK 1951
Cdd:pfam00628    1 YCAVCGKSDDGGELVQCDGCDDWFHLACLGPPLDPaeIPSGEWLCPECKPK 51
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
1955-2130 1.24e-17

Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription];


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 87.17  E-value: 1.24e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825 1955 QSIKIKKIHVKGKKTNDSKKTKKGNVAGDTEDEDSASTSSSLKRGSKElkKRKMEETTSLNLSKAESTTSIKKPKKDESR 2034
Cdd:COG5076     62 TSIVDDREPGSMANVNDDLENVGGITYSPFEKNRPESLRFDEIVFLAI--ESVTPESGLGSLLMAHLKTSVKKRKTPKIE 139
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825 2035 DLAL---CSMILTEMET------HEDSWPFLLPVNLKLVPGYKKVIKKPMDFSTIREKLNNGQYPNFETFALDVRLVFDN 2105
Cdd:COG5076    140 DELLyadNKAIAKFKKQlflrdgRFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDN 219
                          170       180
                   ....*....|....*....|....*
gi 1720399825 2106 CETFNEDDSDIGRAGHSMRKYFEKK 2130
Cdd:COG5076    220 CKLYNGPDSSVYVDAKELEKYFLKL 244
TPH pfam13868
Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of ...
877-1028 2.79e-16

Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain.


Pssm-ID: 464007 [Multi-domain]  Cd Length: 341  Bit Score: 82.66  E-value: 2.79e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  877 QAAQIKLLRKLQKQEQARVAKEAKKQQAIMAAEEKRKQKEQMKIIKQQEKIKRIQQIRMEKELRAQqiLEEKELRRQQAV 956
Cdd:pfam13868   16 LAAKCNKERDAQIAEKKRIKAEEKEEERRLDEMMEEERERALEEEEEKEEERKEERKRYRQELEEQ--IEEREQKRQEEY 93
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  957 LLKHQE------------LERHRLDMERERRRQHVM--LMKAMEARKKAEEKERLKQEKRDEKRLNKERKLEQRRLELEM 1022
Cdd:pfam13868   94 EEKLQEreqmdeiveriqEEDQAEAEEKLEKQRQLReeIDEFNEEQAEWKELEKEEEREEDERILEYLKEKAEREEEREA 173

                   ....*.
gi 1720399825 1023 AKELKK 1028
Cdd:pfam13868  174 EREEIE 179
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
1903-1948 1.17e-14

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 69.93  E-value: 1.17e-14
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 1720399825  1903 YCQICRKGDNEELLLLCDGCDKGCHTYCHRPKITT-IPDGDWFCPAC 1948
Cdd:smart00249    1 YCSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEeEPDGKWYCPKC 47
DDT smart00571
domain in different transcription and chromosome remodeling factors;
1055-1118 3.02e-14

domain in different transcription and chromosome remodeling factors;


Pssm-ID: 214726  Cd Length: 63  Bit Score: 69.20  E-value: 3.02e-14
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1720399825  1055 TTFSDCLMVVQFLRNFGKVLGFDVNIDVpnLSVLQEGLLNIgDSMGEVQDLLVRLLSAAVCDPG 1118
Cdd:smart00571    2 EAFGDLLMVYEFLRSFGKVLGLSPFRAT--LEDFIAALKCR-DQNGLLTEVHVVLLRAILKDEG 62
PTZ00121 PTZ00121
MAEBL; Provisional
863-1032 1.82e-13

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 76.72  E-value: 1.82e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  863 AKLLRKlqAQEIARQAAQIKLLRKLQKQEQARVAKEAKKQQAIMAAEEKRKQKEQMKI--IKQQEKIKRIQQIRMEKE-- 938
Cdd:PTZ00121  1499 ADEAKK--AAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAeeLKKAEEKKKAEEAKKAEEdk 1576
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  939 ---LRAQQILEEKELRRQQAVLLKHQELERHRLDmerERRRQHVMLMKAMEARKKAEEK---ERLKQEKRDEKRLNKERK 1012
Cdd:PTZ00121  1577 nmaLRKAEEAKKAEEARIEEVMKLYEEEKKMKAE---EAKKAEEAKIKAEELKKAEEEKkkvEQLKKKEAEEKKKAEELK 1653
                          170       180
                   ....*....|....*....|
gi 1720399825 1013 LEQRRLELEMAKELKKPKED 1032
Cdd:PTZ00121  1654 KAEEENKIKAAEEAKKAEED 1673
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
866-1021 6.51e-12

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 71.12  E-value: 6.51e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  866 LRKLQAQEIARQAAQIKL-LRKLQKQEQARVAKEAKKQQAIMAAEEKRKQKEQMKIIKQQEKIKRIQQIRMEKELRAQQI 944
Cdd:COG1196    306 RLEERRRELEERLEELEEeLAELEEELEELEEELEELEEELEEAEEELEEAEAELAEAEEALLEAEAELAEAEEELEELA 385
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1720399825  945 LEEKELRRQQAVLLKHQELERHRLDMERERRRQHVMLMKAMEARKKAEEKERLKQEKRDEKRLNKERKLEQRRLELE 1021
Cdd:COG1196    386 EELLEALRAAAELAAQLEELEEAEEALLERLERLEEELEELEEALAELEEEEEEEEEALEEAAEEEAELEEEEEALL 462
MBD pfam01429
Methyl-CpG binding domain; The Methyl-CpG binding domain (MBD) binds to DNA that contains one ...
753-802 7.97e-11

Methyl-CpG binding domain; The Methyl-CpG binding domain (MBD) binds to DNA that contains one or more symmetrically methylated CpGs. DNA methylation in animals is associated with alterations in chromatin structure and silencing of gene expression. MBD has negligible non-specific affinity for DNA. In vitro foot-printing with MeCP2 showed the MBD can protect a 12 nucleotide region surrounding a methyl CpG pair. MBDs are found in several Methyl-CpG binding proteins and also DNA demethylase.


Pssm-ID: 396147 [Multi-domain]  Cd Length: 76  Bit Score: 59.68  E-value: 7.97e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1720399825  753 VADDQELRIPLDYGWQRETRVRNFGG-RLPGEVAYYAPCGKKLRQCPDMVK 802
Cdd:pfam01429    1 IERKREDRLPLPPGWRREERQRKSGSkAGKVDVFYYSPTGKKLRSKSEVAR 51
tolA_full TIGR02794
TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the ...
870-1025 6.77e-10

TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB. [Transport and binding proteins, Other, Cellular processes, Pathogenesis]


Pssm-ID: 274303 [Multi-domain]  Cd Length: 346  Bit Score: 62.94  E-value: 6.77e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  870 QAQEIARQAAQIKLLRKLQKQEQARVAKEAKKQQAimaaEEKRKQKEQMKIIKQQEKIKRIQQIRMEKELRAQQILEEKE 949
Cdd:TIGR02794   51 QANRIQQQKKPAAKKEQERQKKLEQQAEEAEKQRA----AEQARQKELEQRAAAEKAAKQAEQAAKQAEEKQKQAEEAKA 126
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1720399825  950 LRRQQAVLLKHQELERHRLDMERERRRQHVMLMKAMEARKKAEEKERLKQEKRDEKRLNKER-KLEQRRLELEMAKE 1025
Cdd:TIGR02794  127 KQAAEAKAKAEAEAERKAKEEAAKQAEEEAKAKAAAEAKKKAEEAKKKAEAEAKAKAEAEAKaKAEEAKAKAEAAKA 203
MBD smart00391
Methyl-CpG binding domain; Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, ...
758-802 3.93e-09

Methyl-CpG binding domain; Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, MeCP1) domain


Pssm-ID: 128673  Cd Length: 77  Bit Score: 55.07  E-value: 3.93e-09
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*.
gi 1720399825   758 ELRIPLDYGWQRETRVRNFG-GRLPGEVAYYAPCGKKLRQCPDMVK 802
Cdd:smart00391    3 PLRLPLPCGWRRETKQRKSGrSAGKFDVYYISPCGKKLRSKSELAR 48
DDT pfam02791
DDT domain; The DDT domain is named after (DNA binding homeobox and Different Transcription ...
1056-1116 1.21e-08

DDT domain; The DDT domain is named after (DNA binding homeobox and Different Transcription factors) and is approximately 60 residues in length. Along with the WHIM motifs, it comprises an entirely alpha helical module found in diverse eukaryotic chromatin proteins. Based on the structure of Ioc3, this module is inferred to interact with nucleosomal linker DNA and the SLIDE domain of ISWI proteins. The resulting complex forms a protein ruler that measures out the spacing between two adjacent nucleosomes. In particular, the DDT domain, in combination with the WHIM1 and WHIM2 motifs form the SLIDE domain binding pocket.


Pssm-ID: 460696  Cd Length: 58  Bit Score: 52.89  E-value: 1.21e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1720399825 1056 TFSDCLMVVQFLRNFGKVLGfdvnIDVPNLSVLQEGLLNIGDSMGEVQDLLVRLLSAAVCD 1116
Cdd:pfam02791    2 AFGDLLMVWEFLNSFGEVLG----LSPFTLDDFEEALLCTEEPSELLDEIHCALLKALVRD 58
GBP_C cd16269
Guanylate-binding protein, C-terminal domain; Guanylate-binding protein (GBP), C-terminal ...
865-985 6.68e-07

Guanylate-binding protein, C-terminal domain; Guanylate-binding protein (GBP), C-terminal domain. Guanylate-binding proteins (GBPs) are synthesized after activation of the cell by interferons. The biochemical properties of GBPs are clearly different from those of Ras-like and heterotrimeric GTP-binding proteins. They bind guanine nucleotides with low affinity (micromolar range), are stable in their absence, and have a high turnover GTPase. In addition to binding GDP/GTP, they have the unique ability to bind GMP with equal affinity and hydrolyze GTP not only to GDP, but also to GMP. This C-terminal domain has been shown to mediate inhibition of endothelial cell proliferation by inflammatory cytokines.


Pssm-ID: 293879 [Multi-domain]  Cd Length: 291  Bit Score: 53.35  E-value: 6.68e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  865 LLRKLQAQE-IAR---QAAQIKLLRKLQKQEQARVAKEAKKQQAIMaaEEKRKQKEQMkiIKQQEKI--KRIQQIRMEKE 938
Cdd:cd16269    172 LQEFLQSKEaEAEailQADQALTEKEKEIEAERAKAEAAEQERKLL--EEQQRELEQK--LEDQERSyeEHLRQLKEKME 247
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 1720399825  939 LRAQQILEEKElrRQQAVLLKHQElerhrlDMERERRRQHVMLMKAM 985
Cdd:cd16269    248 EERENLLKEQE--RALESKLKEQE------ALLEEGFKEQAELLQEE 286
WSD pfam15613
Williams-Beuren syndrome DDT (WSD), D-TOX E motif; This family represents the combined ...
1339-1371 6.17e-06

Williams-Beuren syndrome DDT (WSD), D-TOX E motif; This family represents the combined alpha-helical module found in diverse eukaryotic chromatin proteins. Based on the Ioc3 structure, the N-terminus of this module is inferred to interact with nucleosomal linker DNA and the SLIDE domain of ISWI proteins. The resulting complex forms a protein ruler that measures out the spacing between two adjacent nucleosomes. The acidic residue from the GxD signature at the N-terminus is a major determinant of the interaction between the ISWI and WHIM motifs. The N-terminal portion also contacts the inter-nucleosomal linker DNA. The module shows a great domain architectural diversity and is often combined with other modified histone peptide recognizing and DNA binding domains, some of which discriminate methylated DNA. The WSD module constitutes the inter-nucleosomal linker DNA binding site in the major groove of DNA, and was first identified as WSD, the D-TOX E motif of plant homeodomains homologous with the mutant transcription factor causing Williams-Beuren syndrome in association with the DDT-domain.


Pssm-ID: 464775 [Multi-domain]  Cd Length: 69  Bit Score: 45.60  E-value: 6.17e-06
                           10        20        30
                   ....*....|....*....|....*....|....
gi 1720399825 1339 LRSMMFGQDRYRRRYWIL-PQCGGIFVEGMESGE 1371
Cdd:pfam15613    1 IRSLPLGRDRRYNRYWWFdPGTGRLFVESPSDGE 34
WSD pfam15613
Williams-Beuren syndrome DDT (WSD), D-TOX E motif; This family represents the combined ...
1682-1721 3.08e-05

Williams-Beuren syndrome DDT (WSD), D-TOX E motif; This family represents the combined alpha-helical module found in diverse eukaryotic chromatin proteins. Based on the Ioc3 structure, the N-terminus of this module is inferred to interact with nucleosomal linker DNA and the SLIDE domain of ISWI proteins. The resulting complex forms a protein ruler that measures out the spacing between two adjacent nucleosomes. The acidic residue from the GxD signature at the N-terminus is a major determinant of the interaction between the ISWI and WHIM motifs. The N-terminal portion also contacts the inter-nucleosomal linker DNA. The module shows a great domain architectural diversity and is often combined with other modified histone peptide recognizing and DNA binding domains, some of which discriminate methylated DNA. The WSD module constitutes the inter-nucleosomal linker DNA binding site in the major groove of DNA, and was first identified as WSD, the D-TOX E motif of plant homeodomains homologous with the mutant transcription factor causing Williams-Beuren syndrome in association with the DDT-domain.


Pssm-ID: 464775 [Multi-domain]  Cd Length: 69  Bit Score: 43.68  E-value: 3.08e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 1720399825 1682 EEMQFGWWRIID-PEDLKTLLKVLHLRGIREKALQKQIQKH 1721
Cdd:pfam15613   28 ESPSDGEWGVYSsKEQLDALIASLNPRGVRESALKEALEKI 68
COG5141 COG5141
PHD zinc finger-containing protein [General function prediction only];
1903-1949 5.65e-04

PHD zinc finger-containing protein [General function prediction only];


Pssm-ID: 227470 [Multi-domain]  Cd Length: 669  Bit Score: 44.97  E-value: 5.65e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1720399825 1903 YCQICRK-----GDNEELLLLCDGCDKGCHTYCHrpKITTIPDGDWFCPACI 1949
Cdd:COG5141    192 FDDICTKctsthNENSNAIVFCDGCEICVHQSCY--GIQFLPEGFWLCRKCI 241
OmpH smart00935
Outer membrane protein (OmpH-like); This family includes outer membrane proteins such as OmpH ...
870-932 1.38e-03

Outer membrane protein (OmpH-like); This family includes outer membrane proteins such as OmpH among others. Skp (OmpH) has been characterized as a molecular chaperone that interacts with unfolded proteins as they emerge in the periplasm from the Sec translocation machinery.


Pssm-ID: 214922 [Multi-domain]  Cd Length: 140  Bit Score: 41.03  E-value: 1.38e-03
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1720399825   870 QAQEIARQAAQIK-LLRKLQKQ-----EQARVAKEAKKQQAIMAAEEKRKQKEQMKIIKQQEKIKRIQQ 932
Cdd:smart00935   30 RQAELEKLEKELQkLKEKLQKDaatlsEAAREKKEKELQKKVQEFQRKQQKLQQDLQKRQQEELQKILD 98
WHIM1 pfam15612
WSTF, HB1, Itc1p, MBD9 motif 1; A conserved alpha helical motif that along with the WHIM2 and ...
1159-1199 2.65e-03

WSTF, HB1, Itc1p, MBD9 motif 1; A conserved alpha helical motif that along with the WHIM2 and WHIM3 motifs, and the DDT domain comprise an alpha helical module found in diverse eukaryotic chromatin proteins.Based on the Ioc3 structure, this module is inferred to interact with nucleosomal linker DNA and the SLIDE domain of ISWI proteins. The resulting complex forms a protein ruler that measures out the spacing between two adjacent nucleosomes. The conserved basic residue in WHIM1 is involved in packing with the DDT motif. The module shows a great domain architectural diversity and is often combined with other modified histone peptide recognising and DNA binding domains, some of which discriminate methylated DNA.


Pssm-ID: 464774 [Multi-domain]  Cd Length: 46  Bit Score: 37.48  E-value: 2.65e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 1720399825 1159 ELTESLKTKAFQAHTPAQKASILAFLVNELACSKSVVSEID 1199
Cdd:pfam15612    6 GLLETLKKGGYYELSPEEKLKILKALCDLLLSSSAIRDEIE 46
growth_prot_Scy NF041483
polarized growth protein Scy;
863-1032 3.77e-03

polarized growth protein Scy;


Pssm-ID: 469371 [Multi-domain]  Cd Length: 1293  Bit Score: 42.51  E-value: 3.77e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  863 AKLLRKlQAQE-IARQAAQIKLLRKlQKQEQArvakEAKKQQAIMAAEEKRKQKEQMKIIKQQEKIKRIQQIRMEKELR- 940
Cdd:NF041483   515 ATTLRR-QAEEtLERTRAEAERLRA-EAEEQA----EEVRAAAERAARELREETERAIAARQAEAAEELTRLHTEAEERl 588
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  941 --AQQIL-----EEKELRRQQAvllkhQELERHRLDM-------------ERERRRQHVMlMKAMEARKKAE-------- 992
Cdd:NF041483   589 taAEEALadaraEAERIRREAA-----EETERLRTEAaerirtlqaqaeqEAERLRTEAA-ADASAARAEGEnvavrlrs 662
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*
gi 1720399825  993 ----EKERLKQEKRDE-KRLNKERKLEQRRLELEMAKELKKPKED 1032
Cdd:NF041483   663 eaaaEAERLKSEAQESaDRVRAEAAAAAERVGTEAAEALAAAQEE 707
 
Name Accession Description Interval E-value
Bromo_BAZ2A_B_like cd05503
Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B ...
2035-2131 2.43e-64

Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B (BAZ2B) were identified as a novel human bromodomain gene by cDNA library screening. BAZ2A is also known as Tip5 (Transcription termination factor I-interacting protein 5) and hWALp3. The proteins may play roles in transcriptional regulation. Human Tip5 is part of a complex termed NoRC (nucleolar remodeling complex), which induces nucleosome sliding and may play a role in the regulation of the rDNA locus. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99935  Cd Length: 97  Bit Score: 213.39  E-value: 2.43e-64
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825 2035 DLALCSMILTEMETHEDSWPFLLPVNLKLVPGYKKVIKKPMDFSTIREKLNNGQYPNFETFALDVRLVFDNCETFNEDDS 2114
Cdd:cd05503      1 DLALCETILDEMEAHEDAWPFLEPVNTKLVPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDS 80
                           90
                   ....*....|....*..
gi 1720399825 2115 DIGRAGHSMRKYFEKKW 2131
Cdd:cd05503     81 EVGRAGHNMRKFFEKRW 97
BROMO smart00297
bromo domain;
2029-2133 4.76e-35

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 130.09  E-value: 4.76e-35
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  2029 KKDESRDLALCSMILTEMETHEDSWPFLLPVNLKLVPGYKKVIKKPMDFSTIREKLNNGQYPNFETFALDVRLVFDNCET 2108
Cdd:smart00297    2 PKLQKKLQELLKAVLDKLDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNART 81
                            90       100
                    ....*....|....*....|....*
gi 1720399825  2109 FNEDDSDIGRAGHSMRKYFEKKWTD 2133
Cdd:smart00297   82 YNGPDSEVYKDAKKLEKFFEKKLRE 106
Bromodomain cd04369
Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear ...
2035-2131 1.53e-33

Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.


Pssm-ID: 99922 [Multi-domain]  Cd Length: 99  Bit Score: 125.18  E-value: 1.53e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825 2035 DLALCSMILTEMETH--EDSWPFLLPVNLKLVPGYKKVIKKPMDFSTIREKLNNGQYPNFETFALDVRLVFDNCETFNED 2112
Cdd:cd04369      1 LKKKLRSLLDALKKLkrDLSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYNGP 80
                           90
                   ....*....|....*....
gi 1720399825 2113 DSDIGRAGHSMRKYFEKKW 2131
Cdd:cd04369     81 GSPIYKDAKKLEKLFEKLL 99
PHD_BAZ2B cd15630
PHD finger found in bromodomain adjacent to zinc finger domain protein 2B (BAZ2B); BAZ2B, also ...
1902-1950 4.29e-32

PHD finger found in bromodomain adjacent to zinc finger domain protein 2B (BAZ2B); BAZ2B, also termed WALp4, is a bromodomain-containing protein whose biological role is still elusive. It shows high sequence similarly with BAZ2A, which is the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP-and histone H4 tail-dependent fashion. BAZ2B contains a TAM (TIP5/ARBP/MBD) domain, an Apolipophorin-III like domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277100  Cd Length: 49  Bit Score: 119.31  E-value: 4.29e-32
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1720399825 1902 VYCQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIPDGDWFCPACIS 1950
Cdd:cd15630      1 VYCQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIPEGDWFCPACIA 49
Bromo_gcn5_like cd05509
Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates ...
2037-2130 4.15e-31

Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99941 [Multi-domain]  Cd Length: 101  Bit Score: 118.43  E-value: 4.15e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825 2037 ALCSMILTEMETHEDSWPFLLPVNLKLVPGYKKVIKKPMDFSTIREKLNNGQYPNFETFALDVRLVFDNCETFNEDDSDI 2116
Cdd:cd05509      4 TQLKKVLDSLKNHKSAWPFLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPDTEY 83
                           90
                   ....*....|....
gi 1720399825 2117 GRAGHSMRKYFEKK 2130
Cdd:cd05509     84 YKCANKLEKFFWKK 97
PHD_BAZ2A_like cd15545
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) and 2B ...
1903-1948 7.25e-31

PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) and 2B (BAZ2B); BAZ2A, also termed transcription termination factor I-interacting protein 5 (TTF-I-interacting protein 5, or Tip5), or WALp3, is an epigenetic regulator. It has been implicated in epigenetic rRNA gene silencing, as the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP- and histone H4 tail-dependent fashion. BAZ2A has also been shown to be broadly overexpressed in prostate cancer, to regulate numerous protein-coding genes and to cooperate with EZH2 (enhancer of zeste homolog 2) to maintain epigenetic silencing at genes repressed in prostate cancer metastasis. Its overexpression is tightly associated with a prostate cancer subtype displaying CpG island methylator phenotype (CIMP) in tumors and with prostate cancer recurrence in patients. BAZ2B, also termed WALp4, is a bromodomain-containing protein whose biological role is still elusive. It shows high sequence similarly with BAZ2A. Both BAZ2A and BAZ2B contain a TAM (TIP5/ARBP/MBD) domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain. BAZ2B also harbors an extra Apolipophorin-III like domain in its N-terminal region.


Pssm-ID: 277020 [Multi-domain]  Cd Length: 46  Bit Score: 115.87  E-value: 7.25e-31
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1720399825 1903 YCQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIPDGDWFCPAC 1948
Cdd:cd15545      1 SCQICRSGDNEDQLLLCDGCDRGYHTYCFKPKMTNVPEGDWFCPEC 46
Bromo_Acf1_like cd05504
Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was ...
2036-2130 3.17e-30

Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was identified as a novel human bromodomain gene by cDNA library screening. The Drosophila homologue, Acf1, is part of the CHRAC (chromatin accessibility complex) and regulates ISWI-induced nucleosome remodeling. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99936  Cd Length: 115  Bit Score: 116.34  E-value: 3.17e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825 2036 LALCSMILTEMETHEDSWPFLLPVNLKLVPGYKKVIKKPMDFSTIREKLNNGQYPNFETFALDVRLVFDNCETFNEDDSD 2115
Cdd:cd05504     14 LSALEQLLVEIVKHKDSWPFLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNPEHTS 93
                           90
                   ....*....|....*
gi 1720399825 2116 IGRAGHSMRKYFEKK 2130
Cdd:cd05504     94 VYKAGTRLQRFFIKR 108
Bromo_tif1_like cd05502
Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of ...
2034-2130 4.91e-28

Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of the tripartite motif (TRIM) protein family, which is characterized by a particular domain architecture. It functions by recruiting coactivators and/or corepressors to modulate transcription. Vertebrate Tif1-gamma, also labeled E3 ubiquitin-protein ligase TRIM33, plays a role in the control of hematopoiesis. Its homologue in Xenopus laevis, Ectodermin, has been shown to function in germ-layer specification and control of cell growth during embryogenesis. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99934 [Multi-domain]  Cd Length: 109  Bit Score: 110.07  E-value: 4.91e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825 2034 RDLALCSMILTEMETHEDSWPFLLPVNlKLVPGYKKVIKKPMDFSTIREKL---NNGQYPNFETFALDVRLVFDNCETFN 2110
Cdd:cd05502      4 IDQRKCERLLLELYCHELSLPFHEPVS-PSVPNYYKIIKTPMDLSLIRKKLqpkSPQHYSSPEEFVADVRLMFKNCYKFN 82
                           90       100
                   ....*....|....*....|
gi 1720399825 2111 EDDSDIGRAGHSMRKYFEKK 2130
Cdd:cd05502     83 EEDSEVAQAGKELELFFEEQ 102
PHD_BAZ2A cd15629
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A); BAZ2A, also ...
1904-1949 1.27e-27

PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A); BAZ2A, also termed transcription termination factor I-interacting protein 5 (TTF-I-interacting protein 5, or Tip5), or WALp3, is an epigenetic regulator. It has been implicated in epigenetic rRNA gene silencing, as the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP- and histone H4 tail-dependent fashion. BAZ2A has also been shown to be broadly overexpressed in prostate cancer, to regulate numerous protein-coding genes and to cooperate with EZH2 (enhancer of zeste homolog 2) to maintain epigenetic silencing at genes repressed in prostate cancer metastasis. Its overexpression is tightly associated with a prostate cancer subtype displaying CpG island methylator phenotype (CIMP) in tumors and with prostate cancer recurrence in patients. It contains a TAM (TIP5/ARBP/MBD) domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277099  Cd Length: 47  Bit Score: 106.86  E-value: 1.27e-27
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1720399825 1904 CQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIPDGDWFCPACI 1949
Cdd:cd15629      2 CLVCRKGDNDEYLLLCDGCDRGCHMYCHRPKMLQVPEGDWFCPNCV 47
Bromo_Brdt_II_like cd05498
Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET ...
2036-2131 1.82e-27

Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99930  Cd Length: 102  Bit Score: 108.13  E-value: 1.82e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825 2036 LALCSMILTEM--ETHED-SWPFLLPVN---LKLvPGYKKVIKKPMDFSTIREKLNNGQYPNFETFALDVRLVFDNCETF 2109
Cdd:cd05498      2 LKFCSGILKELfsKKHKAyAWPFYKPVDpeaLGL-HDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKY 80
                           90       100
                   ....*....|....*....|..
gi 1720399825 2110 NEDDSDIGRAGHSMRKYFEKKW 2131
Cdd:cd05498     81 NPPDHPVHAMARKLQDVFEDRW 102
Bromo_BDF1_2_II cd05499
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast ...
2035-2131 5.12e-26

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99931  Cd Length: 102  Bit Score: 103.90  E-value: 5.12e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825 2035 DLALCSMILTEM---ETHEDSWPFLLPVN--LKLVPGYKKVIKKPMDFSTIREKLNNGQYPNFETFALDVRLVFDNCETF 2109
Cdd:cd05499      1 ELKFCEEVLKELmkpKHSAYNWPFLDPVDpvALNIPNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTF 80
                           90       100
                   ....*....|....*....|..
gi 1720399825 2110 NEDDSDIGRAGHSMRKYFEKKW 2131
Cdd:cd05499     81 NPEGTDVYMMGHQLEEVFNDKW 102
HAT_MBD cd01397
Methyl-CpG binding domains (MBD) present in putative chromatin remodelling factor such as ...
758-827 1.97e-25

Methyl-CpG binding domains (MBD) present in putative chromatin remodelling factor such as BAZ2A; BAZ2A contains a MBD, DDT, PHD-type zinc finger and Bromo domain suggesting that BAZ2A might be associated with histone acetyltransferase (HAT) activity. The Drosophila melanogaster toutatis protein, a putative subunit of the chromatin-remodeling complex, and other such proteins in this group share a similar domain architecture with BAZ2A, as does the Caenorhabditis elegans flectin homolog.


Pssm-ID: 238691 [Multi-domain]  Cd Length: 73  Bit Score: 101.33  E-value: 1.97e-25
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1720399825  758 ELRIPLDYGWQRETRVRNFGGRLPGEVAYYAPCGKKLRQCPDMVKGMQW---CLLKEEDVIPRIRAMDGRRGR 827
Cdd:cd01397      1 ELRVPLELGWRRETRIRGLGGRIQGEVAYYAPCGKKLRQYPEVIKYLSKngiSLLSRENFSFSARAPVGDFYE 73
Bromo_plant1 cd05506
Bromodomain, uncharacterized subfamily specific to plants. Might function as a global ...
2039-2131 9.69e-24

Bromodomain, uncharacterized subfamily specific to plants. Might function as a global transcription factor. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99938  Cd Length: 99  Bit Score: 97.40  E-value: 9.69e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825 2039 CSMILTEMETHEDSWPFLLPVNLKL--VPGYKKVIKKPMDFSTIREKLNNGQYPNFETFALDVRLVFDNCETFNEDDSDI 2116
Cdd:cd05506      5 CGTLLRKLMKHKWGWVFNAPVDVVAlgLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPPGNDV 84
                           90
                   ....*....|....*
gi 1720399825 2117 GRAGHSMRKYFEKKW 2131
Cdd:cd05506     85 HTMAKELLKIFETRW 99
Bromo_TFIID cd05511
Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, ...
2038-2130 2.79e-22

Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, a large multi-domain complex, which initiates the assembly of the transcription machinery. TAFII250 contains two bromodomains that specifically bind to acetylated histone H4. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99943 [Multi-domain]  Cd Length: 112  Bit Score: 93.87  E-value: 2.79e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825 2038 LCSM---ILTEMETHEDSWPFLLPVNLKLVPGYKKVIKKPMDFSTIREKLNNGQYPNFETFALDVRLVFDNCETFNEDDS 2114
Cdd:cd05511      1 LSFIldeIVNELKNLPDSWPFHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNGPDS 80
                           90
                   ....*....|....*.
gi 1720399825 2115 DIGRAGHSMRKYFEKK 2130
Cdd:cd05511     81 VYTKKAKEMLELAEEL 96
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
2039-2121 4.80e-22

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 91.99  E-value: 4.80e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825 2039 CSMILTEMETHEDSWPFLLPVNLKLVPGYKKVIKKPMDFSTIREKLNNGQYPNFETFALDVRLVFDNCETFNEDDSDIGR 2118
Cdd:pfam00439    1 CLEILDKLMEHPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYK 80

                   ...
gi 1720399825 2119 AGH 2121
Cdd:pfam00439   81 AAE 83
Bromo_BDF1_2_I cd05500
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast ...
2051-2130 4.99e-22

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99932  Cd Length: 103  Bit Score: 92.76  E-value: 4.99e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825 2051 DSWPFLLPVN-LKL-VPGYKKVIKKPMDFSTIREKLNNGQYPNFETFALDVRLVFDNCETFNEDDSDIGRAGHSMRKYFE 2128
Cdd:cd05500     21 DARPFLVPVDpVKLnIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLTFNGPEHPVSQMGKRLQAAFE 100

                   ..
gi 1720399825 2129 KK 2130
Cdd:cd05500    101 KH 102
PHD_BAZ1A cd15627
PHD finger found in bromodomain adjacent to zinc finger domain protein 1A (BAZ1A); BAZ1A, also ...
1904-1948 3.06e-21

PHD finger found in bromodomain adjacent to zinc finger domain protein 1A (BAZ1A); BAZ1A, also termed ATP-dependent chromatin-remodeling protein, or ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), or CHRAC subunit ACF1, or Williams syndrome transcription factor-related chromatin-remodeling factor 180 (WCRF180), or WALp1, is a subunit of the conserved imitation switch (ISWI)-family ATP-dependent chromatin assembly and remodeling factor (ACF)/chromatin accessibility complex (CHRAC) chromatin remodeling complex, which is required for DNA replication through heterochromatin. It alters the remodeling properties of the ATPase motor protein sucrose nonfermenting-2 homolog (SNF2H). Moreover, BAZ1A and its complexes play important roles in DNA double-strand break (DSB) repair. It is essential for averting improper gene expression during spermatogenesis. It also regulates transcriptional repression of vitamin D3 receptor-regulated genes. BAZ1A contains a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277097 [Multi-domain]  Cd Length: 46  Bit Score: 88.60  E-value: 3.06e-21
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1720399825 1904 CQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIPDGDWFCPAC 1948
Cdd:cd15627      2 CRICRRKGDAEKMLLCDGCDRGHHMYCLRPPLKKVPEGDWFCPDC 46
PHD_RSF1 cd15543
PHD finger found in Remodeling and spacing factor 1 (Rsf-1); Rsf-1, also termed HBV ...
1903-1948 1.06e-20

PHD finger found in Remodeling and spacing factor 1 (Rsf-1); Rsf-1, also termed HBV pX-associated protein 8, or Hepatitis B virus X-associated protein alpha (HBxAPalpha), or p325 subunit of RSF chromatin-remodeling complex, is a novel nuclear protein with histone chaperon function. It is a subunit of an ISWI chromatin remodeling complex, remodeling and spacing factor (RSF), and plays a role in mediating ATPase-dependent chromatin remodeling and conferring tumor aggressiveness in common carcinomas. As an ataxia-telangiectasia mutated (ATM)-dependent chromatin remodeler, Rsf-1 facilitates DNA damage checkpoints and homologous recombination repair. It regulates the mitotic spindle checkpoint and chromosome instability through the association with serine/threonine kinase BubR1 (BubR1) and Hepatitis B virus (HBV) X protein (HBx) in the chromatin fraction during mitosis. It also interacts with cyclin E1 and promotes tumor development. Rsf-1 contains a plant homeodomain (PHD) finger.


Pssm-ID: 277018 [Multi-domain]  Cd Length: 46  Bit Score: 86.94  E-value: 1.06e-20
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1720399825 1903 YCQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIPDGDWFCPAC 1948
Cdd:cd15543      1 PCRKCGLSDHPEWILLCDRCDAGYHTACLRPPLMIIPDGNWFCPPC 46
PHD_BAZ1A_like cd15544
PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, ...
1904-1948 1.64e-19

PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, also termed ATP-dependent chromatin-remodeling protein, or ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), or CHRAC subunit ACF1, or Williams syndrome transcription factor-related chromatin-remodeling factor 180 (WCRF180), or WALp1, is a subunit of the conserved imitation switch (ISWI)-family ATP-dependent chromatin assembly and remodeling factor (ACF)/chromatin accessibility complex (CHRAC) chromatin remodeling complex, which is required for DNA replication through heterochromatin. It alters the remodeling properties of the ATPase motor protein sucrose nonfermenting-2 homolog (SNF2H). Moreover, BAZ1A and its complexes play important roles in DNA double-strand break (DSB) repair. It is essential for averting improper gene expression during spermatogenesis. It also regulates transcriptional repression of vitamin D3 receptor-regulated genes. BAZ1B, also termed Tyrosine-protein kinase BAZ1B, or Williams syndrome transcription factor (WSTF), or Williams-Beuren syndrome chromosomal region 10 protein, Williams-Beuren syndrome chromosomal region 9 protein, or WALp2, is a multifunctional protein implicated in several nuclear processes, including replication, transcription, and the DNA damage response. BAZ1B/WSTF, together with the imitation switch (ISWI) ATPase, forms a WSTF-ISWI chromatin remodeling complex (WICH), which transiently associates with the human inactive X chromosome (Xi) during late S-phase prior to BRCA1 and gamma-H2AX. Moreover, BAZ1B/WSTF, SNF2h, and nuclear myosin 1 (NM1) forms the chromatin remodeling complex B-WICH that is involved in regulating rDNA transcription. Both BAZ1A and BAZ1B contain a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277019  Cd Length: 46  Bit Score: 83.61  E-value: 1.64e-19
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1720399825 1904 CQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIPDGDWFCPAC 1948
Cdd:cd15544      2 CKVCRKKGDPDNMILCDGCDKAFHLYCLRPALREVPSGDWFCPAC 46
PHD1_Lid2p_like cd15519
PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar ...
1904-1948 5.08e-19

PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar proteins; Lid2p is a trimethyl H3K4 (H3K4me3) demethylase responsible for H3K4 hypomethylation in heterochromatin. It interacts with the histone lysine-9 methyltransferase, Clr4, through the Dos1/Clr8-Rik1 complex, and mediates H3K9 methylation and small RNA production. It also acts cooperatively with the histone modification enzymes Set1 and Lsd1 and plays an essential role in cross-talk between H3K4 and H3K9 methylation in euchromatin. Lid2p contains a JmjC domain, three PHD fingers and a JmjN domain. This model corresponds to the first PHD finger.


Pssm-ID: 276994 [Multi-domain]  Cd Length: 46  Bit Score: 82.13  E-value: 5.08e-19
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1720399825 1904 CQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIPDGDWFCPAC 1948
Cdd:cd15519      2 CEVCGLDDNEGEVLLCDGCDAEYHTSCLDPPLGEIPPGTWFCPSC 46
PHD1_KDM5A_like cd15515
PHD finger 1 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and similar ...
1904-1948 7.96e-19

PHD finger 1 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and similar proteins; The JARID subfamily within the JmjC proteins includes Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and a Drosophila homolog, protein little imaginal discs (Lid). KDM5A was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5B has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. Both KDM5A and KDM5B function as trimethylated histone H3 lysine 4 (H3K4me3) demethylases. KDM5C is a H3K4 trimethyl-histone demethylase that catalyzes demethylation of H3K4me3 and H3K4me2 to H3K4me1. It plays a role in neuronal survival and dendrite development. KDM5C defects are associated with X-linked mental retardation (XLMR). KDM5D is a male-specific antigen that shows a demethylase activity specific for di- and tri-methylated histone H3K4 (H3K4me2 and H3K4me3), and has a male-specific function as a histone H3K4 demethylase by recruiting a meiosis-regulatory protein, MSH5, to condensed DNA. KDM5D directly interacts with a polycomb-like protein Ring6a/MBLR, and plays a role in regulation of transcriptional initiation through H3K4 demethylation. This family also includes Drosophila melanogaster protein little imaginal discs (Lid) that functions as a JmjC-dependent H3K4me3 demethylase, which is required for dMyc-induced cell growth. It positively regulates Hox gene expression in S2 cells. Members in this family contain the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as two or three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 276990  Cd Length: 46  Bit Score: 81.67  E-value: 7.96e-19
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1720399825 1904 CQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIPDGDWFCPAC 1948
Cdd:cd15515      2 CQVCGRGDDEDKLLLCDGCDDSYHTFCLIPPLPDIPPGDWRCPKC 46
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
1903-1951 8.29e-18

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 78.69  E-value: 8.29e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1720399825 1903 YCQICRKGDNEELLLLCDGCDKGCHTYCHRPKITT--IPDGDWFCPACISK 1951
Cdd:pfam00628    1 YCAVCGKSDDGGELVQCDGCDDWFHLACLGPPLDPaeIPSGEWLCPECKPK 51
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
1955-2130 1.24e-17

Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription];


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 87.17  E-value: 1.24e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825 1955 QSIKIKKIHVKGKKTNDSKKTKKGNVAGDTEDEDSASTSSSLKRGSKElkKRKMEETTSLNLSKAESTTSIKKPKKDESR 2034
Cdd:COG5076     62 TSIVDDREPGSMANVNDDLENVGGITYSPFEKNRPESLRFDEIVFLAI--ESVTPESGLGSLLMAHLKTSVKKRKTPKIE 139
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825 2035 DLAL---CSMILTEMET------HEDSWPFLLPVNLKLVPGYKKVIKKPMDFSTIREKLNNGQYPNFETFALDVRLVFDN 2105
Cdd:COG5076    140 DELLyadNKAIAKFKKQlflrdgRFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDN 219
                          170       180
                   ....*....|....*....|....*
gi 1720399825 2106 CETFNEDDSDIGRAGHSMRKYFEKK 2130
Cdd:COG5076    220 CKLYNGPDSSVYVDAKELEKYFLKL 244
Bromo_SPT7_like cd05510
Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the ...
2039-2125 1.54e-17

Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA, and SLIK. SAGA is involved in the RNA polymerase II-dependent transcriptional regulation of about 10% of all yeast genes. The SPT7 bromodomain has been shown to weakly interact with acetylated histone H3, but not H4. The human representative of this subfamily is cat eye syndrome critical region protein 2 (CECR2). Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99942 [Multi-domain]  Cd Length: 112  Bit Score: 80.18  E-value: 1.54e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825 2039 CSMILTEMETH-EDSWPFLLPVNLKLVPGYKKVIKKPMDFSTIREKLNNGQYPNFETFALDVRLVFDNCETFNEDDSDIG 2117
Cdd:cd05510     12 LDKVLNELKTYtEHSTPFLTKVSKREAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCLLYNSDPSHPL 91

                   ....*....
gi 1720399825 2118 RA-GHSMRK 2125
Cdd:cd05510     92 RRhANFMKK 100
Bromo_brd1_like cd05512
Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein ...
2055-2124 2.34e-16

Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein assumed to be a transcriptional regulator. BRD1 has been implicated with brain development and susceptibility to schizophrenia and bipolar affective disorder. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99944  Cd Length: 98  Bit Score: 76.28  E-value: 2.34e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825 2055 FLLPVNLKLVPGYKKVIKKPMDFSTIREKLNNGQYPNFETFALDVRLVFDNCETFNEDDSDIGRAGHSMR 2124
Cdd:cd05512     22 FSEPVDLSEVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYNAKDTIFYRAAVRLR 91
TPH pfam13868
Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of ...
877-1028 2.79e-16

Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain.


Pssm-ID: 464007 [Multi-domain]  Cd Length: 341  Bit Score: 82.66  E-value: 2.79e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  877 QAAQIKLLRKLQKQEQARVAKEAKKQQAIMAAEEKRKQKEQMKIIKQQEKIKRIQQIRMEKELRAQqiLEEKELRRQQAV 956
Cdd:pfam13868   16 LAAKCNKERDAQIAEKKRIKAEEKEEERRLDEMMEEERERALEEEEEKEEERKEERKRYRQELEEQ--IEEREQKRQEEY 93
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  957 LLKHQE------------LERHRLDMERERRRQHVM--LMKAMEARKKAEEKERLKQEKRDEKRLNKERKLEQRRLELEM 1022
Cdd:pfam13868   94 EEKLQEreqmdeiveriqEEDQAEAEEKLEKQRQLReeIDEFNEEQAEWKELEKEEEREEDERILEYLKEKAEREEEREA 173

                   ....*.
gi 1720399825 1023 AKELKK 1028
Cdd:pfam13868  174 EREEIE 179
Bromo_WSTF_like cd05505
Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The ...
2035-2116 2.82e-16

Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The Williams-Beuren syndrome deletion transcript 9 is a putative transcriptional regulator. WSTF was found to play a role in vitamin D-mediated transcription as part of two chromatin remodeling complexes, WINAC and WICH. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99937  Cd Length: 97  Bit Score: 76.04  E-value: 2.82e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825 2035 DLALCSMILTEMETHEDSWPFLLPVNLKLVPGYKKVIKKPMDFSTIREKLNNGQYPNFETFALDVRLVFDNCETFNEDDS 2114
Cdd:cd05505      1 ELQKCEEILSKILKYRFSWPFREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYENGS 80

                   ..
gi 1720399825 2115 DI 2116
Cdd:cd05505     81 YV 82
TPH pfam13868
Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of ...
835-1028 3.92e-16

Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain.


Pssm-ID: 464007 [Multi-domain]  Cd Length: 341  Bit Score: 82.27  E-value: 3.92e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  835 RAREESRMKRRKgrppnvgsaefldntdaKLLRKLQAQ-EIARQAAQIKLLRKLQKQEQ----ARVAKEAKKQQAIMAAE 909
Cdd:pfam13868  109 RIQEEDQAEAEE-----------------KLEKQRQLReEIDEFNEEQAEWKELEKEEEreedERILEYLKEKAEREEER 171
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  910 E-------KRKQKEQMKIIKQQEKI------------KRIQQIRMEKELRAQQILEEKELRRQQAV---LLKHQELERHR 967
Cdd:pfam13868  172 EaereeieEEKEREIARLRAQQEKAqdekaerdelraKLYQEEQERKERQKEREEAEKKARQRQELqqaREEQIELKERR 251
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1720399825  968 LDMERERRRQhvMLMKAMEARKKAEEKERLKQEKRDEKRL------------NKERKLEQRRLELEMAKELKK 1028
Cdd:pfam13868  252 LAEEAEREEE--EFERMLRKQAEDEEIEQEEAEKRRMKRLehrrelekqieeREEQRAAEREEELEEGERLRE 322
PHD1_Lid_like cd15605
PHD finger 1 found in Drosophila melanogaster protein little imaginal discs (Lid) and similar ...
1904-1948 5.25e-16

PHD finger 1 found in Drosophila melanogaster protein little imaginal discs (Lid) and similar proteins; Drosophila melanogaster Lid, also termed Retinoblastoma-binding protein 2 homolog, is identified genetically as a trithorax group (trxG) protein that is a Drosophila homolog of the human protein JARID1A/kdm5A, a member of the JARID subfamily within the JmjC proteins. Lid functions as a JmjC-dependent trimethyl histone H3K4 (H3K4me3) demethylase, which is required for dMyc-induced cell growth. It positively regulates Hox gene expression in S2 cells. Lid contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger of Lid.


Pssm-ID: 277078  Cd Length: 46  Bit Score: 73.64  E-value: 5.25e-16
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1720399825 1904 CQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIPDGDWFCPAC 1948
Cdd:cd15605      2 CHTCGRGDGEESMLLCDGCDDSYHTFCLLPPLSEVPKGDWRCPKC 46
PHD_PHRF1 cd15536
PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1); PHRF1, also ...
1903-1948 6.48e-16

PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1); PHRF1, also termed KIAA1542, or CTD-binding SR-like protein rA9, is a ubiquitin ligase that induces the ubiquitination of TGIF (TG-interacting factor) at lysine 130. It acts as a tumor suppressor that promotes the transforming growth factor (TGF)-beta cytostatic program through selective release of TGIF-driven promyelocytic leukemia protein (PML) inactivation. PHRF1 contains a plant homeodomain (PHD) finger and a RING finger.


Pssm-ID: 277011  Cd Length: 46  Bit Score: 73.22  E-value: 6.48e-16
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1720399825 1903 YCQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIPDGDWFCPAC 1948
Cdd:cd15536      1 YCEVCGRSDREDRLLLCDGCDAGYHMECLTPPLDEVPIEEWFCPEC 46
PHD_BAZ1B cd15628
PHD finger found in bromodomain adjacent to zinc finger domain protein 1B (BAZ1B); BAZ1B, also ...
1904-1948 7.53e-16

PHD finger found in bromodomain adjacent to zinc finger domain protein 1B (BAZ1B); BAZ1B, also termed Tyrosine-protein kinase BAZ1B, or Williams syndrome transcription factor (WSTF), or Williams-Beuren syndrome chromosomal region 10 protein, Williams-Beuren syndrome chromosomal region 9 protein, or WALp2, is a multifunctional protein implicated in several nuclear processes, including replication, transcription, and the DNA damage response. BAZ1B/WSTF, together with the imitation switch (ISWI) ATPase, forms a WSTF-ISWI chromatin remodeling complex (WICH), which transiently associates with the human inactive X chromosome (Xi) during late S-phase prior to BRCA1 and gamma-H2AX. Moreover, BAZ1B/WSTF, SNF2h, and nuclear myosin 1 (NM1) forms the chromatin remodeling complex B-WICH that is involved in regulating rDNA transcription. BAZ1B contains a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277098  Cd Length: 46  Bit Score: 73.24  E-value: 7.53e-16
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1720399825 1904 CQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIPDGDWFCPAC 1948
Cdd:cd15628      2 CKVCRKKGEDDKLILCDECNQAFHLFCLRPALYEVPDGEWMCPAC 46
DUF5401 pfam17380
Family of unknown function (DUF5401); This is a family of unknown function found in ...
835-1024 1.42e-15

Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.


Pssm-ID: 375164 [Multi-domain]  Cd Length: 722  Bit Score: 82.86  E-value: 1.42e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  835 RAREESRMKRRKGRPPNVGSAEFLDNTDAKLLRKLQAQEIARQAAQIKLLRKLQ---KQEQARVAKEAKKQQAIMAAEEK 911
Cdd:pfam17380  376 RMRELERLQMERQQKNERVRQELEAARKVKILEEERQRKIQQQKVEMEQIRAEQeeaRQREVRRLEEERAREMERVRLEE 455
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  912 RKQKEQMKIIKQQEKIKRIQQIRMEKELRAQQILEekELRRQqavLLKHQELERHRLDMERERRRQhvMLMKAMEARKKA 991
Cdd:pfam17380  456 QERQQQVERLRQQEEERKRKKLELEKEKRDRKRAE--EQRRK---ILEKELEERKQAMIEEERKRK--LLEKEMEERQKA 528
                          170       180       190
                   ....*....|....*....|....*....|...
gi 1720399825  992 EEKERLKQEKRDEKRLNKERKlEQRRLELEMAK 1024
Cdd:pfam17380  529 IYEEERRREAEEERRKQQEME-ERRRIQEQMRK 560
Bromo_Brdt_I_like cd05497
Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET ...
2049-2130 1.85e-15

Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99929  Cd Length: 107  Bit Score: 74.00  E-value: 1.85e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825 2049 HEDSWPFLLPVN-LKL-VPGYKKVIKKPMDFSTIREKLNNGQYPNFETFALDVRLVFDNCETFNEDDSDIGRAGHSMRKY 2126
Cdd:cd05497     20 HKFAWPFQQPVDaVKLnLPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYNKPGDDVVLMAQTLEKL 99

                   ....
gi 1720399825 2127 FEKK 2130
Cdd:cd05497    100 FLQK 103
PHD1_KDM5A cd15602
PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone ...
1904-1951 4.80e-15

PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone demethylase JARID1A, Jumonji/ARID domain-containing protein 1A, or Retinoblastoma-binding protein 2 (RBBP-2 or RBP2)) was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5A functions as a trimethylated histone H3 lysine 4 (H3K4me3) demethylase that belongs to the JARID subfamily within the JmjC proteins. It also displays DNA-binding activities that can recognize the specific DNA sequence CCGCCC. KDM5A contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277075  Cd Length: 49  Bit Score: 71.13  E-value: 4.80e-15
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1720399825 1904 CQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIPDGDWFCPACISK 1951
Cdd:cd15602      2 CLFCGRGNNEDKLLLCDGCDDSYHTFCLIPPLPDVPKGDWRCPKCVAE 49
Bromo_cbp_like cd05495
Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase ...
2050-2128 8.39e-15

Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase acting on histone, which gives a specific tag for transcriptional activation and also acetylates non-histone proteins. CREBBP binds specifically to phosphorylated CREB protein and augments the activity of phosphorylated CREB to activate transcription of cAMP-responsive genes. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99927  Cd Length: 108  Bit Score: 72.09  E-value: 8.39e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825 2050 EDSWPFLLPVNLKL--VPGYKKVIKKPMDFSTIREKLNNGQYPNFETFALDVRLVFDNCETFNEDDSDIGRAGHSMRKYF 2127
Cdd:cd05495     20 PESLPFRQPVDPKLlgIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNAWLYNRKTSRVYKYCTKLAEVF 99

                   .
gi 1720399825 2128 E 2128
Cdd:cd05495    100 E 100
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
1903-1948 1.17e-14

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 69.93  E-value: 1.17e-14
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 1720399825  1903 YCQICRKGDNEELLLLCDGCDKGCHTYCHRPKITT-IPDGDWFCPAC 1948
Cdd:smart00249    1 YCSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEeEPDGKWYCPKC 47
DUF5401 pfam17380
Family of unknown function (DUF5401); This is a family of unknown function found in ...
866-1022 1.34e-14

Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.


Pssm-ID: 375164 [Multi-domain]  Cd Length: 722  Bit Score: 79.78  E-value: 1.34e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  866 LRKLQAQEIARQAAQIKLLRKLQ-----KQEQARVAKEAKKQQAIMAAEEKRKQKEQM----KIIKQQEKIKRIQQIRME 936
Cdd:pfam17380  362 LERIRQEEIAMEISRMRELERLQmerqqKNERVRQELEAARKVKILEEERQRKIQQQKvemeQIRAEQEEARQREVRRLE 441
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  937 KElRAQQI--LEEKELRRQQavllkhqELERHRLDmERERRRQHVMLMKAMEARKKAEEKER--LKQEKRDEKRLNKERK 1012
Cdd:pfam17380  442 EE-RAREMerVRLEEQERQQ-------QVERLRQQ-EEERKRKKLELEKEKRDRKRAEEQRRkiLEKELEERKQAMIEEE 512
                          170
                   ....*....|
gi 1720399825 1013 LEQRRLELEM 1022
Cdd:pfam17380  513 RKRKLLEKEM 522
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
2034-2118 1.91e-14

Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. The structure(2DKW) in this alignment is an uncharacterized protein predicted from analysis of cDNA clones from human fetal liver


Pssm-ID: 99957  Cd Length: 112  Bit Score: 71.23  E-value: 1.91e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825 2034 RDLALC-SMILTEMETHEDSWPFLLPVNLKLVPGYKKVIKKPMDFSTIREKLNNGQYPNFETFALDVRLVFDNCETFNED 2112
Cdd:cd05528      2 RELRLFlRDVLKRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNPD 81

                   ....*.
gi 1720399825 2113 DSDIGR 2118
Cdd:cd05528     82 RDPADK 87
PHD1_KDM5C_5D cd15604
PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D); The family ...
1904-1948 1.94e-14

PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D); The family includes KDM5C and KDM5D, both of which belong to the JARID subfamily within the JmjC proteins. KDM5C (also termed Histone demethylase JARID1C, Jumonji/ARID domain-containing protein 1C, SmcX, or Xe169) is a H3K4 trimethyl-histone demethylase that catalyzes demethylation of H3K4me3 and H3K4me2 to H3K4me1. It plays a role in neuronal survival and dendrite development. KDM5C defects are associated with X-linked mental retardation (XLMR). KDM5D (also termed Histocompatibility Y antigen (H-Y), Histone demethylase JARID1D, Jumonji/ARID domain-containing protein 1D, or SmcY) is a male-specific antigen that shows a demethylase activity specific for di- and tri-methylated histone H3K4 (H3K4me3 andH3K4me2), and has a male-specific function as a histone H3K4 demethylase by recruiting a meiosis-regulatory protein, MSH5, to condensed DNA. KDM5D directly interacts with a polycomb-like protein Ring6a/MBLR, and plays a role in regulation of transcriptional initiation through H3K4 demethylation. Both KDM5C and KDM5D contain the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as two plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277077  Cd Length: 46  Bit Score: 69.10  E-value: 1.94e-14
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1720399825 1904 CQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIPDGDWFCPAC 1948
Cdd:cd15604      2 CRMCSRGDEDDKLLLCDGCDDNYHTFCLLPPLPEPPKGIWRCPKC 46
TPH pfam13868
Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of ...
862-1033 2.19e-14

Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain.


Pssm-ID: 464007 [Multi-domain]  Cd Length: 341  Bit Score: 76.88  E-value: 2.19e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  862 DAKLLRKLQAQEIARQAAQIK--LLRKLQKQEQARVAKEAKKQQAIMAAEEKRKQKEQMKIIKQQEK------IKRIQQI 933
Cdd:pfam13868   30 EKKRIKAEEKEEERRLDEMMEeeRERALEEEEEKEEERKEERKRYRQELEEQIEEREQKRQEEYEEKlqereqMDEIVER 109
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  934 RMEKELRAQQILEEKELRRQQAVLLKHQELERHRldmERERRRQHVMLMKAMEARKKAEEKERLKQEKRDEKRLNKERKL 1013
Cdd:pfam13868  110 IQEEDQAEAEEKLEKQRQLREEIDEFNEEQAEWK---ELEKEEEREEDERILEYLKEKAEREEEREAEREEIEEEKEREI 186
                          170       180
                   ....*....|....*....|
gi 1720399825 1014 EQRRLELEMAKELKKPKEDM 1033
Cdd:pfam13868  187 ARLRAQQEKAQDEKAERDEL 206
Bromo_WDR9_II cd05496
Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
2039-2110 2.87e-14

Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99928  Cd Length: 119  Bit Score: 70.95  E-value: 2.87e-14
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1720399825 2039 CSMILTEMETHEDSWPFLLPVNLKLVPGYKKVIKKPMDFSTIREKLNNGQYPNFETFALDVRLVFDNCETFN 2110
Cdd:cd05496     10 CKELVNLMWDCEDSEPFRQPVDLLKYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSKSYT 81
DDT smart00571
domain in different transcription and chromosome remodeling factors;
1055-1118 3.02e-14

domain in different transcription and chromosome remodeling factors;


Pssm-ID: 214726  Cd Length: 63  Bit Score: 69.20  E-value: 3.02e-14
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1720399825  1055 TTFSDCLMVVQFLRNFGKVLGFDVNIDVpnLSVLQEGLLNIgDSMGEVQDLLVRLLSAAVCDPG 1118
Cdd:smart00571    2 EAFGDLLMVYEFLRSFGKVLGLSPFRAT--LEDFIAALKCR-DQNGLLTEVHVVLLRAILKDEG 62
TPH pfam13868
Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of ...
862-1028 3.10e-14

Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain.


Pssm-ID: 464007 [Multi-domain]  Cd Length: 341  Bit Score: 76.50  E-value: 3.10e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  862 DAKLLRKLQAQEIARQAAQIKLLRKLQKQEQARVAKE---AKKQQAIMAAEEKRKQKEQM-KIIKQQEKIK--RIQQIRM 935
Cdd:pfam13868  168 EEEREAEREEIEEEKEREIARLRAQQEKAQDEKAERDelrAKLYQEEQERKERQKEREEAeKKARQRQELQqaREEQIEL 247
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  936 EKELRAQQILEEKELRrqQAVLLKHQELERhRLDMERERRRQ--------------HVMLMKAMEARKKAEEKERLKQEK 1001
Cdd:pfam13868  248 KERRLAEEAEREEEEF--ERMLRKQAEDEE-IEQEEAEKRRMkrlehrrelekqieEREEQRAAEREEELEEGERLREEE 324
                          170       180
                   ....*....|....*....|....*..
gi 1720399825 1002 RDekrlnkerklEQRRLELEMAKELKK 1028
Cdd:pfam13868  325 AE----------RRERIEEERQKKLKE 341
PHD2_KAT6A_6B cd15527
PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, ...
1904-1948 3.63e-14

PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, also termed histone acetyltransferase KAT6A, YBF2/SAS3, SAS2 and TIP60 protein 3 (MYST-3), or runt-related transcription factor-binding protein 2, or zinc finger protein 220, is a MYST-type histone acetyltransferase (HAT) that functions as a coactivator for acute myeloid leukemia 1 protein (AML1)- and p53-dependent transcription. It possesses intrinsic HAT activity to acetylate both itself and lysine (K) residues on histone H2B, histone H3 (K14) and histone H4 (K5, K8, K12 and K16) in vitro and H3K9 in vivo. MOZ-related factor (MORF), also termed MOZ2, or histone acetyltransferase KAT6B, or MOZ, YBF2/SAS3, SAS2 and TIP60 protein 4 (MYST4), is a ubiquitously expressed transcriptional regulator with intrinsic HAT activity. It can interact with the Runt-domain transcription factor Runx2 and form a tetrameric complex with BRPFs, ING5, and EAF6. Both MOZ and MORF are catalytic subunits of HAT complexes that are required for normal developmental programs, such as hematopoiesis, neurogenesis, and skeletogenesis, and are also implicated in human leukemias. MOZ is also the catalytic subunit of a tetrameric inhibitor of growth 5 (ING5) complex, which specifically acetylates nucleosomal histone H3K14. Moreover, MOZ and MORF are involved in regulating transcriptional activation mediated by Runx2 (or Cbfa1), a Runt-domain transcription factor known to play important roles in T cell lymphomagenesis and bone development, and its homologs. MOZ contains a linker histone 1 and histone 5 domains and two plant homeodomain (PHD) fingers. In contrast, MORF contains an N-terminal region containing two PHD fingers, a putative HAT domain, an acidic region, and a C-terminal Ser/Met-rich domain. The family corresponds to the first PHD finger.


Pssm-ID: 277002  Cd Length: 46  Bit Score: 68.17  E-value: 3.63e-14
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1720399825 1904 CQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIPDGDWFCPAC 1948
Cdd:cd15527      2 CSVCQDSGNADNLLFCDACDKGFHMECHDPPLTRMPKGKWVCQIC 46
TPH pfam13868
Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of ...
864-1039 3.92e-14

Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain.


Pssm-ID: 464007 [Multi-domain]  Cd Length: 341  Bit Score: 76.11  E-value: 3.92e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  864 KLLRKLQAQEIARQAAQI-KLLRKLQKQEQARVAKEAKKQQAIM-----AAEEKRKQKEQMKIiKQQEKIKRIQQIRMEK 937
Cdd:pfam13868   86 EQKRQEEYEEKLQEREQMdEIVERIQEEDQAEAEEKLEKQRQLReeideFNEEQAEWKELEKE-EEREEDERILEYLKEK 164
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  938 ELRAQQILEEKE------------LRRQQAVLLKHQ-ELERHRLD-MERERRRQHVMLMKaMEARKKAEEKERLKQEKRD 1003
Cdd:pfam13868  165 AEREEEREAEREeieeekereiarLRAQQEKAQDEKaERDELRAKlYQEEQERKERQKER-EEAEKKARQRQELQQAREE 243
                          170       180       190
                   ....*....|....*....|....*....|....*..
gi 1720399825 1004 EKRLNKERKLEQRRLELEMAKE-LKKPKEDMCLADQK 1039
Cdd:pfam13868  244 QIELKERRLAEEAEREEEEFERmLRKQAEDEEIEQEE 280
MBD cd00122
MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of ...
758-802 4.37e-14

MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1. The MBDs present in putative chromatin remodelling subunit, BAZ2A, and putative histone methyltransferase, CLLD8, represent two phylogenetically distinct groups within the MBD protein family.


Pssm-ID: 238069  Cd Length: 62  Bit Score: 68.50  E-value: 4.37e-14
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1720399825  758 ELRIPLDYGWQRETRVRNFGGRLPGEVAYYAPCGKKLRQCPDMVK 802
Cdd:cd00122      1 PLRDPLPPGWKRELVIRKSGSAGKGDVYYYSPCGKKLRSKPEVAR 45
PHD1_KDM5B cd15603
PHD finger 1 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis ...
1904-1948 6.92e-14

PHD finger 1 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis antigen 31 (CT31), Histone demethylase JARID1B, Jumonji/ARID domain-containing protein 1B (JARID1B), PLU-1, or retinoblastoma-binding protein 2 homolog 1 (RBP2-H1 or RBBP2H1A)) is a member of the JARID subfamily within the JmjC proteins. It has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of pregnant females and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. KDM5B acts as a histone demethylase that catalyzes the removal of trimethylation of lysine 4 on histone H3 (H3K4me3), induced by polychlorinated biphenyls (PCBs). It also mediates demethylation of H3K4me2 and H3K4me1. Moreover, KDM5B functions as a negative regulator of hematopoietic stem cell (HSC) self-renewal and progenitor cell activity. KDM5B has also been shown to interact with the DNA binding transcription factors BF-1 and PAX9, as well as TIEG1/KLF10 (transforming growth factor-beta inducible early gene-1/Kruppel-like transcription factor 10), and possibly function as a transcriptional corepressor. KDM5B contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277076  Cd Length: 46  Bit Score: 67.67  E-value: 6.92e-14
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1720399825 1904 CQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIPDGDWFCPAC 1948
Cdd:cd15603      2 CLVCGSGNDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 46
Bromo_brd7_like cd05513
Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown ...
2055-2114 1.43e-13

Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown to inhibit cell growth and the progression of the cell cycle by regulating cell-cycle genes at the transcriptional level. BRD7 has been identified as a gene involved in nasopharyngeal carcinoma. The protein interacts with acetylated histone H3 via its bromodomain. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99945  Cd Length: 98  Bit Score: 68.21  E-value: 1.43e-13
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825 2055 FLLPVNLKLVPGYKKVIKKPMDFSTIREKLNNGQYPNFETFALDVRLVFDNCETFNEDDS 2114
Cdd:cd05513     22 FAFPVTDFIAPGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYNKPDT 81
PTZ00121 PTZ00121
MAEBL; Provisional
863-1032 1.82e-13

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 76.72  E-value: 1.82e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  863 AKLLRKlqAQEIARQAAQIKLLRKLQKQEQARVAKEAKKQQAIMAAEEKRKQKEQMKI--IKQQEKIKRIQQIRMEKE-- 938
Cdd:PTZ00121  1499 ADEAKK--AAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAeeLKKAEEKKKAEEAKKAEEdk 1576
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  939 ---LRAQQILEEKELRRQQAVLLKHQELERHRLDmerERRRQHVMLMKAMEARKKAEEK---ERLKQEKRDEKRLNKERK 1012
Cdd:PTZ00121  1577 nmaLRKAEEAKKAEEARIEEVMKLYEEEKKMKAE---EAKKAEEAKIKAEELKKAEEEKkkvEQLKKKEAEEKKKAEELK 1653
                          170       180
                   ....*....|....*....|
gi 1720399825 1013 LEQRRLELEMAKELKKPKED 1032
Cdd:PTZ00121  1654 KAEEENKIKAAEEAKKAEED 1673
PTZ00121 PTZ00121
MAEBL; Provisional
868-1032 2.40e-13

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 76.33  E-value: 2.40e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  868 KLQAQEIARQAAQIKLLRKLQKQEQARVAKEAKKQQAIMAAEEKRKQKEQMKI--IKQQEKIKRIQQIRMEKELRAQQil 945
Cdd:PTZ00121  1496 KKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKAdeLKKAEELKKAEEKKKAEEAKKAE-- 1573
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  946 EEKELRRQQAVLLKHQELERHRLDM---ERERRRQHVMLMKAMEARKKAEEKERLKQEKRDEKRLNKERKLEQRRlelem 1022
Cdd:PTZ00121  1574 EDKNMALRKAEEAKKAEEARIEEVMklyEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKK----- 1648
                          170
                   ....*....|
gi 1720399825 1023 AKELKKPKED 1032
Cdd:PTZ00121  1649 AEELKKAEEE 1658
TPH pfam13868
Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of ...
864-1033 2.53e-13

Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain.


Pssm-ID: 464007 [Multi-domain]  Cd Length: 341  Bit Score: 73.41  E-value: 2.53e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  864 KLLRKLQAQEIARQAAQIKLLRKLQKQeqarvaKEAKKQQAIMAAEEKRKQKEQMK--IIKQQEKIKRIQQIRMEKELRA 941
Cdd:pfam13868   55 RALEEEEEKEEERKEERKRYRQELEEQ------IEEREQKRQEEYEEKLQEREQMDeiVERIQEEDQAEAEEKLEKQRQL 128
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  942 QQileekELRRQQAVLLKHQELERHRLDMERERRRQHVMLMKAMEARKKA------EEKERLKQEKRD--EKRLNKERKL 1013
Cdd:pfam13868  129 RE-----EIDEFNEEQAEWKELEKEEEREEDERILEYLKEKAEREEEREAereeieEEKEREIARLRAqqEKAQDEKAER 203
                          170       180
                   ....*....|....*....|....
gi 1720399825 1014 EQRRLELEM----AKELKKPKEDM 1033
Cdd:pfam13868  204 DELRAKLYQeeqeRKERQKEREEA 227
Bromo_polybromo_V cd05515
Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which ...
2044-2116 2.61e-13

Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99946  Cd Length: 105  Bit Score: 67.71  E-value: 2.61e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1720399825 2044 TEMETHEDSWPFL-LPvNLKLVPGYKKVIKKPMDFSTIREKLNNGQYPNFETFALDVRLVFDNCETFNEDDSDI 2116
Cdd:cd05515     16 TDGRGRRLSLIFMrLP-SKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACKYNEPDSQI 88
PTZ00121 PTZ00121
MAEBL; Provisional
832-1032 3.47e-13

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 75.56  E-value: 3.47e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  832 DRPRAREESRMKRRKGRPPNVGSAEFLDNTDAKLLRKLQAQEIARQAAQIKLLR--KLQKQEQARVAKEAK-KQQAIMAA 908
Cdd:PTZ00121  1549 DELKKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEeeKKMKAEEAKKAEEAKiKAEELKKA 1628
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  909 EEKRKQKEQMKiIKQQEKIKRIQQIRMEKE---LRAQQILEEKELRRQQAVLLKHQElerhrldmERERRRQHVMLMKAM 985
Cdd:PTZ00121  1629 EEEKKKVEQLK-KKEAEEKKKAEELKKAEEenkIKAAEEAKKAEEDKKKAEEAKKAE--------EDEKKAAEALKKEAE 1699
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*..
gi 1720399825  986 EARKKAEEKERLKQEKRDEKRLNKERklEQRRLELEMAKelKKPKED 1032
Cdd:PTZ00121  1700 EAKKAEELKKKEAEEKKKAEELKKAE--EENKIKAEEAK--KEAEED 1742
PHD2_KMT2C_like cd15510
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
1904-1948 3.53e-13

PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobilitygroup)-binding motif, and two FY-rich regions. This model corresponds to the second PHD finger.


Pssm-ID: 276985  Cd Length: 46  Bit Score: 65.53  E-value: 3.53e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1720399825 1904 CQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIPDGDWFCPAC 1948
Cdd:cd15510      2 CQACRQPGDDTKMLVCETCDKGYHTSCLRPVMSSIPKYGWKCKNC 46
PHD2_CHD_II cd15532
PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
1903-1948 3.59e-13

PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD proteins includes chromodomain-helicase-DNA-binding protein CHD3, CHD4, and CHD5, which are nuclear and ubiquitously expressed chromatin remodelling ATPases generally associated with histone deacetylases (HDACs). They are involved in DNA Double Strand Break (DSB) signaling, DSB repair and/or p53-dependent pathways such as apoptosis and senescence, as well as in the maintenance of genomic stability, and/or cancer prevention. They function as subunits of the Nucleosome Remodelling and Deacetylase (NuRD) complex, which is generally associated with gene repression, heterochromatin formation, and overall chromatin compaction. In contrast to the class I CHD enzymes (CHD1 and CHD2), class II CHD proteins lack identifiable DNA-binding domains, but possess a C-terminal coiled-coil region. Moreover, in addition to the tandem chromodomains and a helicase domain, they all harbor tandem plant homeodomain (PHD) zinc fingers involved in the recognition of methylated histone tails. This model corresponds to the second PHD finger.


Pssm-ID: 277007 [Multi-domain]  Cd Length: 43  Bit Score: 65.38  E-value: 3.59e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1720399825 1903 YCQICRKGDNeelLLLCDGCDKGCHTYCHRPKITTIPDGDWFCPAC 1948
Cdd:cd15532      1 FCRVCKDGGE---LLCCDGCPSSYHLHCLNPPLAEIPDGDWFCPRC 43
PTZ00121 PTZ00121
MAEBL; Provisional
833-1032 1.24e-12

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 74.02  E-value: 1.24e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  833 RPRAREESRMKRRKGRPPNVGSAEfldntDAKLLRKLQAQEIARQAAQIKLLRKLQKQEQARVAKEAKKQQAIMAAEEKR 912
Cdd:PTZ00121  1496 KKKADEAKKAAEAKKKADEAKKAE-----EAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAK 1570
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  913 KQKE-------QMKIIKQQEKiKRI---------------QQIRMEKE--LRAQQILEEKELRRQQAVLLKHQELERHRl 968
Cdd:PTZ00121  1571 KAEEdknmalrKAEEAKKAEE-ARIeevmklyeeekkmkaEEAKKAEEakIKAEELKKAEEEKKKVEQLKKKEAEEKKK- 1648
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1720399825  969 dMERERRRQHVMLMKAMEARKKAEEKERLKQE--KRDEKRLNKERKLEQRRLELEMAKELKKPKED 1032
Cdd:PTZ00121  1649 -AEELKKAEEENKIKAAEEAKKAEEDKKKAEEakKAEEDEKKAAEALKKEAEEAKKAEELKKKEAE 1713
ATAD3_N pfam12037
ATPase family AAA domain-containing protein 3, N-terminal; This is the conserved N-terminal ...
863-1025 1.51e-12

ATPase family AAA domain-containing protein 3, N-terminal; This is the conserved N-terminal domain of ATPase family AAA domain-containing protein 3 (ATAD3) which is involved in dimerization and interacts with the inner surface of the outer mitochondrial membrane. This domain is found associated with the AAA ATPase domain (pfam00004). ATAD3 is essential for mitochondrial network organization, mitochondrial metabolism and cell growth at organizm and cellular level. It may also play an important role in mitochondrial protein synthesis.


Pssm-ID: 463442 [Multi-domain]  Cd Length: 264  Bit Score: 70.01  E-value: 1.51e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  863 AKLLRKLQAQEIARQAAQiklLRKLQKQ----EQARVAKEAKKQQAIMAAEEKRKQ-KEQMKIIKQQEKIKRIQ------ 931
Cdd:pfam12037   32 AKAARELESSPHAKKALE---LMKKQEQtrqaELQAKIKEYEAAQEQLKIERQRVEyEERRKTLQEETKQKQQRaqyqde 108
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  932 --QIRMEKELRAQQILEEKELRRQQAVLLKHQEL---------ERHRLDMERERRRQHVMlmkamearkkAEEKERLKQE 1000
Cdd:pfam12037  109 laRKRYQDQLEAQRRRNEELLRKQEESVAKQEAMriqaqrrqtEEHEAELRRETERAKAE----------AEAEARAKEE 178
                          170       180
                   ....*....|....*....|....*
gi 1720399825 1001 krdekRLNKERKLEQRRLELEMAKE 1025
Cdd:pfam12037  179 -----RENEDLNLEQLREKANEERE 198
PHD2_KMT2D cd15595
PHD finger 2 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
1904-1948 2.26e-12

PHD finger 2 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such asHOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the second PHD finger.


Pssm-ID: 277070  Cd Length: 46  Bit Score: 63.09  E-value: 2.26e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1720399825 1904 CQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIPDGDWFCPAC 1948
Cdd:cd15595      2 CQTCRKPGEDSKMLVCEACDKGYHTFCLKPAMESLPTDSWKCKAC 46
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
1903-1948 2.54e-12

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


Pssm-ID: 276966 [Multi-domain]  Cd Length: 48  Bit Score: 63.10  E-value: 2.54e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1720399825 1903 YCQICRK-GDNEELLLLCDGCDKGCHTYCHRPKITT-IPDGDWFCPAC 1948
Cdd:cd15489      1 SCIVCGKgGDLGGELLQCDGCGKWFHADCLGPPLSSfVPNGKWICPVC 48
DUF4670 pfam15709
Domain of unknown function (DUF4670); This family of proteins is found in eukaryotes. Proteins ...
872-1043 2.89e-12

Domain of unknown function (DUF4670); This family of proteins is found in eukaryotes. Proteins in this family are typically between 373 and 763 amino acids in length.


Pssm-ID: 464815 [Multi-domain]  Cd Length: 522  Bit Score: 71.52  E-value: 2.89e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  872 QEIARQAAQIKLLRKLQKQEQAR-VAKEAKKQQAIMAAEEKRKQKEQMKIIkQQEKIKRIQQIRMEKELRAQQILEEKEL 950
Cdd:pfam15709  313 EERSEEDPSKALLEKREQEKASRdRLRAERAEMRRLEVERKRREQEEQRRL-QQEQLERAEKMREELELEQQRRFEEIRL 391
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  951 RRQQavllkhqeLERHRLDMERERRRQHVMLmkamearKKAEEKERLKQEKRDEKRLNKERKLEQRRLELEMAKELKKPK 1030
Cdd:pfam15709  392 RKQR--------LEEERQRQEEEERKQRLQL-------QAAQERARQQQEEFRRKLQELQRKKQQEEAERAEAEKQRQKE 456
                          170
                   ....*....|....
gi 1720399825 1031 EDMCLA-DQKPLPE 1043
Cdd:pfam15709  457 LEMQLAeEQKRLME 470
DUF5401 pfam17380
Family of unknown function (DUF5401); This is a family of unknown function found in ...
872-1032 5.39e-12

Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.


Pssm-ID: 375164 [Multi-domain]  Cd Length: 722  Bit Score: 71.31  E-value: 5.39e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  872 QEIARQAAQIKLLRKLQKQEQARVAkEAKKQQAIMAAEEK--RKQKEQMKIIKQQEKIKRIQQIRMEK---ELRAQQILE 946
Cdd:pfam17380  303 QEKEEKAREVERRRKLEEAEKARQA-EMDRQAAIYAEQERmaMERERELERIRQEERKRELERIRQEEiamEISRMRELE 381
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  947 EKELRRQQAVLLKHQELE--RHRLDMERERRRQHVMLMKAMEARKKAEEKERLKQEKRDEKRlnKERKLEQRRL-ELEMA 1023
Cdd:pfam17380  382 RLQMERQQKNERVRQELEaaRKVKILEEERQRKIQQQKVEMEQIRAEQEEARQREVRRLEEE--RAREMERVRLeEQERQ 459

                   ....*....
gi 1720399825 1024 KELKKPKED 1032
Cdd:pfam17380  460 QQVERLRQQ 468
PTZ00121 PTZ00121
MAEBL; Provisional
835-1038 6.06e-12

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 71.71  E-value: 6.06e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  835 RAREESRMKRRKGRPPNVGSAEflDNTDAKLLRKLQAQEIARQAAQIKLLRKLQ---KQEQARVAKEAKKQQAIMAAEEK 911
Cdd:PTZ00121  1110 KAEEARKAEEAKKKAEDARKAE--EARKAEDARKAEEARKAEDAKRVEIARKAEdarKAEEARKAEDAKKAEAARKAEEV 1187
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  912 RKQKEqmkiIKQQEKIKRIQQIR-MEKELRAQQILEEKELRRQQAVL----LKHQELERHRLDMER--ERRRQHVMLMKA 984
Cdd:PTZ00121  1188 RKAEE----LRKAEDARKAEAARkAEEERKAEEARKAEDAKKAEAVKkaeeAKKDAEEAKKAEEERnnEEIRKFEEARMA 1263
                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1720399825  985 MEARKKAEEKERLKQEKRDEKRLNKERKLEQRRL--ELEMAKELKKPKEDMCLADQ 1038
Cdd:PTZ00121  1264 HFARRQAAIKAEEARKADELKKAEEKKKADEAKKaeEKKKADEAKKKAEEAKKADE 1319
PHD2_KMT2C cd15594
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
1904-1948 6.17e-12

PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the second PHD finger.


Pssm-ID: 277069  Cd Length: 46  Bit Score: 61.88  E-value: 6.17e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1720399825 1904 CQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIPDGDWFCPAC 1948
Cdd:cd15594      2 CQTCRQPGDDNKMLVCDTCDKGYHTFCLQPVMTTIPKNGWKCKNC 46
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
866-1021 6.51e-12

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 71.12  E-value: 6.51e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  866 LRKLQAQEIARQAAQIKL-LRKLQKQEQARVAKEAKKQQAIMAAEEKRKQKEQMKIIKQQEKIKRIQQIRMEKELRAQQI 944
Cdd:COG1196    306 RLEERRRELEERLEELEEeLAELEEELEELEEELEELEEELEEAEEELEEAEAELAEAEEALLEAEAELAEAEEELEELA 385
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1720399825  945 LEEKELRRQQAVLLKHQELERHRLDMERERRRQHVMLMKAMEARKKAEEKERLKQEKRDEKRLNKERKLEQRRLELE 1021
Cdd:COG1196    386 EELLEALRAAAELAAQLEELEEAEEALLERLERLEEELEELEEALAELEEEEEEEEEALEEAAEEEAELEEEEEALL 462
PTZ00121 PTZ00121
MAEBL; Provisional
819-1031 7.48e-12

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 71.33  E-value: 7.48e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  819 RAMDGRRGRPP-NPDRPRAREESRMKRRKGRPPNVGSAEfldntDAKLLRKLQAQEIARQAAQIKLLRKLQKQEQARVAK 897
Cdd:PTZ00121  1147 KAEDAKRVEIArKAEDARKAEEARKAEDAKKAEAARKAE-----EVRKAEELRKAEDARKAEAARKAEEERKAEEARKAE 1221
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  898 EAKKQQAIMAAEEKRKQKEQMKI---IKQQEKIKRIQQIRMEKELRAQQILEEKELRRQQAVLLKHQELERHRLDMERER 974
Cdd:PTZ00121  1222 DAKKAEAVKKAEEAKKDAEEAKKaeeERNNEEIRKFEEARMAHFARRQAAIKAEEARKADELKKAEEKKKADEAKKAEEK 1301
                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1720399825  975 RRQHVMLMKAMEARKKAEEKERLKQEKRDEKRLNKERKLEQRRLELEMAKELKKPKE 1031
Cdd:PTZ00121  1302 KKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADE 1358
PHD_UHRF1_2 cd15525
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and ...
1904-1948 9.13e-12

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and UHRF2; UHRF1 is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumour suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of transcription factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF2 was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) by interacting with the HBV core protein and promoting its degradation. Both UHRF1 and UHRF2 contain an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger.


Pssm-ID: 277000  Cd Length: 47  Bit Score: 61.62  E-value: 9.13e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1720399825 1904 CQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIPDGD-WFCPAC 1948
Cdd:cd15525      2 CHVCGGKQDPEKQLLCDECDMAYHLYCLDPPLTSLPDDDeWYCPDC 47
Bromo_SP100C_like cd05501
Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major ...
2067-2135 9.60e-12

Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major component of PML-SP100 nuclear bodies (NBs), which are poorly understood. It is covalently modified by SUMO-1 and may play a role in processes at the chromatin level. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99933  Cd Length: 102  Bit Score: 63.22  E-value: 9.60e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1720399825 2067 YKKVIKKPMDFSTIREKLNNGQYPNFETFALDVRLVFDNCETFNEDDsDIGRAGHSMRKYFEKKWTDTF 2135
Cdd:cd05501     33 YCQGIKEPMWLNKVKERLNERVYHTVEGFVRDMRLIFHNHKLFYKDD-DFGQVGITLEKKFEKNFKEVF 100
PTZ00121 PTZ00121
MAEBL; Provisional
819-1031 1.48e-11

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 70.17  E-value: 1.48e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  819 RAMDGRRGRPPNPDRPRAREESRMKRRKGRPPNVGSAEFLDNTDAKLLRKLQAQEI-ARQAAQIKLLRKLQKQEQARVAK 897
Cdd:PTZ00121  1565 KAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIkAEELKKAEEEKKKVEQLKKKEAE 1644
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  898 EAKKqqaimaAEEKRKQKEQMKIIKQQEKIKRIQQIRMEKELR---------AQQILEEKELRRQQAVLLKHQELERHRl 968
Cdd:PTZ00121  1645 EKKK------AEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKkaeedekkaAEALKKEAEEAKKAEELKKKEAEEKKK- 1717
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1720399825  969 dMERERRRQHVMLMKAMEARKKAEEKERLKQE-KRDEKRLNKERKLeqRRLELEMAKELKKPKE 1031
Cdd:PTZ00121  1718 -AEELKKAEEENKIKAEEAKKEAEEDKKKAEEaKKDEEEKKKIAHL--KKEEEKKAEEIRKEKE 1778
PTZ00121 PTZ00121
MAEBL; Provisional
820-1038 2.10e-11

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 69.78  E-value: 2.10e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  820 AMDGRRGRPPNPDRPRAREESRMKRRKGRPPNVGSAE---FLDNTDAKLLRKLQAQEIARQAAQIK----LLRKlqKQEQ 892
Cdd:PTZ00121  1263 AHFARRQAAIKAEEARKADELKKAEEKKKADEAKKAEekkKADEAKKKAEEAKKADEAKKKAEEAKkkadAAKK--KAEE 1340
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  893 ARVAKEAKKQQAIMAAEEKRKQKEQMKI--IKQQEKIKRIQQIR--MEKELRAQQILEEKELRRQQAVLLKHQELERHRL 968
Cdd:PTZ00121  1341 AKKAAEAAKAEAEAAADEAEAAEEKAEAaeKKKEEAKKKADAAKkkAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKA 1420
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  969 DmerERRRQHVMLMKAMEARKKAEEKERLKQEKRDEKRLNKERKLEQRRLELEMAKELKKPKEDMCLADQ 1038
Cdd:PTZ00121  1421 D---EAKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAKKADE 1487
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
855-1025 2.28e-11

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 69.58  E-value: 2.28e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  855 AEFLDNTDAKLLRKLQAQEIARQAAQIKLLR------KLQKQEQARVAKEAKKQQAIMAAEEKRKQKEQMKIIKQQEKIK 928
Cdd:COG1196    248 LEELEAELEELEAELAELEAELEELRLELEEleleleEAQAEEYELLAELARLEQDIARLEERRRELEERLEELEEELAE 327
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  929 RIQQIRMEKELRAQQILEEKELRRQQAVLLKHQELERHRLDMERERRRQHVMLMKAMEARKKAEEKERLKQEKRDEKRLN 1008
Cdd:COG1196    328 LEEELEELEEELEELEEELEEAEEELEEAEAELAEAEEALLEAEAELAEAEEELEELAEELLEALRAAAELAAQLEELEE 407
                          170
                   ....*....|....*..
gi 1720399825 1009 KERKLEQRRLELEMAKE 1025
Cdd:COG1196    408 AEEALLERLERLEEELE 424
Bromo_WDR9_I_like cd05529
Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
2019-2118 2.29e-11

Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99958  Cd Length: 128  Bit Score: 63.12  E-value: 2.29e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825 2019 AESTTSIKKP-----KKDESRDLALCSMILTE----METHEDSW--PFLLPVNLKL-VPGYKKVIKKPMDFSTIREKLNN 2086
Cdd:cd05529      1 LYNPLSSEWElfdpgWEQPHIRDEERERLISGldklLLSLQLEIaeYFEYPVDLRAwYPDYWNRVPVPMDLETIRSRLEN 80
                           90       100       110
                   ....*....|....*....|....*....|..
gi 1720399825 2087 GQYPNFETFALDVRLVFDNCETFNEDDSDIGR 2118
Cdd:cd05529     81 RYYRSLEALRHDVRLILSNAETFNEPNSEIAK 112
PHD1_MTF2_PHF19_like cd15499
PHD finger 1 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) ...
1904-1949 2.34e-11

PHD finger 1 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) family proteins MTF2, PHF19, and similar proteins; The family includes two PCL family proteins, metal-response element-binding transcription factor 2 (MTF2/PCL2) and PHF19/PCL3, which are homologs of PHD finger protein1 (PHF1). PCL family proteins are accessory components of the polycomb repressive complex 2 (PRC2) core complex and all contain an N-terminal Tudor domain followed by two PHD fingers, and a C-terminal MTF2 domain. They specifically recognize tri-methylated H3K36 (H3K36me3) through their N-terminal Tudor domains. The interaction between their Tudor domains and H3K36me3 is critical for both the targeting and spreading of PRC2 into active chromatin regions and for the maintenance of optimal repression of poised developmental genes where PCL proteins, H3K36me3, and H3K27me3 coexist. Moreover, unlike other PHD finger-containing proteins, the first PHD fingers of PCL proteins do not display histone H3K4 binding affinity and they do not affect the Tudor domain binding to histones. This model corresponds to the first PHD finger.


Pssm-ID: 276974  Cd Length: 53  Bit Score: 60.59  E-value: 2.34e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1720399825 1904 CQICRKGDNEEL--LLLCDGCDKGCHTYCHRPKITTIP---DGDWFCPACI 1949
Cdd:cd15499      2 CSICGGAEARDGneILICDKCDKGYHQLCHSPKVRTSPlegDEKWFCSRCV 52
PTZ00121 PTZ00121
MAEBL; Provisional
835-1032 2.53e-11

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 69.40  E-value: 2.53e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  835 RAREESRMKRRKGRppnvgsAEFLDNTDAKLLRKLQAQEIaRQAAQIKL---LRKLQKQEQARVAKEAKK--QQAIMAAE 909
Cdd:PTZ00121  1613 KKAEEAKIKAEELK------KAEEEKKKVEQLKKKEAEEK-KKAEELKKaeeENKIKAAEEAKKAEEDKKkaEEAKKAEE 1685
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  910 EKRKQKEQMKiiKQQEKIKRIQQIRM---EKELRAQQILEEKELRRQQAVLLKHQElerhrldmERERRrqhvmlmKAME 986
Cdd:PTZ00121  1686 DEKKAAEALK--KEAEEAKKAEELKKkeaEEKKKAEELKKAEEENKIKAEEAKKEA--------EEDKK-------KAEE 1748
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*.
gi 1720399825  987 ARKKAEEKERLKQEKRDEkrlnkERKLEQRRLELEMAKELKKPKED 1032
Cdd:PTZ00121  1749 AKKDEEEKKKIAHLKKEE-----EKKAEEIRKEKEAVIEEELDEED 1789
Bromo_brd8_like cd05507
Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with ...
2042-2124 2.67e-11

Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with the thyroid hormone receptor in a ligand-dependent fashion and enhances thyroid hormone-dependent activation from thyroid response elements. Brd8 is thought to be a nuclear receptor coactivator. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99939  Cd Length: 104  Bit Score: 62.00  E-value: 2.67e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825 2042 ILTEMETHEDSWPFLLPVNLKLVPGYKKVIKKPMDFSTIREKLNNGQYPNFETFALDVRLVFDNCETFNEDDSDIGRAGH 2121
Cdd:cd05507     11 VYRTLASHRYASVFLKPVTEDIAPGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQRDVLLMFQNAIMYNSSDHDVYLMAV 90

                   ...
gi 1720399825 2122 SMR 2124
Cdd:cd05507     91 EMQ 93
PTZ00121 PTZ00121
MAEBL; Provisional
859-1038 3.99e-11

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 69.01  E-value: 3.99e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  859 DNTDAKLLRKLQAQEIARQAAQIKLLRKLQKQ-EQARVAKEAKKQqaimaAEEKRKQKEQMKiiKQQEKIKRIQQIR-ME 936
Cdd:PTZ00121  1434 DEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKaEEAKKADEAKKK-----AEEAKKADEAKK--KAEEAKKKADEAKkAA 1506
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  937 KELRAQQILEEKELRRQQAVLLKHQELERHRLDMERERRRQHVMLMKAMEARkKAEEKERLKQEKRDEKRLNKE------ 1010
Cdd:PTZ00121  1507 EAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEELK-KAEEKKKAEEAKKAEEDKNMAlrkaee 1585
                          170       180       190
                   ....*....|....*....|....*....|....*....
gi 1720399825 1011 -RKLEQRRLELEM----------AKELKKPKEDMCLADQ 1038
Cdd:PTZ00121  1586 aKKAEEARIEEVMklyeeekkmkAEEAKKAEEAKIKAEE 1624
PHD2_d4 cd15530
PHD finger 2 found in d4 gene family proteins; The family includes proteins coded by three ...
1903-1948 5.54e-11

PHD finger 2 found in d4 gene family proteins; The family includes proteins coded by three members of the d4 gene family, DPF1 (neuro-d4), DPF2 (ubi-d4/Requiem), and DPF3 (cer-d4), which function as transcription factors and are involved in transcriptional regulation of genes by changing the condensed/decondensed state of chromatin in the nucleus. DPF2 is ubiquitously expressed and it acts as a transcription factor that may participate in developmentally programmed cell death. DPF1 and DPF3 are expressed predominantly in neural tissues, and they may be involved in the transcription regulation of neuro-specific gene clusters. The d4 family proteins show distinct domain organization with domain 2/3 in the N-terminal region, a Cys2His2 (C2H2) zinc finger or Kruppel-type zinc finger in the central part and two adjacent plant homeodomain (PHD) fingers (d4-domain) in the C-terminal part of the molecule. This model corresponds to the second PHD finger.


Pssm-ID: 277005  Cd Length: 46  Bit Score: 59.32  E-value: 5.54e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1720399825 1903 YCQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIPDGDWFCPAC 1948
Cdd:cd15530      1 SCSLCGTSENDDQLLFCDDCDRGYHMYCLSPPMSEPPEGSWSCHLC 46
PHD1_AIRE cd15539
PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune ...
1903-1948 7.08e-11

PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune polyendocrinopathy candidiasis ectodermal dystrophy (APECED) protein, functions as a regulator of gene transcription in the thymus. It is essential for prevention of autoimmunity. AIRE plays a critical role in the induction of central tolerance. It promotes self-tolerance through tissue-specific antigen (TSA) expression. It also acts as an active regulator of chondrocyte differentiation. AIRE contains a homogeneously-staining region (HSR) or caspase-recruitment domain (CARD), a nuclear localization signal (NLS), a SAND (for Sp100, AIRE, nuclear phosphoprotein 41/75 or NucP41/75, and deformed epidermal auto regulatory factor 1 or Deaf1) domain, two plant homeodomain (PHD) fingers, and four LXXLL (where L stands for leucine) motifs. This model corresponds to the first PHD finger that recognizes the unmethylated tail of histone H3 and targets AIRE-dependent genes.


Pssm-ID: 277014 [Multi-domain]  Cd Length: 43  Bit Score: 59.00  E-value: 7.08e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1720399825 1903 YCQICRKGDNeelLLLCDGCDKGCHTYCHRPKITTIPDGDWFCPAC 1948
Cdd:cd15539      1 ECAVCGDGGE---LLCCDGCPRAFHLACLVPPLTLIPSGTWRCSSC 43
MBD pfam01429
Methyl-CpG binding domain; The Methyl-CpG binding domain (MBD) binds to DNA that contains one ...
753-802 7.97e-11

Methyl-CpG binding domain; The Methyl-CpG binding domain (MBD) binds to DNA that contains one or more symmetrically methylated CpGs. DNA methylation in animals is associated with alterations in chromatin structure and silencing of gene expression. MBD has negligible non-specific affinity for DNA. In vitro foot-printing with MeCP2 showed the MBD can protect a 12 nucleotide region surrounding a methyl CpG pair. MBDs are found in several Methyl-CpG binding proteins and also DNA demethylase.


Pssm-ID: 396147 [Multi-domain]  Cd Length: 76  Bit Score: 59.68  E-value: 7.97e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1720399825  753 VADDQELRIPLDYGWQRETRVRNFGG-RLPGEVAYYAPCGKKLRQCPDMVK 802
Cdd:pfam01429    1 IERKREDRLPLPPGWRREERQRKSGSkAGKVDVFYYSPTGKKLRSKSEVAR 51
PTZ00121 PTZ00121
MAEBL; Provisional
833-1038 8.08e-11

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 67.86  E-value: 8.08e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  833 RPRAREESRMKRRKGRPPNVGSAEFLDNTDAKLLRKLQAQEiARQAAQIKLLRKLQKQEQARVAKEAKK-QQAIMAAEEK 911
Cdd:PTZ00121  1236 KKDAEEAKKAEEERNNEEIRKFEEARMAHFARRQAAIKAEE-ARKADELKKAEEKKKADEAKKAEEKKKaDEAKKKAEEA 1314
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  912 RKQKEQMK-----------IIKQQEKIKRIQQIRMEKELRAQQILEEKElRRQQAVLLKHQElERHRLDMERERRRQhvm 980
Cdd:PTZ00121  1315 KKADEAKKkaeeakkkadaAKKKAEEAKKAAEAAKAEAEAAADEAEAAE-EKAEAAEKKKEE-AKKKADAAKKKAEE--- 1389
                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1720399825  981 LMKAMEARKKAEE-KERLKQEKRDEKRLNKERKLEQRRLELEMAKELKKPKEDMCLADQ 1038
Cdd:PTZ00121  1390 KKKADEAKKKAEEdKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADE 1448
YqiK COG2268
Uncharacterized membrane protein YqiK, contains Band7/PHB/SPFH domain [Function unknown];
851-1009 1.01e-10

Uncharacterized membrane protein YqiK, contains Band7/PHB/SPFH domain [Function unknown];


Pssm-ID: 441869 [Multi-domain]  Cd Length: 439  Bit Score: 66.43  E-value: 1.01e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  851 NVGSAEFLDNTDAKLLRKLQAQEIAR--QAAQIKLLRKLQKQEQARVAKEAKKQQAIMAAEEKRKQKEQMKIIKQQEKIK 928
Cdd:COG2268    202 RIAEAEAERETEIAIAQANREAEEAEleQEREIETARIAEAEAELAKKKAEERREAETARAEAEAAYEIAEANAEREVQR 281
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  929 RIQQIRMEKELRAQQILEEKELRRQQAVLLKHQELERHRLDmERERRRQHVMLMKAM-EA---RKKAEEKERLKQEKRDE 1004
Cdd:COG2268    282 QLEIAEREREIELQEKEAEREEAELEADVRKPAEAEKQAAE-AEAEAEAEAIRAKGLaEAegkRALAEAWNKLGDAAILL 360

                   ....*
gi 1720399825 1005 KRLNK 1009
Cdd:COG2268    361 MLIEK 365
DUF5401 pfam17380
Family of unknown function (DUF5401); This is a family of unknown function found in ...
867-1031 1.45e-10

Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.


Pssm-ID: 375164 [Multi-domain]  Cd Length: 722  Bit Score: 66.69  E-value: 1.45e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  867 RKLQAQEIARQAAqikllrkLQKQ-----EQARVAKEAKKQQAIMAAEEKRKQKEQmkiIKQQE---------KIKRIQQ 932
Cdd:pfam17380  316 RKLEEAEKARQAE-------MDRQaaiyaEQERMAMERERELERIRQEERKRELER---IRQEEiameisrmrELERLQM 385
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  933 IRMEKELRAQQILE--------EKElrRQQAVLLKHQELERHRLDMERERRRQhvmlMKAMEaRKKAEEKERLKQEKRDE 1004
Cdd:pfam17380  386 ERQQKNERVRQELEaarkvkilEEE--RQRKIQQQKVEMEQIRAEQEEARQRE----VRRLE-EERAREMERVRLEEQER 458
                          170       180       190
                   ....*....|....*....|....*....|.
gi 1720399825 1005 K----RLnKERKLEQRRLELEMAKELKKPKE 1031
Cdd:pfam17380  459 QqqveRL-RQQEEERKRKKLELEKEKRDRKR 488
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
862-1031 1.92e-10

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 66.50  E-value: 1.92e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  862 DAKLLRKLQAQEIARQAAQIKLlRKLQKQEQARVAKEAKKQQAIMAAEEKRKQKEQMKIIKQQEKIKRIQQIRMEKELRA 941
Cdd:COG1196    234 LRELEAELEELEAELEELEAEL-EELEAELAELEAELEELRLELEELELELEEAQAEEYELLAELARLEQDIARLEERRR 312
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  942 QQILEEKELRRQQAVLLKH-----QELERHRLDMERERRRQHVMLMKAMEARKKAEEKERLKQEKRDEKRLNKERKLEQR 1016
Cdd:COG1196    313 ELEERLEELEEELAELEEEleeleEELEELEEELEEAEEELEEAEAELAEAEEALLEAEAELAEAEEELEELAEELLEAL 392
                          170
                   ....*....|....*
gi 1720399825 1017 RLELEMAKELKKPKE 1031
Cdd:COG1196    393 RAAAELAAQLEELEE 407
Bromo_polybromo_IV cd05518
Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which ...
2062-2130 2.31e-10

Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99949 [Multi-domain]  Cd Length: 103  Bit Score: 59.38  E-value: 2.31e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1720399825 2062 KLVPGYKKVIKKPMDFSTIREKLNNGQYPNFETFALDVRLVFDNCETFNEDDSDIGRAGHSMRKYFEKK 2130
Cdd:cd05518     34 KDYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHYNEEGSQVYEDANILEKVLKEK 102
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
866-1025 2.41e-10

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 66.11  E-value: 2.41e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  866 LRKLQAQEIARQAAQIKLLRKLQKQEQARVAKEAKKQQAIMAAEEKRKQKEQMKIIKQQEKIKRIQQ---------IRME 936
Cdd:COG1196    222 LKELEAELLLLKLRELEAELEELEAELEELEAELEELEAELAELEAELEELRLELEELELELEEAQAeeyellaelARLE 301
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  937 KELRAQQILEEKELRRQQAVLLKHQELERHRLDMERERRRQHVMLMKAMEARKKAEEKERLKQEKRDE---KRLNKERKL 1013
Cdd:COG1196    302 QDIARLEERRRELEERLEELEEELAELEEELEELEEELEELEEELEEAEEELEEAEAELAEAEEALLEaeaELAEAEEEL 381
                          170
                   ....*....|..
gi 1720399825 1014 EQRRLELEMAKE 1025
Cdd:COG1196    382 EELAEELLEALR 393
Bromo_SNF2L2 cd05516
Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI ...
2054-2116 2.65e-10

Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone receptors to boost transcriptional activation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99947  Cd Length: 107  Bit Score: 59.36  E-value: 2.65e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1720399825 2054 PFL-LPVNlKLVPGYKKVIKKPMDFSTIREKLNNGQYPNFETFALDVRLVFDNCETFNEDDSDI 2116
Cdd:cd05516     27 VFIqLPSR-KELPEYYELIRKPVDFKKIKERIRNHKYRSLEDLEKDVMLLCQNAQTFNLEGSLI 89
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
858-1028 2.86e-10

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 65.73  E-value: 2.86e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  858 LDNTDAKLLRkLQA--QEIARQaaqiklLRKLQKQeqARVAKEAkkqqaimaaeekRKQKEQMKIIKQQEKIKRIQQIRM 935
Cdd:COG1196    181 LEATEENLER-LEDilGELERQ------LEPLERQ--AEKAERY------------RELKEELKELEAELLLLKLRELEA 239
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  936 EKELRAQQILEEKELRRQQAVLLKHQELERHRLDMERERRRQHVMLMKAmEARKKAEEKERLKQEKRDEKRLNKERKLEQ 1015
Cdd:COG1196    240 ELEELEAELEELEAELEELEAELAELEAELEELRLELEELELELEEAQA-EEYELLAELARLEQDIARLEERRRELEERL 318
                          170
                   ....*....|...
gi 1720399825 1016 RRLELEMAKELKK 1028
Cdd:COG1196    319 EELEEELAELEEE 331
PHD_UHRF1 cd15616
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1); ...
1904-1948 4.19e-10

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1); UHRF1 (also termed inverted CCAAT box-binding protein of 90 kDa, nuclear protein 95, nuclear zinc finger protein Np95 (Np95), RING finger protein 106, transcription factor ICBP90, or E3 ubiquitin-protein ligase UHRF1) is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumour suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of transcription factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF1 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET and RING finger associated (SRA) domain, and a C-terminal RING-finger domain. It specifically binds to hemimethylated DNA, double-stranded CpG dinucleotides, and recruits the maintenance methyltransferase DNMT1 to its hemimethylated DNA substrate through its SRA domain. UHRF1-dependent H3K23 ubiquitylation has an essential role in maintaining DNA methylation and replication. The tandem Tudor domain directs UHRF1 binding to the heterochromatin mark histone H3K9me3 and the PHD finger targets UHRF1 to unmodified histone H3 in euchromatic regions. The RING-finger domain exhibit both autocatalytic E3 ubiquitin (Ub) ligase activity and activity against histone H3 and DNMT1.


Pssm-ID: 277088  Cd Length: 47  Bit Score: 56.90  E-value: 4.19e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1720399825 1904 CQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIP-DGDWFCPAC 1948
Cdd:cd15616      2 CHVCGGKQDPDKQLMCDECDMAFHIYCLNPPLSSIPdDEDWYCPEC 47
PHD2_PHF10 cd15529
PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed ...
1904-1948 4.26e-10

PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed BRG1-associated factor 45a (BAF45a), or XAP135, is a ubiquitously expressed transcriptional regulator that is required for maintaining the undifferentiated status of neuroblasts. It contains a SAY (supporter of activation of yellow) domain and two adjacent plant homeodomain (PHD) fingers. This model corresponds to the second PHD finger.


Pssm-ID: 277004  Cd Length: 44  Bit Score: 56.55  E-value: 4.26e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1720399825 1904 CQICRKGDNEELLLLCDGCDKGCHTYChrPKITTIPDGDWFCPAC 1948
Cdd:cd15529      2 CTKCGDPHDEDKMMFCDQCDRGYHTFC--VGLRSIPDGRWICPLC 44
PHD5_KMT2C_like cd15513
PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in ...
1904-1949 4.49e-10

PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in KMT2D; KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the fifth PHD finger of KMT2C and the fourth PHD finger of KMT2D.


Pssm-ID: 276988  Cd Length: 47  Bit Score: 56.72  E-value: 4.49e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1720399825 1904 CQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIPDGDWFCPACI 1949
Cdd:cd15513      2 CEGCGKASDESRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWCV 47
PTZ00121 PTZ00121
MAEBL; Provisional
835-1032 4.97e-10

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 65.16  E-value: 4.97e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  835 RAREESRMKRRKGRPPNVGSAEFldntDAKllRKLQAQEIARQAaqIKLLRKLQKQEQARVAKEAKKQQAIMAAEEKRKQ 914
Cdd:PTZ00121  1059 KAEAKAHVGQDEGLKPSYKDFDF----DAK--EDNRADEATEEA--FGKAEEAKKTETGKAEEARKAEEAKKKAEDARKA 1130
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  915 KEqmkiIKQQEKIKRIQQIRMEKELRAQQILEEKELRRQQAVLLKHQELERHRLDMERERRRQHVMLMKAMEARK----- 989
Cdd:PTZ00121  1131 EE----ARKAEDARKAEEARKAEDAKRVEIARKAEDARKAEEARKAEDAKKAEAARKAEEVRKAEELRKAEDARKaeaar 1206
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*
gi 1720399825  990 KAEEKERLKQEKR--DEKRLNKERKLEQRRLELEMAKELKKPKED 1032
Cdd:PTZ00121  1207 KAEEERKAEEARKaeDAKKAEAVKKAEEAKKDAEEAKKAEEERNN 1251
Bromo_ASH1 cd05525
Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the ...
2042-2128 5.23e-10

Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the trithorax-group in Drosophila melanogaster, an epigenetic transcriptional regulator of HOX genes. Drosophila ASH1 has been shown to methylate specific lysines in histones H3 and H4. Mammalian ASH1 has been shown to methylate histone H3. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99955 [Multi-domain]  Cd Length: 106  Bit Score: 58.56  E-value: 5.23e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825 2042 ILTEMETHEDSW------PFL-LPVNLKlVPGYKKVIKKPMDFSTIREKLNNGQYPNFETFALDVRLVFDNCETFNEDDS 2114
Cdd:cd05525     10 ICDAIITYKDSNgqslaiPFInLPSKKK-NPDYYERITDPVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNAEKYYGRKS 88
                           90
                   ....*....|....
gi 1720399825 2115 DIGRAGHSMRKYFE 2128
Cdd:cd05525     89 PIGRDVCRLRKAYY 102
PTZ00121 PTZ00121
MAEBL; Provisional
868-1031 5.68e-10

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 65.16  E-value: 5.68e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  868 KLQAQEIARQAAQIKLLRKLQKQ-EQARVAKEAKKQqaimaAEEKRKQKEQMKIIKQQEKIKRIQQiRMEKELRAQQILE 946
Cdd:PTZ00121  1404 KKKADELKKAAAAKKKADEAKKKaEEKKKADEAKKK-----AEEAKKADEAKKKAEEAKKAEEAKK-KAEEAKKADEAKK 1477
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  947 EKELRRQQAVLLKHQELERHRLDmerERRRQHVMLMKAMEARKKAEEKERLKQEKRDEKRLNKE-RKLEQRRL--ELEMA 1023
Cdd:PTZ00121  1478 KAEEAKKADEAKKKAEEAKKKAD---EAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEaKKAEEKKKadELKKA 1554

                   ....*...
gi 1720399825 1024 KELKKPKE 1031
Cdd:PTZ00121  1555 EELKKAEE 1562
tolA_full TIGR02794
TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the ...
870-1025 6.77e-10

TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB. [Transport and binding proteins, Other, Cellular processes, Pathogenesis]


Pssm-ID: 274303 [Multi-domain]  Cd Length: 346  Bit Score: 62.94  E-value: 6.77e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  870 QAQEIARQAAQIKLLRKLQKQEQARVAKEAKKQQAimaaEEKRKQKEQMKIIKQQEKIKRIQQIRMEKELRAQQILEEKE 949
Cdd:TIGR02794   51 QANRIQQQKKPAAKKEQERQKKLEQQAEEAEKQRA----AEQARQKELEQRAAAEKAAKQAEQAAKQAEEKQKQAEEAKA 126
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1720399825  950 LRRQQAVLLKHQELERHRLDMERERRRQHVMLMKAMEARKKAEEKERLKQEKRDEKRLNKER-KLEQRRLELEMAKE 1025
Cdd:TIGR02794  127 KQAAEAKAKAEAEAERKAKEEAAKQAEEEAKAKAAAEAKKKAEEAKKKAEAEAKAKAEAEAKaKAEEAKAKAEAAKA 203
PTZ00121 PTZ00121
MAEBL; Provisional
833-1031 9.25e-10

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 64.39  E-value: 9.25e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  833 RPRAREESRMKRRKGRPPNVGSAEFLDNTDAKLLRKLQAQEIARQAAQIKLLRKLQKQEQARVAKEAKKQQAIMAAEEKR 912
Cdd:PTZ00121  1073 KPSYKDFDFDAKEDNRADEATEEAFGKAEEAKKTETGKAEEARKAEEAKKKAEDARKAEEARKAEDARKAEEARKAEDAK 1152
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  913 K--------QKEQMKIIKQQEKIKRIQQIRMEKELR-AQQILEEKELRRQQAVlLKHQELERHRLDMERERRRQHVMLMK 983
Cdd:PTZ00121  1153 RveiarkaeDARKAEEARKAEDAKKAEAARKAEEVRkAEELRKAEDARKAEAA-RKAEEERKAEEARKAEDAKKAEAVKK 1231
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1720399825  984 AMEARKKAEEKERLKQEKRDEK-------------RLNKERKLEQRRL--ELEMAKELKKPKE 1031
Cdd:PTZ00121  1232 AEEAKKDAEEAKKAEEERNNEEirkfeearmahfaRRQAAIKAEEARKadELKKAEEKKKADE 1294
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
866-1031 9.74e-10

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 64.19  E-value: 9.74e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  866 LRKLQAQEIARQAAQIKLLRKLQKQEQARVAKEAKKQQAimAAEEKRKQKEQMKIIKQQEKIK-RIQQIRMEKELRAQQI 944
Cdd:COG1196    276 LEELELELEEAQAEEYELLAELARLEQDIARLEERRREL--EERLEELEEELAELEEELEELEeELEELEEELEEAEEEL 353
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  945 LEEKELRRQQAVLLKHQELERHRLDMERERRRQHVMLMKAMEARKKAEEKERLKQEKRDEKRLNkERKLEQRRLELEMAK 1024
Cdd:COG1196    354 EEAEAELAEAEEALLEAEAELAEAEEELEELAEELLEALRAAAELAAQLEELEEAEEALLERLE-RLEEELEELEEALAE 432

                   ....*..
gi 1720399825 1025 ELKKPKE 1031
Cdd:COG1196    433 LEEEEEE 439
PHD_BRPF_JADE_like cd15492
PHD finger found in BRPF proteins, Jade proteins, protein AF-10, AF-17, and similar proteins; ...
1904-1948 1.46e-09

PHD finger found in BRPF proteins, Jade proteins, protein AF-10, AF-17, and similar proteins; The family includes BRPF proteins, Jade proteins, protein AF-10 and AF-17. BRPF proteins are scaffold proteins that form monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complexes with other regulatory subunits, such as inhibitor of growth 5 (ING5) and Esa1-associated factor 6 ortholog (EAF6). BRPF proteins have multiple domains, including a canonical Cys4HisCys3 plant homeodomain (PHD) zinc finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. PHD and ePHD fingers both bind to lysine 4 of histone H3 (K4H3), bromodomains interact with acetylated lysines on N-terminal tails of histones and other proteins, and PWWP domains show histone-binding and chromatin association properties. Jade proteins are required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and EAF6, to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. AF-10, also termed ALL1 (acute lymphoblastic leukemia)-fused gene from chromosome 10 protein, is a transcription factor that has been implicated in the development of leukemia following chromosomal rearrangements between the AF10 gene and one of at least two other genes, MLL and CALM. AF-17, also termed ALL1-fused gene from chromosome 17 protein, is a putative transcription factor that may play a role in multiple signaling pathways. All Jade proteins, AF-10, and AF-17 contain a canonical PHD finger followed by a non-canonical ePHD finger. This model corresponds to the canonical PHD finger.


Pssm-ID: 276967 [Multi-domain]  Cd Length: 46  Bit Score: 55.32  E-value: 1.46e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1720399825 1904 CQICRKGDNEE--LLLLCDGCDKGCHTYCHrpKITTIPDGDWFCPAC 1948
Cdd:cd15492      2 CDVCLDGESEDdnEIVFCDGCNVAVHQSCY--GIPLIPEGDWFCRKC 46
PHD_Phf1p_Phf2p_like cd15502
PHD finger found in Schizosaccharomyces pombe SWM histone demethylase complex subunits Phf1 ...
1904-1948 2.20e-09

PHD finger found in Schizosaccharomyces pombe SWM histone demethylase complex subunits Phf1 (Phf1p) and Phf2 (Phf2p); Phf1p and Phf2p are components of the SWM histone demethylase complex that specifically demethylates histone H3 at lysine 9 (H3K9me2), a specific tag for epigenetic transcriptional activation. They function as corepressors and play roles in regulating heterochromatin propagation and euchromatic transcription. Both Phf1p and Phf2p contain a plant homeodomain (PHD) finger.


Pssm-ID: 276977  Cd Length: 52  Bit Score: 55.13  E-value: 2.20e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1720399825 1904 CQICRKGDNEE--LLLLCDGCDKGCHTYCHRPKITT----IPDGDWFCPAC 1948
Cdd:cd15502      2 CIVCQRGHSPKsnRIVFCDGCNTPYHQLCHDPSIDDevveDPDAEWFCKKC 52
Bromo_polybromo_III cd05520
Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which ...
2054-2130 2.42e-09

Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99951  Cd Length: 103  Bit Score: 56.58  E-value: 2.42e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1720399825 2054 PFL-LPVNlKLVPGYKKVIKKPMDFSTIREKLNNGQYPNFETFALDVRLVFDNCETFNEDDSDIGRAGHSMRKYFEKK 2130
Cdd:cd05520     26 PFLkLPSK-RKYPDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNVPNSRIYKDAEKLQKLMQAK 102
PTZ00121 PTZ00121
MAEBL; Provisional
835-1031 2.43e-09

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 63.24  E-value: 2.43e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  835 RAREESRMKRRKGRPPNVGSAEFLDNTDA---KLLRKLQAQEIARQAAQIKllrklQKQEQARVAKEAKKQ--QAIMAAE 909
Cdd:PTZ00121  1354 AAADEAEAAEEKAEAAEKKKEEAKKKADAakkKAEEKKKADEAKKKAEEDK-----KKADELKKAAAAKKKadEAKKKAE 1428
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  910 EKRKQKEQMKiiKQQEKIKRIQQIRMEKELRAQQILEEKELRRQQAVLLKHQELERHRLDMERERRRQhvMLMKAMEARK 989
Cdd:PTZ00121  1429 EKKKADEAKK--KAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEE--AKKKADEAKK 1504
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*.
gi 1720399825  990 KAEEKERLKQEKRDE--KRLNKERKLEQRRL--ELEMAKELKKPKE 1031
Cdd:PTZ00121  1505 AAEAKKKADEAKKAEeaKKADEAKKAEEAKKadEAKKAEEKKKADE 1550
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
867-1054 2.79e-09

Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 62.48  E-value: 2.79e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  867 RKLQAQEIARQAAQIKLLRKLQKQEQARVAKEAKKQQAIMAAEEKRKQKEQM-----KIIKQQEKIKRIQQIRME---KE 938
Cdd:COG4717     66 PELNLKELKELEEELKEAEEKEEEYAELQEELEELEEELEELEAELEELREElekleKLLQLLPLYQELEALEAElaeLP 145
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  939 LRAQQILEEKELRRQQAVLLKHQELERHRLDMERERRRQHVMLMKAMEARKKAEEKERLKQEKRdekRLNKERKLEQRRL 1018
Cdd:COG4717    146 ERLEELEERLEELRELEEELEELEAELAELQEELEELLEQLSLATEEELQDLAEELEELQQRLA---ELEEELEEAQEEL 222
                          170       180       190
                   ....*....|....*....|....*....|....*.
gi 1720399825 1019 ElEMAKELKKPKEDMCLADQKPLPEWPRIPGLVLSG 1054
Cdd:COG4717    223 E-ELEEELEQLENELEAAALEERLKEARLLLLIAAA 257
MBD smart00391
Methyl-CpG binding domain; Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, ...
758-802 3.93e-09

Methyl-CpG binding domain; Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, MeCP1) domain


Pssm-ID: 128673  Cd Length: 77  Bit Score: 55.07  E-value: 3.93e-09
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*.
gi 1720399825   758 ELRIPLDYGWQRETRVRNFG-GRLPGEVAYYAPCGKKLRQCPDMVK 802
Cdd:smart00391    3 PLRLPLPCGWRRETKQRKSGrSAGKFDVYYISPCGKKLRSKSELAR 48
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
868-1027 4.35e-09

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 61.88  E-value: 4.35e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  868 KLQAQEIARQAAQIKLLRKLQKQEQARVAKEAKKQQAIMAAEEKRKQKEQMKIIKQQEKIKRIQQIRMEKELRAQQILEE 947
Cdd:COG1196    252 EAELEELEAELAELEAELEELRLELEELELELEEAQAEEYELLAELARLEQDIARLEERRRELEERLEELEEELAELEEE 331
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  948 KELRRQQAVLLKHQELERHRLDMERERRRQHVmLMKAMEARKKAEEKERLKQEKRDEKRLNKERKLEQRRLELEMAKELK 1027
Cdd:COG1196    332 LEELEEELEELEEELEEAEEELEEAEAELAEA-EEALLEAEAELAEAEEELEELAEELLEALRAAAELAAQLEELEEAEE 410
PHD_UHRF2 cd15617
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); ...
1904-1948 7.29e-09

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); UHRF2 (also termed Np95/ICBP90-like RING finger protein (NIRF), Np95-like RING finger protein, nuclear protein 97, nuclear zinc finger protein Np97, RING finger protein 107, or E3 ubiquitin-protein ligase UHRF2) was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs,p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) by interacting with the HBV core protein and promoting its degradation. UHRF2 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger.


Pssm-ID: 277089  Cd Length: 47  Bit Score: 53.42  E-value: 7.29e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1720399825 1904 CQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIP-DGDWFCPAC 1948
Cdd:cd15617      2 CYVCGGKQDAHMQLLCDECNMAYHIYCLNPPLDKIPeDEDWYCPSC 47
PHD_TIF1_like cd15541
PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar ...
1903-1948 8.26e-09

PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar proteins; The TIF1 family of transcriptional cofactors includes TIF1alpha (TRIM24), TIF1beta (TRIM28), TIF1gamma (TRIM33), and TIF1delta (TRIM66), which are characterized by an N-terminal RING-finger B-box coiled-coil (RBCC/TRIM) motif and plant homeodomain (PHD) finger followed by a bromodomain in the C-terminal region. TIF1 proteins couple chromatin modifications to transcriptional regulation, signaling, and tumor suppression. They exert a deacetylase-dependent silencing effect when tethered to a promoter region. TIF1alpha, TIF1beta, and TIF1delta can homodimerize and contain a PXVXL motif necessary and sufficient for heterochromatin protein 1(HP1) binding. TIF1alpha and TIF1beta bind nuclear receptors and Kruppel-associated boxes (KRAB) specifically and respectively. In contrast, TIF1delta appears to lack nuclear receptor- and KRAB-binding activity. Moreover, TIF1delta is specifically involved in heterochromatin-mediated gene silencing during postmeiotic phases of spermatogenesis. TIF1gamma is structurally closely related to TIF1alpha and TIF1beta, but has very little functional features in common with them. It does not interact with the KRAB silencing domain of KOX1 or the heterochromatinic proteins HP1alpha, beta, and gamma. It cannot bind to nuclear receptors (NRs). This family also includes Sp100/Sp140 family proteins, the nuclear body SP100 and SP140. Sp110 is a leukocyte-specific component of the nuclear body. It may function as a nuclear hormone receptor transcriptional coactivator that may play a role in inducing differentiation of myeloid cells. It is also involved in resisting intracellular pathogens and functions as an important drug target for preventing intracellular pathogen diseases, such as tuberculosis, hepatic veno-occlusive disease, and intracellular cancers. SP140 is an interferon inducible nuclear leukocyte-specific protein involved in primary biliary cirrhosis and a risk factor in chronic lymphocytic leukemia. It is also implicated in innate immune response to human immunodeficiency virus type 1 (HIV-1) by binding to the virus viral infectivity factor (Vif) protein. Both Sp110 and Sp140 contain a SAND domain, a plant homeodomain (PHD) finger, and a bromodomain (BRD).


Pssm-ID: 277016 [Multi-domain]  Cd Length: 43  Bit Score: 53.12  E-value: 8.26e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1720399825 1903 YCQICRKGDNeelLLLCDGCDKGCHTYCHRPKITTIPDGDWFCPAC 1948
Cdd:cd15541      1 WCAVCQNGGE---LLCCDKCPRVFHLDCHIPPIPEFPSGEWSCSLC 43
DDT pfam02791
DDT domain; The DDT domain is named after (DNA binding homeobox and Different Transcription ...
1056-1116 1.21e-08

DDT domain; The DDT domain is named after (DNA binding homeobox and Different Transcription factors) and is approximately 60 residues in length. Along with the WHIM motifs, it comprises an entirely alpha helical module found in diverse eukaryotic chromatin proteins. Based on the structure of Ioc3, this module is inferred to interact with nucleosomal linker DNA and the SLIDE domain of ISWI proteins. The resulting complex forms a protein ruler that measures out the spacing between two adjacent nucleosomes. In particular, the DDT domain, in combination with the WHIM1 and WHIM2 motifs form the SLIDE domain binding pocket.


Pssm-ID: 460696  Cd Length: 58  Bit Score: 52.89  E-value: 1.21e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1720399825 1056 TFSDCLMVVQFLRNFGKVLGfdvnIDVPNLSVLQEGLLNIGDSMGEVQDLLVRLLSAAVCD 1116
Cdd:pfam02791    2 AFGDLLMVWEFLNSFGEVLG----LSPFTLDDFEEALLCTEEPSELLDEIHCALLKALVRD 58
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
2026-2130 1.55e-08

Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription];


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 59.05  E-value: 1.55e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825 2026 KKPKKDESRDlalcSMILTEMETHEDSWPFLLPVNLKLVPGYKKVIKKPMDFSTIREKLNNGQYPNFETFALDVRLVFDN 2105
Cdd:COG5076    259 PGREEREERE----SVLITNSQAHVGAWPFLRPVSDEEVPDYYKDIRDPMDLSTKELKLRNNYYRPEETFVRDAKLFFDN 334
                           90       100
                   ....*....|....*....|....*
gi 1720399825 2106 CETFNEDDSDIGRAGHSMRKYFEKK 2130
Cdd:COG5076    335 CVMYNGEVTDYYKNANVLEDFVIKK 359
PTZ00121 PTZ00121
MAEBL; Provisional
867-1039 1.63e-08

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 60.15  E-value: 1.63e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  867 RKLQAQEIARQAAQIKLLRKLQKQEQARVAKEAKKQqaimaAEEKRKQKEQMKiiKQQEKIKRIQQIRMekelRAQQILE 946
Cdd:PTZ00121  1364 EKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKK-----AEEDKKKADELK--KAAAAKKKADEAKK----KAEEKKK 1432
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  947 EKELRRQQAVLLKHQELERHrldmERERRRQHVMLMKAMEARKKAEEKERLKQEKRDEKRLNKERKLEQRRLELEMAKEL 1026
Cdd:PTZ00121  1433 ADEAKKKAEEAKKADEAKKK----AEEAKKAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKAAEA 1508
                          170
                   ....*....|...
gi 1720399825 1027 KKPKEDMCLADQK 1039
Cdd:PTZ00121  1509 KKKADEAKKAEEA 1521
tolA_full TIGR02794
TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the ...
872-1032 1.77e-08

TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB. [Transport and binding proteins, Other, Cellular processes, Pathogenesis]


Pssm-ID: 274303 [Multi-domain]  Cd Length: 346  Bit Score: 58.70  E-value: 1.77e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  872 QEIARQAAQIKLLRKLQKQEQARVAKEAKKQQAIMAAEEKRKQKEQMKiiKQQEkikriqqirmekELRAQQILE----- 946
Cdd:TIGR02794   71 KKLEQQAEEAEKQRAAEQARQKELEQRAAAEKAAKQAEQAAKQAEEKQ--KQAE------------EAKAKQAAEakaka 136
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  947 EKELRRQQAVLLKHQ-ELERHRLDMERERRRQHVMLMKAM-EARKKAEEKERLKQEKRDEKRLNKERKLEQRRLEL-EMA 1023
Cdd:TIGR02794  137 EAEAERKAKEEAAKQaEEEAKAKAAAEAKKKAEEAKKKAEaEAKAKAEAEAKAKAEEAKAKAEAAKAKAAAEAAAKaEAE 216

                   ....*....
gi 1720399825 1024 KELKKPKED 1032
Cdd:TIGR02794  217 AAAAAAAEA 225
DR0291 COG1579
Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General ...
859-1028 2.47e-08

Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General function prediction only];


Pssm-ID: 441187 [Multi-domain]  Cd Length: 236  Bit Score: 56.86  E-value: 2.47e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  859 DNTDAKLLRKLQA--QEIARQAAQIK-LLRKLQKQEQARVAKEA---KKQQAIMAAEEKRKQKEQmKIIKQQEKIKRIQ- 931
Cdd:COG1579      2 MPEDLRALLDLQEldSELDRLEHRLKeLPAELAELEDELAALEArleAAKTELEDLEKEIKRLEL-EIEEVEARIKKYEe 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  932 ---QIRMEKELRAQQiLEEKELRRQQAVLlKHQELErhrldmererrrqhvmLMKAMEARKK--AEEKERLKQEKRDEKR 1006
Cdd:COG1579     81 qlgNVRNNKEYEALQ-KEIESLKRRISDL-EDEILE----------------LMERIEELEEelAELEAELAELEAELEE 142
                          170       180
                   ....*....|....*....|..
gi 1720399825 1007 LNKERKLEQRRLELEMAKELKK 1028
Cdd:COG1579    143 KKAELDEELAELEAELEELEAE 164
CCDC34 pfam13904
Coiled-coil domain-containing protein 3; This family is found in eukaryotes; it has several ...
874-1042 2.55e-08

Coiled-coil domain-containing protein 3; This family is found in eukaryotes; it has several conserved tryptophan residues. The function is not known.


Pssm-ID: 464032 [Multi-domain]  Cd Length: 221  Bit Score: 56.64  E-value: 2.55e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  874 IARQAAQIKLLRKLQKQ-EQARVAKEAKKQQAIMAAEEKRKQKEQMKIIKQQEKikriqqirmekELRAQQILEEKELRR 952
Cdd:pfam13904   40 YARKLEGLKLERQPLEAyENWLAAKQRQRQKELQAQKEEREKEEQEAELRKRLA-----------KEKYQEWLQRKARQQ 108
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  953 QQAVLLKHQELERHRLDMERERRRQHVmlmKAMEARKKAEEKERLKQEKRDEKRLNKERKLEQRRLELEMAKEL--KKPK 1030
Cdd:pfam13904  109 TKKREESHKQKAAESASKSLAKPERKV---SQEEAKEVLQEWERKKLEQQQRKREEEQREQLKKEEEEQERKQLaeKAWQ 185
                          170
                   ....*....|..
gi 1720399825 1031 EDMCLADQKPLP 1042
Cdd:pfam13904  186 KWMKNVKNKPKP 197
TolA COG3064
Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis];
862-1038 3.09e-08

Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442298 [Multi-domain]  Cd Length: 485  Bit Score: 58.51  E-value: 3.09e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  862 DAKLLRKLQAQEIARQAAQIKLLRKLQKQEQARVAKEAKKQQAIMAAEEKRKQKEQMKIIKQQEKIKRIQQIrmEKELRA 941
Cdd:COG3064     11 EAAAQERLEQAEAEKRAAAEAEQKAKEEAEEERLAELEAKRQAEEEAREAKAEAEQRAAELAAEAAKKLAEA--EKAAAE 88
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  942 qqilEEKELRRQQAVLLKHQELERhrldmERERRRQHVMLMKAMEARKKAEEKERLK-QEKRDEKRLNKERKLEQRRLEL 1020
Cdd:COG3064     89 ----AEKKAAAEKAKAAKEAEAAA-----AAEKAAAAAEKEKAEEAKRKAEEEAKRKaEEERKAAEAEAAAKAEAEAARA 159
                          170
                   ....*....|....*...
gi 1720399825 1021 EMAKELKKPKEDMCLADQ 1038
Cdd:COG3064    160 AAAAAAAAAAAAARAAAG 177
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
866-1032 3.27e-08

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 59.30  E-value: 3.27e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  866 LRKLQAQEiarQAAQIKLLRKLQKQEQARVAKEAKKQQAIMAAEEKRKQKEQMKIIKQQekIKRIQQIRMEKELRAQQIL 945
Cdd:TIGR02168  805 LDELRAEL---TLLNEEAANLRERLESLERRIAATERRLEDLEEQIEELSEDIESLAAE--IEELEELIEELESELEALL 879
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  946 EEKELRRQQAVLLKH--QELERHRLDMERERRRqhvmLMKAMEARKKAEEKERLKQEKRDEKRLN-KERKLEQRRLELEM 1022
Cdd:TIGR02168  880 NERASLEEALALLRSelEELSEELRELESKRSE----LRRELEELREKLAQLELRLEGLEVRIDNlQERLSEEYSLTLEE 955
                          170
                   ....*....|
gi 1720399825 1023 AKELKKPKED 1032
Cdd:TIGR02168  956 AEALENKIED 965
tolA_full TIGR02794
TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the ...
869-1030 3.30e-08

TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB. [Transport and binding proteins, Other, Cellular processes, Pathogenesis]


Pssm-ID: 274303 [Multi-domain]  Cd Length: 346  Bit Score: 57.93  E-value: 3.30e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  869 LQAQEIARQAAQIKLlrklQKQEQARVAKEAKKQQAIMAAE-EKRKQKEQMKIIKQQEKIKRIQQIRmekelRAQQILEE 947
Cdd:TIGR02794   43 VDPGAVAQQANRIQQ----QKKPAAKKEQERQKKLEQQAEEaEKQRAAEQARQKELEQRAAAEKAAK-----QAEQAAKQ 113
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  948 KELRRQQAVLLKHQELERHRLDMERERRRQhvmlmKAMEARKKAEEkERLKQEKRDEKrlnKERKLEQRRLELEM-AKEL 1026
Cdd:TIGR02794  114 AEEKQKQAEEAKAKQAAEAKAKAEAEAERK-----AKEEAAKQAEE-EAKAKAAAEAK---KKAEEAKKKAEAEAkAKAE 184

                   ....
gi 1720399825 1027 KKPK 1030
Cdd:TIGR02794  185 AEAK 188
PHD1_CHD_II cd15531
PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
1903-1948 4.23e-08

PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD proteins includes chromodomain-helicase-DNA-binding protein CHD3, CHD4, and CHD5, which are nuclear and ubiquitously expressed chromatin remodelling ATPases generally associated with histone deacetylases (HDACs). They are involved in DNA Double Strand Break (DSB) signaling, DSB repair and/or p53-dependent pathways such as apoptosis and senescence, as well as in the maintenance of genomic stability, and/or cancer prevention. They function as subunits of the Nucleosome Remodelling and Deacetylase (NuRD) complex, which is generally associated with gene repression, heterochromatin formation, and overall chromatin compaction. In contrast to the class I CHD enzymes (CHD1 and CHD2), class II CHD proteins lack identifiable DNA-binding domains, but possess a C-terminal coiled-coil region. Moreover, in addition to the tandem chromodomains and a helicase domain, they all harbor tandem plant homeodomain (PHD) zinc fingers involved in the recognition of methylated histone tails. This model corresponds to the first PHD finger.


Pssm-ID: 277006 [Multi-domain]  Cd Length: 43  Bit Score: 51.06  E-value: 4.23e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1720399825 1903 YCQICRKGDNeelLLLCDGCDKGCHTYCHRPKITTIPDGDWFCPAC 1948
Cdd:cd15531      1 YCEVCQQGGE---IILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 43
PHD_PRHA_like cd15504
PHD finger found in Arabidopsis thaliana pathogenesis-related homeodomain protein (PRHA) and ...
1903-1948 5.19e-08

PHD finger found in Arabidopsis thaliana pathogenesis-related homeodomain protein (PRHA) and similar proteins; PRHA is a homeodomain protein encoded by a single-copy Arabidopsis thaliana homeobox gene, prha. It shows the capacity to bind to TAATTG core sequence elements but requires additional adjacent bases for high-affinity binding. PRHA contains a plant homeodomain (PHD) finger, a homeodomain, peptide repeats and a putative leucine zipper dimerization domain.


Pssm-ID: 276979  Cd Length: 53  Bit Score: 51.28  E-value: 5.19e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1720399825 1903 YCQICRKG--DNEELLLLCDG-CDKGCHTYCHRPKITT--IPDGD--WFCPAC 1948
Cdd:cd15504      1 FCAKCQSGeaSPDNDILLCDGgCNRAYHQKCLEPPLLTedIPPEDegWLCPLC 53
DUF4659 pfam15558
Domain of unknown function (DUF4659); This family of proteins is found in eukaryotes. Proteins ...
867-1032 5.69e-08

Domain of unknown function (DUF4659); This family of proteins is found in eukaryotes. Proteins in this family are typically between 427 and 674 amino acids in length. There are two completely conserved residues (D and I) that may be functionally important.


Pssm-ID: 464768 [Multi-domain]  Cd Length: 374  Bit Score: 57.35  E-value: 5.69e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  867 RKLQAQEIAR-QAAQikLLRKLQKQEQARVAKEAKKQQAIMAAEEKRKQKEQmkiikQQEKIKRIQQIRMEKELRAQqil 945
Cdd:pfam15558    7 RKIAALMLARhKEEQ--RMRELQQQAALAWEELRRRDQKRQETLERERRLLL-----QQSQEQWQAEKEQRKARLGR--- 76
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  946 EEKELRRQQAVLLKHQELERHRLDMERERRRQHVMLMKAMEARKKAEEKERLKQEKRDEKRLNKERKLEQRRLELEMA-- 1023
Cdd:pfam15558   77 EERRRADRREKQVIEKESRWREQAEDQENQRQEKLERARQEAEQRKQCQEQRLKEKEEELQALREQNSLQLQERLEEAch 156

                   ....*....
gi 1720399825 1024 KELKKPKED 1032
Cdd:pfam15558  157 KRQLKEREE 165
DUF4670 pfam15709
Domain of unknown function (DUF4670); This family of proteins is found in eukaryotes. Proteins ...
865-1021 6.12e-08

Domain of unknown function (DUF4670); This family of proteins is found in eukaryotes. Proteins in this family are typically between 373 and 763 amino acids in length.


Pssm-ID: 464815 [Multi-domain]  Cd Length: 522  Bit Score: 57.65  E-value: 6.12e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  865 LLRKLQAQEIAR-----QAAQIKLL---RKLQKQ-EQARVAKEAKKQQAIMAAE---EKRKQKEQMKIIKQQEKIKRIQQ 932
Cdd:pfam15709  324 LLEKREQEKASRdrlraERAEMRRLeveRKRREQeEQRRLQQEQLERAEKMREElelEQQRRFEEIRLRKQRLEEERQRQ 403
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  933 IRMEKELRAQ-QILEEKELRRQQAVLLKHQELERHRLDMERERRRQHVMLMKAMEARkKAEEKERL---KQEKRDEKRLN 1008
Cdd:pfam15709  404 EEEERKQRLQlQAAQERARQQQEEFRRKLQELQRKKQQEEAERAEAEKQRQKELEMQ-LAEEQKRLmemAEEERLEYQRQ 482
                          170
                   ....*....|...
gi 1720399825 1009 KERKLEQRRLELE 1021
Cdd:pfam15709  483 KQEAEEKARLEAE 495
tolA PRK09510
cell envelope integrity inner membrane protein TolA; Provisional
871-1039 7.84e-08

cell envelope integrity inner membrane protein TolA; Provisional


Pssm-ID: 236545 [Multi-domain]  Cd Length: 387  Bit Score: 57.12  E-value: 7.84e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  871 AQEIARQAAQIKLLRKLQKQEQARVAKEAKKQQAIMAAEEKR-KQKEQMKIIKQQEKIKRIQQIRMEKElraQQILEEKE 949
Cdd:PRK09510    61 VEQYNRQQQQQKSAKRAEEQRKKKEQQQAEELQQKQAAEQERlKQLEKERLAAQEQKKQAEEAAKQAAL---KQKQAEEA 137
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  950 LRRQQAVLLKHQELERHRLDM-------ERERRRQHVMLMKA-MEARKKAEEKERLKQEKRDEKRLNKERKLEQRRLELE 1021
Cdd:PRK09510   138 AAKAAAAAKAKAEAEAKRAAAaakkaaaEAKKKAEAEAAKKAaAEAKKKAEAEAAAKAAAEAKKKAEAEAKKKAAAEAKK 217
                          170
                   ....*....|....*...
gi 1720399825 1022 MAKELKKPKEDMCLADQK 1039
Cdd:PRK09510   218 KAAAEAKAAAAKAAAEAK 235
PHD1_MTF2 cd15578
PHD finger 1 found in metal-response element-binding transcription factor 2 (MTF2); MTF2, also ...
1904-1950 1.52e-07

PHD finger 1 found in metal-response element-binding transcription factor 2 (MTF2); MTF2, also termed metal regulatory transcription factor 2, or metal-response element DNA-binding protein M96, or polycomb-like protein 2 (PCL2), complexes with the polycomb repressive complex-2 (PRC2) in embryonic stem cells and regulates the transcriptional networks during embryonic stem cell self-renewal and differentiation. It recruits the PRC2 complex to the inactive X chromosome and target loci in embryonic stem cells. Moreover, MTF2 is required for PRC2-mediated Hox cluster repression. It activates the Cdkn2a gene and promotes cellular senescence, thus suppressing the catalytic activity of PRC2 locally. MTF2 consists of an N-terminal Tudor domain followed by two PHD fingers, and a C-terminal MTF2 domain. This model corresponds to the first PHD finger.


Pssm-ID: 277053  Cd Length: 53  Bit Score: 49.70  E-value: 1.52e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1720399825 1904 CQICRKGDNEE--LLLLCDGCDKGCHTYCHRPKITTI---PDGDWFCPACIS 1950
Cdd:cd15578      2 CTVCQDGSSESpnEIVLCDKCGQGYHQLCHNPKIDSSvldPDVPWLCRQCVF 53
PHD_PHF21A cd15523
PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC ...
1903-1948 1.53e-07

PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC complex protein BHC80) along with HDAC1/2, CtBP1, CoREST, and BRAF35, is associated with LSD1, a lysine (K)-specific histone demethylase. It inhibits LSD1-mediated histone demethylation in vitro. PHF21A is predominantly present in the central nervous system and spermatogenic cells and is one of the six components of BRAF-HDAC complex (BHC) involved in REST-dependent transcriptional repression of neuron-specific genes in non-neuronal cells. It acts as a scaffold protein in BHC in neuronal as well as non-neuronal cells and also plays a role in spermatogenesis. PHF21A contains a C-terminal plant homeodomain (PHD) finger that is responsible for the binding directly to each of five other components of BHC, and of organizing BHC mediating transcriptional repression.


Pssm-ID: 276998 [Multi-domain]  Cd Length: 43  Bit Score: 49.32  E-value: 1.53e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1720399825 1903 YCQICRKGDNeelLLLCDGCDKGCHTYCHRPKITTIPDGDWFCPAC 1948
Cdd:cd15523      1 FCSVCRKSGE---LLMCDTCSLVYHLDCLDPPLKTIPKGMWICPKC 43
tolA_full TIGR02794
TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the ...
827-1019 2.78e-07

TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB. [Transport and binding proteins, Other, Cellular processes, Pathogenesis]


Pssm-ID: 274303 [Multi-domain]  Cd Length: 346  Bit Score: 54.85  E-value: 2.78e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  827 RPPNPDRPRAREESRMKRRKGRPPNvgsaeflDNTDAKLLRKLQAQEIARQAAQikllRKLQKQEQARVAKEAKKQQAI- 905
Cdd:TIGR02794   63 AKKEQERQKKLEQQAEEAEKQRAAE-------QARQKELEQRAAAEKAAKQAEQ----AAKQAEEKQKQAEEAKAKQAAe 131
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  906 --MAAEEKRKQKEQMKIIKQQEKikriqqirmEKELRAQQileekELRRQQAVLLKHQELERHRLDMERERRRQHVMLMK 983
Cdd:TIGR02794  132 akAKAEAEAERKAKEEAAKQAEE---------EAKAKAAA-----EAKKKAEEAKKKAEAEAKAKAEAEAKAKAEEAKAK 197
                          170       180       190
                   ....*....|....*....|....*....|....*...
gi 1720399825  984 AMEARKKA--EEKERLKQEKRDEKRLNKERKLEQRRLE 1019
Cdd:TIGR02794  198 AEAAKAKAaaEAAAKAEAEAAAAAAAEAERKADEAELG 235
CCDC66 pfam15236
Coiled-coil domain-containing protein 66; This protein family, named Coiled-coil ...
950-1028 2.78e-07

Coiled-coil domain-containing protein 66; This protein family, named Coiled-coil domain-containing protein 66 (CCDC) refers to a protein domain found in eukaryotes, and is approximately 160 amino acids in length. CCDC66 protein is detected mainly in the inner segments of photoreceptors in many vertebrates including mice and humans. It has been found in dogs, that a mutation in the CCDC66 gene causes generalized progressive retinal atrophy (gPRA). This shows that the protein encoded for by this gene is vital for healthy vision and guards against photoreceptor cell degeneration. The structure of CCDC66 proteins includes a heptad repeat pattern which contains at least one coiled-coil domain. There are at least two or more alpha-helices which form a cable-like structure.


Pssm-ID: 434558 [Multi-domain]  Cd Length: 154  Bit Score: 52.11  E-value: 2.78e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  950 LRRQQAVLLKHQeLErhrldmERERRRQ-----HVMLMKAMEAR--KKAEEKERLKQEK-RDEKRLNKERKLEQRRLELE 1021
Cdd:pfam15236   32 LRGQNALLDPAQ-LE------ERERKRQkalehQNAIKKQLEEKerQKKLEEERRRQEEqEEEERLRREREEEQKQFEEE 104

                   ....*..
gi 1720399825 1022 MAKELKK 1028
Cdd:pfam15236  105 RRKQKEK 111
MAP7 pfam05672
MAP7 (E-MAP-115) family; The organization of microtubules varies with the cell type and is ...
940-1031 3.33e-07

MAP7 (E-MAP-115) family; The organization of microtubules varies with the cell type and is presumably controlled by tissue-specific microtubule-associated proteins (MAPs). The 115-kDa epithelial MAP (E-MAP-115/MAP7) has been identified as a microtubule-stabilising protein predominantly expressed in cell lines of epithelial origin. The binding of this microtubule associated protein is nucleotide independent.


Pssm-ID: 461709 [Multi-domain]  Cd Length: 153  Bit Score: 51.97  E-value: 3.33e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  940 RAQQILEEKelrRQQAVLLKHQELERHRLDMERERRRQHVMLMKAMEARKKAEE-----KERLKQEKRDEKRLNKERKLE 1014
Cdd:pfam05672   11 EAARILAEK---RRQAREQREREEQERLEKEEEERLRKEELRRRAEEERARREEearrlEEERRREEEERQRKAEEEAEE 87
                           90
                   ....*....|....*..
gi 1720399825 1015 QRRLELEMAKELKKPKE 1031
Cdd:pfam05672   88 REQREQEEQERLQKQKE 104
YqiK COG2268
Uncharacterized membrane protein YqiK, contains Band7/PHB/SPFH domain [Function unknown];
876-1025 3.89e-07

Uncharacterized membrane protein YqiK, contains Band7/PHB/SPFH domain [Function unknown];


Pssm-ID: 441869 [Multi-domain]  Cd Length: 439  Bit Score: 54.88  E-value: 3.89e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  876 RQAAQIKllrKLQKQEQARVAKEAKKQQAimaaeEKRKQKEQMKIiKQQEKIKRIQQIRMEKELRAQQILEEKELRRQQA 955
Cdd:COG2268    192 RKIAEII---RDARIAEAEAERETEIAIA-----QANREAEEAEL-EQEREIETARIAEAEAELAKKKAEERREAETARA 262
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1720399825  956 VLLKHQELERHRLDMERERRRQHVMLMKAMEARKKAEEKERLKQEKRDEKRL--NKERKLEQRRLELEMAKE 1025
Cdd:COG2268    263 EAEAAYEIAEANAEREVQRQLEIAEREREIELQEKEAEREEAELEADVRKPAeaEKQAAEAEAEAEAEAIRA 334
Bromo_polybromo_I cd05524
Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which ...
2065-2115 3.97e-07

Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99954 [Multi-domain]  Cd Length: 113  Bit Score: 50.41  E-value: 3.97e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1720399825 2065 PGYKKVIKKPMDFSTIREKLNNGQYPNFETFALDVRLVFDNCETFNEDDSD 2115
Cdd:cd05524     39 PEYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNAKAYYKPDSP 89
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
867-1026 4.40e-07

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 55.45  E-value: 4.40e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  867 RKLQAQEIARQAAQIKLLRKLQKQEQARVAKEAKKQQAI-MAAEEKRKQKEQMK----IIKQQEKIKRIQQIRMEKELRA 941
Cdd:TIGR02168  332 LDELAEELAELEEKLEELKEELESLEAELEELEAELEELeSRLEELEEQLETLRskvaQLELQIASLNNEIERLEARLER 411
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  942 QQILEEKELRRQQAVLLKHQELERHRLDMERERRRQhvMLMKAMEARKKAEEKERLKQEKRDEKR---LNKERKLEQRRL 1018
Cdd:TIGR02168  412 LEDRRERLQQEIEELLKKLEEAELKELQAELEELEE--ELEELQEELERLEEALEELREELEEAEqalDAAERELAQLQA 489

                   ....*...
gi 1720399825 1019 ELEMAKEL 1026
Cdd:TIGR02168  490 RLDSLERL 497
Bromo_ZMYND11 cd05492
Bromodomain; ZMYND11_like sub-family. ZMYND11 or BS69 is a ubiquitously expressed nuclear ...
2065-2125 5.95e-07

Bromodomain; ZMYND11_like sub-family. ZMYND11 or BS69 is a ubiquitously expressed nuclear protein that has been shown to associate with chromatin. It interacts with chromatin remodeling factors and might play a role in chromatin remodeling and gene expression. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99924  Cd Length: 109  Bit Score: 50.07  E-value: 5.95e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1720399825 2065 PGYKKVIKKPMDFSTIREKLNNGQYPNFETFALDVRLVFDNCETFNEDDSDIGRAGHSMRK 2125
Cdd:cd05492     37 PKRRRLIHTHLDVADIQEKINSEKYTSLEEFKADALLLLHNTAIFHGADSEQYDAARWLYR 97
GBP_C cd16269
Guanylate-binding protein, C-terminal domain; Guanylate-binding protein (GBP), C-terminal ...
865-985 6.68e-07

Guanylate-binding protein, C-terminal domain; Guanylate-binding protein (GBP), C-terminal domain. Guanylate-binding proteins (GBPs) are synthesized after activation of the cell by interferons. The biochemical properties of GBPs are clearly different from those of Ras-like and heterotrimeric GTP-binding proteins. They bind guanine nucleotides with low affinity (micromolar range), are stable in their absence, and have a high turnover GTPase. In addition to binding GDP/GTP, they have the unique ability to bind GMP with equal affinity and hydrolyze GTP not only to GDP, but also to GMP. This C-terminal domain has been shown to mediate inhibition of endothelial cell proliferation by inflammatory cytokines.


Pssm-ID: 293879 [Multi-domain]  Cd Length: 291  Bit Score: 53.35  E-value: 6.68e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  865 LLRKLQAQE-IAR---QAAQIKLLRKLQKQEQARVAKEAKKQQAIMaaEEKRKQKEQMkiIKQQEKI--KRIQQIRMEKE 938
Cdd:cd16269    172 LQEFLQSKEaEAEailQADQALTEKEKEIEAERAKAEAAEQERKLL--EEQQRELEQK--LEDQERSyeEHLRQLKEKME 247
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 1720399825  939 LRAQQILEEKElrRQQAVLLKHQElerhrlDMERERRRQHVMLMKAM 985
Cdd:cd16269    248 EERENLLKEQE--RALESKLKEQE------ALLEEGFKEQAELLQEE 286
tolA PRK09510
cell envelope integrity inner membrane protein TolA; Provisional
859-1039 7.08e-07

cell envelope integrity inner membrane protein TolA; Provisional


Pssm-ID: 236545 [Multi-domain]  Cd Length: 387  Bit Score: 54.04  E-value: 7.08e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  859 DNTDAKLLRKLQAQEIAR--QAAQIKLLRKLQKQEQARV-AKEAKKQQAIMAAEEKRKQK---EQMKIIKQQEKIKRIQQ 932
Cdd:PRK09510    73 SAKRAEEQRKKKEQQQAEelQQKQAAEQERLKQLEKERLaAQEQKKQAEEAAKQAALKQKqaeEAAAKAAAAAKAKAEAE 152
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  933 IRMEKELrAQQILEEKELRRQQAVLLKHQELERHRLDMERERRrqhvmlmKAMEARKKAEEKERLKQEKRDEKRLNKERK 1012
Cdd:PRK09510   153 AKRAAAA-AKKAAAEAKKKAEAEAAKKAAAEAKKKAEAEAAAK-------AAAEAKKKAEAEAKKKAAAEAKKKAAAEAK 224
                          170       180
                   ....*....|....*....|....*..
gi 1720399825 1013 LEQrrlelEMAKELKKPKEDMCLADQK 1039
Cdd:PRK09510   225 AAA-----AKAAAEAKAAAEKAAAAKA 246
DUF4659 pfam15558
Domain of unknown function (DUF4659); This family of proteins is found in eukaryotes. Proteins ...
869-1031 8.44e-07

Domain of unknown function (DUF4659); This family of proteins is found in eukaryotes. Proteins in this family are typically between 427 and 674 amino acids in length. There are two completely conserved residues (D and I) that may be functionally important.


Pssm-ID: 464768 [Multi-domain]  Cd Length: 374  Bit Score: 53.50  E-value: 8.44e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  869 LQAQEIARQAAQIKLLR--KLQKQEQARVAKEAKKQQAIMAAEEKRKQKEQ--------MKIIKQQEKIKRIQQIRmEKE 938
Cdd:pfam15558  145 LQLQERLEEACHKRQLKerEEQKKVQENNLSELLNHQARKVLVDCQAKAEEllrrlsleQSLQRSQENYEQLVEER-HRE 223
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  939 LRAQQILEEKELRRQQAVLLKHQELERHRLDM---ERERRRQHVMLMKAMEARKKAEEKERLKQEKRDEKRLNKERKLEQ 1015
Cdd:pfam15558  224 LREKAQKEEEQFQRAKWRAEEKEEERQEHKEAlaeLADRKIQQARQVAHKTVQDKAQRARELNLEREKNHHILKLKVEKE 303
                          170
                   ....*....|....*.
gi 1720399825 1016 RRLELEMAKELKKPKE 1031
Cdd:pfam15558  304 EKCHREGIKEAIKKKE 319
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
863-1024 8.69e-07

Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 443969 [Multi-domain]  Cd Length: 377  Bit Score: 53.61  E-value: 8.69e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  863 AKLLRKLQAQ--EIARQAAQIKLLRKLQKQEQARVAKEAKKQQAIMAAEEKRKQKEQMKIIKQQEKIKRI--QQIRMEKE 938
Cdd:COG4942     19 ADAAAEAEAEleQLQQEIAELEKELAALKKEEKALLKQLAALERRIAALARRIRALEQELAALEAELAELekEIAELRAE 98
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  939 LRAQQILEEKELRRQQ--------AVLLKHQELER--HRLDMERERRRQHVMLMKAMEARKK--AEEKERLKQEKRDEKR 1006
Cdd:COG4942     99 LEAQKEELAELLRALYrlgrqpplALLLSPEDFLDavRRLQYLKYLAPARREQAEELRADLAelAALRAELEAERAELEA 178
                          170
                   ....*....|....*...
gi 1720399825 1007 LNKERKLEQRRLELEMAK 1024
Cdd:COG4942    179 LLAELEEERAALEALKAE 196
DUF4670 pfam15709
Domain of unknown function (DUF4670); This family of proteins is found in eukaryotes. Proteins ...
863-1024 9.85e-07

Domain of unknown function (DUF4670); This family of proteins is found in eukaryotes. Proteins in this family are typically between 373 and 763 amino acids in length.


Pssm-ID: 464815 [Multi-domain]  Cd Length: 522  Bit Score: 53.80  E-value: 9.85e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  863 AKLLRKLQAQEIARQAAQIKLLRKLQKQEQARVAKEAKKQQAIMAAEEKRKQKEqmkiikQQEKIKRIQQIRMEKELRAQ 942
Cdd:pfam15709  371 AEKMREELELEQQRRFEEIRLRKQRLEEERQRQEEEERKQRLQLQAAQERARQQ------QEEFRRKLQELQRKKQQEEA 444
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  943 QILEEKElRRQQAVLLKHQELERHRLDMERERRRQHVmlmkameaRKKAEEKERLKQEKrDEKRLNKErklEQRRLELEM 1022
Cdd:pfam15709  445 ERAEAEK-QRQKELEMQLAEEQKRLMEMAEEERLEYQ--------RQKQEAEEKARLEA-EERRQKEE---EAARLALEE 511

                   ..
gi 1720399825 1023 AK 1024
Cdd:pfam15709  512 AM 513
Lebercilin pfam15619
Ciliary protein causing Leber congenital amaurosis disease; Lebercilin is a family of ...
864-1013 1.25e-06

Ciliary protein causing Leber congenital amaurosis disease; Lebercilin is a family of eukaryotic ciliary proteins. Mutations in the gene, LCA5, are implicated in the disease Leber congenital amaurosis. In photoreceptors, lebercilin is uniquely localized at the cilium that bridges the inner and outer segments. Lebercilin functions as an integral element of selective protein transport through photoreceptor cilia. Lebercilin specifically interacts with the intraflagellar transport (IFT), and disruption of IFT can lead to Leber congenital amaurosis.


Pssm-ID: 464776 [Multi-domain]  Cd Length: 193  Bit Score: 51.06  E-value: 1.25e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  864 KLLRKLQAqeiaRQAAQIK--------LLRKLQKQ-EQARVAKE--AKKQQAIMAAEEKRKQKEqMKIIKQQEKIKRIQQ 932
Cdd:pfam15619   35 RLLKRLQK----RQEKALGkyegteseLPQLIARHnEEVRVLRErlRRLQEKERDLERKLKEKE-AELLRLRDQLKRLEK 109
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  933 IRMEKELRAQQILEEKeLRRQQAVLL----KHQELERHRLDMERERRRQHVMLM-KAMEARKK----AEEKERLKQekrd 1003
Cdd:pfam15619  110 LSEDKNLAEREELQKK-LEQLEAKLEdkdeKIQDLERKLELENKSFRRQLAAEKkKHKEAQEEvkilQEEIERLQQ---- 184
                          170
                   ....*....|
gi 1720399825 1004 eKRLNKERKL 1013
Cdd:pfam15619  185 -KLKEKEREL 193
PHD1_PHF12 cd15533
PHD finger 1 found in PHD finger protein 12 (PHF12); PHF12, also termed PHD factor 1 (Pf1), is ...
1903-1948 1.28e-06

PHD finger 1 found in PHD finger protein 12 (PHF12); PHF12, also termed PHD factor 1 (Pf1), is a plant homeodomain (PHD) zinc finger-containing protein that bridges the transducin-like enhancer of split (TLE) corepressor to the mSin3A-histone deacetylase (HDAC)-complex, and further represses transcription at targeted genes. PHF12 also interacts with MRG15 (mortality factor-related genes on chromosome 15), a member of the mortality factor (MORF) family of proteins implicated in regulating cellular senescence. PHF12 contains two plant-homeodomain (PHD) zinc fingers followed by a polybasic region. The PHD fingers function downstream of phosphoinositide signaling triggered by the interaction between polybasic regions and phosphoinositides. This model corresponds to the first PHD finger.


Pssm-ID: 277008 [Multi-domain]  Cd Length: 45  Bit Score: 46.97  E-value: 1.28e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1720399825 1903 YCQICRKGDNeelLLLCDGCDKGCHTYCHRPKI--TTIPDGDWFCPAC 1948
Cdd:cd15533      1 YCDSCGEGGD---LLCCDRCPASFHLQCCNPPLdeEDLPPGEWLCHRC 45
PHD_TAF3 cd15522
PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3); TAF3 (also termed ...
1903-1948 1.58e-06

PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3); TAF3 (also termed 140 kDa TATA box-binding protein-associated factor, TBP-associated factor 3, transcription initiation factor TFIID 140 kDa subunit (TAF140), or TAFII-140, is an integral component of TFIID) is a general initiation factor (GTF) that plays a key role in preinitiation complex (PIC) assembly through core promoter recognition. The interaction of H3K4me3 with TAF3 directs global TFIID recruitment to active genes, which regulates gene-selective functions of p53 in response to genotoxic stress. TAF3 is highly enriched in embryonic stem cells and is required for endoderm lineage differentiation and prevents premature specification of neuroectoderm and mesoderm. Moreover, TAF3, along with TRF3, forms a complex that is essential for myogenic differentiation. TAF3 contains a plant homeodomain (PHD) finger. This family also includes Drosophila melanogaster BIP2 (Bric-a-brac interacting protein 2) protein, which functions as an interacting partner of D. melanogaster p53 (Dmp53).


Pssm-ID: 276997 [Multi-domain]  Cd Length: 46  Bit Score: 46.51  E-value: 1.58e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1720399825 1903 YCQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIPDGDWFCPAC 1948
Cdd:cd15522      1 ICPICKKPDDGSPMIGCDECDDWYHWECVGITDEPPEEDDWFCPKC 46
ERM_helical pfam20492
Ezrin/radixin/moesin, alpha-helical domain; The ERM family consists of three closely-related ...
910-1033 1.72e-06

Ezrin/radixin/moesin, alpha-helical domain; The ERM family consists of three closely-related proteins, ezrin, radixin and moesin. Ezrin was first identified as a constituent of microvilli, radixin as a barbed, end-capping actin-modulating protein from isolated junctional fractions, and moesin as a heparin binding protein. A tumour suppressor molecule responsible for neurofibromatosis type 2 (NF2) is highly similar to ERM proteins and has been designated merlin (moesin-ezrin-radixin-like protein). ERM molecules contain 3 domains, an N-terminal globular domain, an extended alpha-helical domain and a charged C-terminal domain (pfam00769). Ezrin, radixin and merlin also contain a polyproline linker region between the helical and C-terminal domains. The N-terminal domain is highly conserved and is also found in merlin, band 4.1 proteins and members of the band 4.1 superfamily, designated the FERM domain. ERM proteins crosslink actin filaments with plasma membranes. They co-localize with CD44 at actin filament plasma membrane interaction sites, associating with CD44 via their N-terminal domains and with actin filaments via their C-terminal domains. This is the alpha-helical domain, which is involved in intramolecular masking of protein-protein interaction sites, regulating the activity of this proteins.


Pssm-ID: 466641 [Multi-domain]  Cd Length: 120  Bit Score: 48.76  E-value: 1.72e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  910 EKRKQKEQMKIIKQQEKIKriqqiRMEKELRAQQ--ILEEKELRRQqavllkhQELERHRLdmERERRRQHVMLMK-AME 986
Cdd:pfam20492    5 EREKQELEERLKQYEEETK-----KAQEELEESEetAEELEEERRQ-------AEEEAERL--EQKRQEAEEEKERlEES 70
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|
gi 1720399825  987 ARKKAEEKERLKQEKRDEKRLNKERKLEQRRLELEMAK---ELKKPKEDM 1033
Cdd:pfam20492   71 AEMEAEEKEQLEAELAEAQEEIARLEEEVERKEEEARRlqeELEEAREEE 120
TolA COG3064
Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis];
870-1032 2.21e-06

Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442298 [Multi-domain]  Cd Length: 485  Bit Score: 52.73  E-value: 2.21e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  870 QAQEIARQAAQIKLLRKLQKQEQARVAKEAKKQQAIMAAEEKRKQKEQmkiiKQQEKIKRIQQIRMEKELRAQQILEEKE 949
Cdd:COG3064      1 AQEALEEKAAEAAAQERLEQAEAEKRAAAEAEQKAKEEAEEERLAELE----AKRQAEEEAREAKAEAEQRAAELAAEAA 76
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  950 LRRQQAvllkhqelERHRLDMERERRRQHVMLMKAMEARKKAEEKERLKQEKRDEKRLNK-----ERKLEQRRLELEMAK 1024
Cdd:COG3064     77 KKLAEA--------EKAAAEAEKKAAAEKAKAAKEAEAAAAAEKAAAAAEKEKAEEAKRKaeeeaKRKAEEERKAAEAEA 148

                   ....*...
gi 1720399825 1025 ELKKPKED 1032
Cdd:COG3064    149 AAKAEAEA 156
PHD_TIF1alpha cd15622
PHD finger found in transcription intermediary factor 1-alpha (TIF1-alpha); TIF1-alpha, also ...
1903-1948 2.28e-06

PHD finger found in transcription intermediary factor 1-alpha (TIF1-alpha); TIF1-alpha, also termed tripartite motif-containing protein 24 (TRIM24), or E3 ubiquitin-protein ligase TRIM24, or RING finger protein 82, belongs to the TRIM/RBCC protein family. It interacts specifically and in a ligand-dependent manner with the ligand binding domain (LBD) of several nuclear receptors (NRs), including retinoid X (RXR), retinoic acid (RAR), vitamin D3 (VDR), estrogen (ER), and progesterone (PR) receptors. It also associates with heterochromatin-associated factors HP1alpha, MOD1 (HP1beta) and MOD2 (HP1gamma), as well as vertebrate Kruppel-type (C2H2) zinc finger proteins that contain transcriptional silencing domain KRAB. TIF1-alpha is a ligand-dependent co-repressor of retinoic acid receptor (RAR) that interacts with multiple nuclear receptors in vitro via an LXXLL motif, and further acts as a gatekeeper of liver carcinogenesis. It also functions as an E3-ubiquitin ligase targeting p53 and is broadly associated with chromatin silencing. Moreover, it is a chromatin regulator that recognizes specific, combinatorial histone modifications through its C-terminal plant homeodomain (PHD)-Bromodomain (Bromo) region. In addition, it interacts with chromatin and estrogen receptor to activate estrogen-dependent genes associated with cellular proliferation and tumor development. TIF1-alpha contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), a plant homeodomain (PHD) finger, followed by a bromodomain in the C-terminal region.


Pssm-ID: 277092  Cd Length: 43  Bit Score: 46.21  E-value: 2.28e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1720399825 1903 YCQICRKGDNeelLLLCDGCDKGCHTYCHRPKITTIPDGDWFCPAC 1948
Cdd:cd15622      1 WCAVCQNGGE---LLCCEKCPKVFHLSCHVPTLMNFPSGEWICTFC 43
Bromo_Rsc1_2_II cd05522
Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
2065-2127 2.30e-06

Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99953 [Multi-domain]  Cd Length: 104  Bit Score: 48.01  E-value: 2.30e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1720399825 2065 PGYKKVIKKPMDFSTIREKLNNGQYPNFETFALDVRLVFDNCETFNEDDSDIGRAGHSMRKYF 2127
Cdd:cd05522     38 PEYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYNENDSQEYKDAVLLEKEA 100
CAF-1_p150 pfam11600
Chromatin assembly factor 1 complex p150 subunit, N-terminal; CAF-1_p150 is a polypeptide ...
884-1030 2.44e-06

Chromatin assembly factor 1 complex p150 subunit, N-terminal; CAF-1_p150 is a polypeptide subunit of CAF-1, which functions in depositing newly synthesized and acetylated histones H3/H4 into chromatin during DNA replication and repair. CAF-1_p150 includes the HP1 interaction site, the PEST, KER and ED interacting sites. CAF-1_p150 interacts directly with newly synthesized and acetylated histones through the acidic KER and ED domains. The PEST domain is associated with proteins that undergo rapid proteolysis.


Pssm-ID: 402959 [Multi-domain]  Cd Length: 164  Bit Score: 49.69  E-value: 2.44e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  884 LRKLQKQEQARVAKEAKKQQAIMAAEEKRKQKEQMKiiKQQEKIKRIQQIRMEKELRAQQILEEKElrrqqavllkhqEL 963
Cdd:pfam11600   18 LEKDKERLRRQLKLEAEKEEKERLKEEAKAEKERAK--EEARRKKEEEKELKEKERREKKEKDEKE------------KA 83
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1720399825  964 ERHRLDMERERRRQHVMLMKAMEARKKAEEKeRLKQEkrdEKRLNKERKleqrrlelEMAKELKKPK 1030
Cdd:pfam11600   84 EKLRLKEEKRKEKQEALEAKLEEKRKKEEEK-RLKEE---EKRIKAEKA--------EITRFLQKPK 138
FliJ COG2882
Flagellar biosynthesis chaperone FliJ [Cell motility];
882-1023 3.00e-06

Flagellar biosynthesis chaperone FliJ [Cell motility];


Pssm-ID: 442129 [Multi-domain]  Cd Length: 142  Bit Score: 48.75  E-value: 3.00e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  882 KLLRKLQKQEQARVAKEAKKQQAIMAAEEKRKQKEQmkiiKQQEKIKRIQQiRMEKELRAQQILE--------EKELRRQ 953
Cdd:COG2882      9 TLLDLAEKEEDEAARELGQAQQALEQAEEQLEQLEQ----YREEYEQRLQQ-KLQQGLSAAQLRNyqqfiarlDEAIEQQ 83
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  954 QavllkhQELERHRLDMERERRRqhvmLMKAMeARKKAEEKerLKqEKRDEKRLNKERKLEQRRLElEMA 1023
Cdd:COG2882     84 Q------QQVAQAEQQVEQARQA----WLEAR-QERKALEK--LK-ERRREEERQEENRREQKELD-ELA 138
CCDC66 pfam15236
Coiled-coil domain-containing protein 66; This protein family, named Coiled-coil ...
904-1002 3.03e-06

Coiled-coil domain-containing protein 66; This protein family, named Coiled-coil domain-containing protein 66 (CCDC) refers to a protein domain found in eukaryotes, and is approximately 160 amino acids in length. CCDC66 protein is detected mainly in the inner segments of photoreceptors in many vertebrates including mice and humans. It has been found in dogs, that a mutation in the CCDC66 gene causes generalized progressive retinal atrophy (gPRA). This shows that the protein encoded for by this gene is vital for healthy vision and guards against photoreceptor cell degeneration. The structure of CCDC66 proteins includes a heptad repeat pattern which contains at least one coiled-coil domain. There are at least two or more alpha-helices which form a cable-like structure.


Pssm-ID: 434558 [Multi-domain]  Cd Length: 154  Bit Score: 49.02  E-value: 3.03e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  904 AIMAAEEKRKQK--EQMKIIKQQ-EKIKRIQQIRMEKELRAQQiLEEKELRRQQAVLLKHQELERHRLdMERE---RRRQ 977
Cdd:pfam15236   42 AQLEERERKRQKalEHQNAIKKQlEEKERQKKLEEERRRQEEQ-EEEERLRREREEEQKQFEEERRKQ-KEKEeamTRKT 119
                           90       100
                   ....*....|....*....|....*.
gi 1720399825  978 HVMLmkamEARKKAEE-KERLKQEKR 1002
Cdd:pfam15236  120 QALL----QAMQKAQElAQRLKQEQR 141
Bromo_SNF2 cd05519
Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in ...
2055-2130 3.99e-06

Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in transcriptional activation, it is the catalytic component of the SWI/SNF ATP-dependent chromatin remodeling complex. The protein is essential for the regulation of gene expression (both positive and negative) of a large number of genes. The SWI/SNF complex changes chromatin structure by altering DNA-histone contacts within the nucleosome, which results in a re-positioning of the nucleosome and facilitates or represses the binding of gene-specific transcription factors. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99950  Cd Length: 103  Bit Score: 47.33  E-value: 3.99e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1720399825 2055 FLLPVNLKLVPGYKKVIKKPMDFSTIREKLNNGQYPNFETFALDVRLVFDNCETFNEDDSDIGRAGHSMRKYFEKK 2130
Cdd:cd05519     27 FLEKPSKKLYPDYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANARTYNQEGSIVYEDAVEMEKAFKKK 102
DUF5401 pfam17380
Family of unknown function (DUF5401); This is a family of unknown function found in ...
835-995 4.00e-06

Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.


Pssm-ID: 375164 [Multi-domain]  Cd Length: 722  Bit Score: 52.05  E-value: 4.00e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  835 RAREESRMKRRKGRPpnvgsaefLDNTDAKLLRKLQAQEIARQAAQIKLLRKLQKQEQARVAKEAKKQ------------ 902
Cdd:pfam17380  433 RQREVRRLEEERARE--------MERVRLEEQERQQQVERLRQQEEERKRKKLELEKEKRDRKRAEEQrrkilekeleer 504
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  903 -QAIMAAEEKRKQKEQmKIIKQQEKIKRIQQIRM-EKELRAQQILEEKelRRQQAVLLKHQElERHRLD-MERERRrqhv 979
Cdd:pfam17380  505 kQAMIEEERKRKLLEK-EMEERQKAIYEEERRREaEEERRKQQEMEER--RRIQEQMRKATE-ERSRLEaMERERE---- 576
                          170
                   ....*....|....*.
gi 1720399825  980 MLMKAMEARKKAEEKE 995
Cdd:pfam17380  577 MMRQIVESEKARAEYE 592
PHD1_Rco1 cd15535
PHD finger 1 found in Saccharomyces cerevisiae transcriptional regulatory protein Rco1 and ...
1903-1948 4.85e-06

PHD finger 1 found in Saccharomyces cerevisiae transcriptional regulatory protein Rco1 and similar proteins; Rco1 is a component of the Rpd3S histone deacetylase complex that plays an important role at actively transcribed genes. Rco1 contains two plant homeodomain (PHD) fingers, which are required for the methylation of histone H3 lysine 36 (H3K36) nucleosome recognition by Rpd3S. This model corresponds to the first PHD finger.


Pssm-ID: 277010 [Multi-domain]  Cd Length: 45  Bit Score: 45.10  E-value: 4.85e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1720399825 1903 YCQIC-RKGdneeLLLLCDGCDKGCHTYCHRPKIT--TIPDGDWFCPAC 1948
Cdd:cd15535      1 FCSACgGYG----SFLCCDGCPRSFHFSCLDPPLEedNLPDDEWFCNEC 45
PDCD7 pfam16021
Programmed cell death protein 7;
835-1010 4.94e-06

Programmed cell death protein 7;


Pssm-ID: 464979 [Multi-domain]  Cd Length: 305  Bit Score: 50.88  E-value: 4.94e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  835 RAREESRMKRRKgrppnvgsaefldnTDAKLLRKLQAQEIARQAAQIK--LLRKLQKQEQARVAKEAKKQQAIMAAEEKR 912
Cdd:pfam16021   74 RQKKRLRRKRRK--------------EERKEEKKEEQERRAEREAKIDkwRRKQIQEVEEKKRERELKLAADAVLSEVRK 139
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  913 KQKEQMKIIKQQEKIKRIQQIRMEKELRaQQILEEKELRRQ-QAVLLKHQELERHRLDM-ERERRRQHVML-MKAMEARK 989
Cdd:pfam16021  140 KQADAKRMLDILRSLEKLRKLRKEAARR-KGIKPESECDEAfESHLEKLRSVWKKRTEEySAEEKALKVMLeGEQEEERK 218
                          170       180
                   ....*....|....*....|.
gi 1720399825  990 KAEEKerlKQEKRDEKRLNKE 1010
Cdd:pfam16021  219 RRREK---RQKKEREEFLQKK 236
PHD_JADE cd15573
PHD finger found in proteins Jade-1, Jade-2, Jade-3, and similar proteins; This family ...
1904-1948 4.96e-06

PHD finger found in proteins Jade-1, Jade-2, Jade-3, and similar proteins; This family includes proteins Jade-1 (PHF17), Jade-2 (PHF15), and Jade-3 (PHF16), each of which is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and EAF6 to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. This family also contains Drosophila melanogaster PHD finger protein rhinoceros (RNO). It is a novel plant homeodomain (PHD)-containing nuclear protein that may function as a transcription factor that antagonizes Ras signaling by regulating transcription of key EGFR/Ras pathway regulators in the Drosophila eye. All Jade proteins contain a canonical Cys4HisCys3 PHD finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, both of which are zinc-binding motifs. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277048 [Multi-domain]  Cd Length: 46  Bit Score: 45.09  E-value: 4.96e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1720399825 1904 CQICRKGDNEE--LLLLCDGCDKGCHTYCHrpKITTIPDGDWFCPAC 1948
Cdd:cd15573      2 CDVCRSPDSEEgnEMVFCDKCNICVHQACY--GIQKIPEGSWLCRTC 46
GBP_C cd16269
Guanylate-binding protein, C-terminal domain; Guanylate-binding protein (GBP), C-terminal ...
883-1017 4.98e-06

Guanylate-binding protein, C-terminal domain; Guanylate-binding protein (GBP), C-terminal domain. Guanylate-binding proteins (GBPs) are synthesized after activation of the cell by interferons. The biochemical properties of GBPs are clearly different from those of Ras-like and heterotrimeric GTP-binding proteins. They bind guanine nucleotides with low affinity (micromolar range), are stable in their absence, and have a high turnover GTPase. In addition to binding GDP/GTP, they have the unique ability to bind GMP with equal affinity and hydrolyze GTP not only to GDP, but also to GMP. This C-terminal domain has been shown to mediate inhibition of endothelial cell proliferation by inflammatory cytokines.


Pssm-ID: 293879 [Multi-domain]  Cd Length: 291  Bit Score: 50.65  E-value: 4.98e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  883 LLRKLQKQEqarvakeaKKQQAIMAAE----EKRKQKEQMKIikQQEKIKRIQQIRMEKELRAQQILEEKElRRQQavll 958
Cdd:cd16269    172 LQEFLQSKE--------AEAEAILQADqaltEKEKEIEAERA--KAEAAEQERKLLEEQQRELEQKLEDQE-RSYE---- 236
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1720399825  959 khQELERHRLDMERERRRQHVMLMKAMEARKKaeEKERLKQEKRDEKRLNKERKLEQRR 1017
Cdd:cd16269    237 --EHLRQLKEKMEEERENLLKEQERALESKLK--EQEALLEEGFKEQAELLQEEIRSLK 291
MAP7 pfam05672
MAP7 (E-MAP-115) family; The organization of microtubules varies with the cell type and is ...
875-1015 5.14e-06

MAP7 (E-MAP-115) family; The organization of microtubules varies with the cell type and is presumably controlled by tissue-specific microtubule-associated proteins (MAPs). The 115-kDa epithelial MAP (E-MAP-115/MAP7) has been identified as a microtubule-stabilising protein predominantly expressed in cell lines of epithelial origin. The binding of this microtubule associated protein is nucleotide independent.


Pssm-ID: 461709 [Multi-domain]  Cd Length: 153  Bit Score: 48.50  E-value: 5.14e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  875 ARQAAQIKLLRKLQKQEQARVAKEAKKQQAIMA----------AEEKRKQKEQMKIIKQQEKIKRIQQIRMEKELRAQQI 944
Cdd:pfam05672   23 AREQREREEQERLEKEEEERLRKEELRRRAEEErarreeearrLEEERRREEEERQRKAEEEAEEREQREQEEQERLQKQ 102
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1720399825  945 LEEKELRRQqavllkhQELERHRLdmERERRRQHvmlmkamearkkaEEKERLKQEKRDEKRLNKERKLEQ 1015
Cdd:pfam05672  103 KEEAEAKAR-------EEAERQRQ--EREKIMQQ-------------EEQERLERKKRIEEIMKRTRKSDQ 151
PHD4_NSD cd15567
PHD finger 4 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
1903-1948 5.33e-06

PHD finger 4 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The nuclear receptor binding SET domain (NSD) protein is a family of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1, that are critical in maintaining chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising to help suppress cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and they play non-redundant roles during development. NSD1 plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. NSD2 is involved in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). This model corresponds to the fourth PHD finger.


Pssm-ID: 277042 [Multi-domain]  Cd Length: 41  Bit Score: 44.93  E-value: 5.33e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1720399825 1903 YCQICRKGDNeelLLLCDGCDKGCHTYCHrpKITTIPDGDWFCPAC 1948
Cdd:cd15567      1 WCFICSEGGS---LICCESCPASFHPECL--GLEPPPEGKFYCEDC 41
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
835-1027 5.94e-06

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 51.86  E-value: 5.94e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  835 RAREESRMKRRKGRPPNVGSAEFLDNTDAKLLRKLQAQEIARQAAQIKLLRKLQKQEQARVAKEAKKQQAIMAAEEKRKQ 914
Cdd:COG1196    629 AARLEAALRRAVTLAGRLREVTLEGEGGSAGGSLTGGSRRELLAALLEAEAELEELAERLAEEELELEEALLAEEEEERE 708
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  915 KEQMKIIKQQEKI---KRIQQIRMEKELRAQQILEEKELRRQQAV-----LLKHQELERHRLDMERERRRqhvmL----M 982
Cdd:COG1196    709 LAEAEEERLEEELeeeALEEQLEAEREELLEELLEEEELLEEEALeelpePPDLEELERELERLEREIEA----LgpvnL 784
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*....
gi 1720399825  983 KAMEARKKAEE-KERLKQEKRDekrLNKERK-LEQ--RRLELEMAKELK 1027
Cdd:COG1196    785 LAIEEYEELEErYDFLSEQRED---LEEAREtLEEaiEEIDRETRERFL 830
PRK12704 PRK12704
phosphodiesterase; Provisional
912-1028 5.99e-06

phosphodiesterase; Provisional


Pssm-ID: 237177 [Multi-domain]  Cd Length: 520  Bit Score: 51.32  E-value: 5.99e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  912 RKQKEQMKIIKQQEKIKRIQQirmEKELRAQQILEEKELRRQQAVLLKHQELERhrldmERERRRQHVmlmKAMEARKKA 991
Cdd:PRK12704    25 RKKIAEAKIKEAEEEAKRILE---EAKKEAEAIKKEALLEAKEEIHKLRNEFEK-----ELRERRNEL---QKLEKRLLQ 93
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 1720399825  992 EEkERLKQ-----EKRDEKRLNKERKLEQRRLELE-MAKELKK 1028
Cdd:PRK12704    94 KE-ENLDRklellEKREEELEKKEKELEQKQQELEkKEEELEE 135
WSD pfam15613
Williams-Beuren syndrome DDT (WSD), D-TOX E motif; This family represents the combined ...
1339-1371 6.17e-06

Williams-Beuren syndrome DDT (WSD), D-TOX E motif; This family represents the combined alpha-helical module found in diverse eukaryotic chromatin proteins. Based on the Ioc3 structure, the N-terminus of this module is inferred to interact with nucleosomal linker DNA and the SLIDE domain of ISWI proteins. The resulting complex forms a protein ruler that measures out the spacing between two adjacent nucleosomes. The acidic residue from the GxD signature at the N-terminus is a major determinant of the interaction between the ISWI and WHIM motifs. The N-terminal portion also contacts the inter-nucleosomal linker DNA. The module shows a great domain architectural diversity and is often combined with other modified histone peptide recognizing and DNA binding domains, some of which discriminate methylated DNA. The WSD module constitutes the inter-nucleosomal linker DNA binding site in the major groove of DNA, and was first identified as WSD, the D-TOX E motif of plant homeodomains homologous with the mutant transcription factor causing Williams-Beuren syndrome in association with the DDT-domain.


Pssm-ID: 464775 [Multi-domain]  Cd Length: 69  Bit Score: 45.60  E-value: 6.17e-06
                           10        20        30
                   ....*....|....*....|....*....|....
gi 1720399825 1339 LRSMMFGQDRYRRRYWIL-PQCGGIFVEGMESGE 1371
Cdd:pfam15613    1 IRSLPLGRDRRYNRYWWFdPGTGRLFVESPSDGE 34
DUF4659 pfam15558
Domain of unknown function (DUF4659); This family of proteins is found in eukaryotes. Proteins ...
864-1022 6.86e-06

Domain of unknown function (DUF4659); This family of proteins is found in eukaryotes. Proteins in this family are typically between 427 and 674 amino acids in length. There are two completely conserved residues (D and I) that may be functionally important.


Pssm-ID: 464768 [Multi-domain]  Cd Length: 374  Bit Score: 50.81  E-value: 6.86e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  864 KLLRKLQAQEiARQAAQIKLLRKLQKQEQARvaKEAKKQQAIMAaEEKRKQKEQMKIIKQQEKIKRIQQIRMEKELRAQQ 943
Cdd:pfam15558   52 RRLLLQQSQE-QWQAEKEQRKARLGREERRR--ADRREKQVIEK-ESRWREQAEDQENQRQEKLERARQEAEQRKQCQEQ 127
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  944 ILEEKELRRQqavllKHQELERHRLdMERERRRQHVMLMKAMEARKKAEE---KERLKQEKRdEKRLNKERKLEQ--RRL 1018
Cdd:pfam15558  128 RLKEKEEELQ-----ALREQNSLQL-QERLEEACHKRQLKEREEQKKVQEnnlSELLNHQAR-KVLVDCQAKAEEllRRL 200

                   ....
gi 1720399825 1019 ELEM 1022
Cdd:pfam15558  201 SLEQ 204
PHD_TIF1gamma cd15624
PHD finger found in transcriptional intermediary factor 1 gamma (TIF1gamma); TIF1gamma, also ...
1903-1948 7.39e-06

PHD finger found in transcriptional intermediary factor 1 gamma (TIF1gamma); TIF1gamma, also termed tripartite motif-containing 33 (trim33), or ectodermin, or RFG7, or PTC7, is an E3-ubiquitin ligase that functions as a regulator of transforming growth factor beta (TGFbeta) signaling; it inhibits the Smad4-mediated TGFbeta response by interaction with Smad2/3 or ubiquitylation of Smad4. Moreover, TIF1gamma is an important regulator of transcription during hematopoiesis, as well as a key factor of tumorigenesis. Like other TIF1 family members, TIF1gamma also contains an intrinsic transcriptional silencing function. It can control erythroid cell fate by regulating transcription elongation. It can bind to the anaphase-promoting complex/cyclosome (APC/C) and promotes mitosis. TIF1gamma contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), a plant homeodomain (PHD) finger, followed by a bromodomain in the C-terminal region.


Pssm-ID: 277094  Cd Length: 46  Bit Score: 44.65  E-value: 7.39e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1720399825 1903 YCQICRKGDNeelLLLCDGCDKGCHTYCHRPKITTIPDGDWFCPAC 1948
Cdd:cd15624      1 WCAVCQNGGD---LLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFC 43
sbcc TIGR00618
exonuclease SbcC; All proteins in this family for which functions are known are part of an ...
864-1041 7.43e-06

exonuclease SbcC; All proteins in this family for which functions are known are part of an exonuclease complex with sbcD homologs. This complex is involved in the initiation of recombination to regulate the levels of palindromic sequences in DNA. 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: 129705 [Multi-domain]  Cd Length: 1042  Bit Score: 51.51  E-value: 7.43e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  864 KLLRKLQAQEiarQAAQIKLLRKLQKQEQA----RVAKEAKKQQAIMAAEEKRKQKEQMKIIKQQEK------IKRIQQI 933
Cdd:TIGR00618  229 KHLREALQQT---QQSHAYLTQKREAQEEQlkkqQLLKQLRARIEELRAQEAVLEETQERINRARKAaplaahIKAVTQI 305
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  934 RMEKElRAQQILEEKELRRQQAvLLKHQELERHRLDMERERRRQHVMLMKAMEARKKAEE----KERLKQEKRDEKRLNK 1009
Cdd:TIGR00618  306 EQQAQ-RIHTELQSKMRSRAKL-LMKRAAHVKQQSSIEEQRRLLQTLHSQEIHIRDAHEVatsiREISCQQHTLTQHIHT 383
                          170       180       190
                   ....*....|....*....|....*....|..
gi 1720399825 1010 ERKLEQRRLELEMAKELKKPKEDMCLADQKPL 1041
Cdd:TIGR00618  384 LQQQKTTLTQKLQSLCKELDILQREQATIDTR 415
COG2433 COG2433
Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only];
887-1026 8.25e-06

Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only];


Pssm-ID: 441980 [Multi-domain]  Cd Length: 644  Bit Score: 51.01  E-value: 8.25e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  887 LQKQEQARVAKEAKKQQAIMAAEEKRKQKEQMKIIKQQEKIKRIQQIRmeKELRAQqiLEEKElrrqqavllkhQELERH 966
Cdd:COG2433    382 LEELIEKELPEEEPEAEREKEHEERELTEEEEEIRRLEEQVERLEAEV--EELEAE--LEEKD-----------ERIERL 446
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  967 RLDMERERRRQHVMLMKAMEARKKAEEKERLKQEKRDEKRLNKERKLEQRRLElEMAKEL 1026
Cdd:COG2433    447 ERELSEARSEERREIRKDREISRLDREIERLERELEEERERIEELKRKLERLK-ELWKLE 505
CAF-1_p150 pfam11600
Chromatin assembly factor 1 complex p150 subunit, N-terminal; CAF-1_p150 is a polypeptide ...
902-1040 8.98e-06

Chromatin assembly factor 1 complex p150 subunit, N-terminal; CAF-1_p150 is a polypeptide subunit of CAF-1, which functions in depositing newly synthesized and acetylated histones H3/H4 into chromatin during DNA replication and repair. CAF-1_p150 includes the HP1 interaction site, the PEST, KER and ED interacting sites. CAF-1_p150 interacts directly with newly synthesized and acetylated histones through the acidic KER and ED domains. The PEST domain is associated with proteins that undergo rapid proteolysis.


Pssm-ID: 402959 [Multi-domain]  Cd Length: 164  Bit Score: 48.15  E-value: 8.98e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  902 QQAIMAAEEKRKQKEQmKIIKQQEKIKRIQQIRMEKELRAQQILEEKELRRQQAVllKHQELERHRLDMERERRRQHVML 981
Cdd:pfam11600    4 QKSVQSQEEKEKQRLE-KDKERLRRQLKLEAEKEEKERLKEEAKAEKERAKEEAR--RKKEEEKELKEKERREKKEKDEK 80
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1720399825  982 MKAMEARKKaEEKERLKQEKRDEKRLNKERKLEQRRLElEMAKELKKPKEDMCLADQKP 1040
Cdd:pfam11600   81 EKAEKLRLK-EEKRKEKQEALEAKLEEKRKKEEEKRLK-EEEKRIKAEKAEITRFLQKP 137
SMC_N pfam02463
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The ...
872-1031 9.23e-06

RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.


Pssm-ID: 426784 [Multi-domain]  Cd Length: 1161  Bit Score: 51.13  E-value: 9.23e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  872 QEIARQAAQIKLLRKLQKQEQARVAKE----AKKQQAIMAAEEKRKQK--EQMKIIKQQEKIKRIQQIRMEKELRaQQIL 945
Cdd:pfam02463  141 GGKIEIIAMMKPERRLEIEEEAAGSRLkrkkKEALKKLIEETENLAELiiDLEELKLQELKLKEQAKKALEYYQL-KEKL 219
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  946 EEKELRRQQAVLLKHQELERHRLDMERERRRQHVMLMKAMEarKKAEEKERLKQEKRDEKrlNKERKLEQRRLELEMAKE 1025
Cdd:pfam02463  220 ELEEEYLLYLDYLKLNEERIDLLQELLRDEQEEIESSKQEI--EKEEEKLAQVLKENKEE--EKEKKLQEEELKLLAKEE 295

                   ....*.
gi 1720399825 1026 LKKPKE 1031
Cdd:pfam02463  296 EELKSE 301
PHD1_BPTF cd15559
PHD finger 1 found in bromodomain and PHD finger-containing transcription factor (BPTF); BPTF, ...
1903-1948 1.18e-05

PHD finger 1 found in bromodomain and PHD finger-containing transcription factor (BPTF); BPTF, also termed nucleosome-remodeling factor subunit BPTF, or fetal Alz-50 clone 1 protein (FAC1), or fetal Alzheimer antigen, functions as a transcriptional regulator that exhibits altered expression and subcellular localization during neuronal development and neurodegenerative diseases such as Alzheimer's disease. It interacts with the human orthologue of the Kelch-like Ech-associated protein (Keap1). Its function and subcellular localization can be regulated by Keap1. Moreover, BPTF is a novel DNA-binding protein that recognizes the DNA sequence CACAACAC and represses transcription through this site in a phosphorylation-dependent manner. Furthermore, BPTF interacts with the Myc-associated zinc finger protein (ZF87/MAZ) and alters its transcriptional activity, which has been implicated in gene regulation in neurodegeneration. Some family members contain two or three plant homeodomain (PHD) fingers, which may be involved in complex formation with histone H3 trimethylated at K4 (H3K4me3). This family corresponds to the first PHD finger.


Pssm-ID: 277034 [Multi-domain]  Cd Length: 43  Bit Score: 43.94  E-value: 1.18e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1720399825 1903 YCQICRK-GDneelLLLCDGCDKGCHTYCHRPKITTIPDGDWFCPAC 1948
Cdd:cd15559      1 HCRVCHKlGD----LLCCETCSAVYHLECVDPPLEEVPEEDWQCEVC 43
ClassIIa_HDAC_Gln-rich-N cd10149
Glutamine-rich N-terminal helical domain of various Class IIa histone deacetylases (HDAC4, ...
895-981 1.50e-05

Glutamine-rich N-terminal helical domain of various Class IIa histone deacetylases (HDAC4, HDAC5 and HDCA9); This superfamily consists of a glutamine-rich N-terminal helical extension to certain Class IIa histone deacetylases (HDACs), including HDAC4, HDAC5 and HDAC9; it is missing in HDAC7. It is referred to as the glutamine-rich domain, and confers responsiveness to calcium signals and mediates interactions with transcription factors and cofactors. This domain is able to repress transcription independently of the HDAC's C-terminal, zinc-dependent catalytic domain. It has many intra- and inter-helical interactions which are possibly involved in reversible assembly and disassembly of proteins. HDACs regulate diverse cellular processes through enzymatic deacetylation of histone as well as non-histone proteins, in particular deacetylating N(6)-acetyl-lysine residues.


Pssm-ID: 197397 [Multi-domain]  Cd Length: 90  Bit Score: 45.45  E-value: 1.50e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  895 VAKEAKKQQAIMAAEEKRKQKEQMKII---KQQEKIKRIQQIRMEKELRAQQilEEKELRRQQAVLLKHQELERHRLDME 971
Cdd:cd10149      3 VLREQQLQQELLALKQQQQIQKQLLIAefqKQHENLTRQHEAQLQEHIKQQQ--EMLAIKQQQELLEKQRKLEQQRQEQE 80
                           90
                   ....*....|
gi 1720399825  972 RERRRQHVML 981
Cdd:cd10149     81 LEKQRREQQL 90
PHD_JADE3 cd15681
PHD finger found in protein Jade-3 and similar proteins; Jade-3, also termed PHD finger ...
1904-1949 1.63e-05

PHD finger found in protein Jade-3 and similar proteins; Jade-3, also termed PHD finger protein 16 (PHF16), is a plant homeodomain (PHD) zinc finger protein that is closely related to Jade-1, which functions as an essential regulator of multiple cell signaling pathways. Like Jade-1, Jade-3 is required for ING4 and ING5 to associate with histone acetyl transferase (HAT) HBO1 and Eaf6 to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. Jade-3 contains a canonical Cys4HisCys3 PHD domain followed by a non-canonical extended PHD (ePHD) domain, Cys2HisCys5HisCys2His, both of which are zinc-binding motifs. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277151 [Multi-domain]  Cd Length: 50  Bit Score: 43.81  E-value: 1.63e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1720399825 1904 CQICRKGDNEE--LLLLCDGCDKGCHTYCHrpKITTIPDGDWFCPACI 1949
Cdd:cd15681      2 CDVCRSPDSEEgnDMVFCDKCNICVHQACY--GILKVPEGSWLCRTCV 47
PHD_SPP1 cd16039
PHD finger found in Set1 complex component SPP1; Set1C component SPP1, also called COMPASS ...
1903-1948 1.73e-05

PHD finger found in Set1 complex component SPP1; Set1C component SPP1, also called COMPASS component Spp1, or Complex proteins associated with set1 protein Spp1, or Suppressor of PRP protein 1, is a component of the COMPASS complex that links histone methylation to initiation of meiotic recombination. It induces double-strand break (DSB) formation by tethering to recombinationally cold regions. SPP1 interacts with H3K4me3 and Mer2, a protein required for DSB formation, to promote recruitment of potential meiotic DSB sites to the chromosomal axis. SPP1 contains a PHD finger, a zinc binding motif.


Pssm-ID: 277186  Cd Length: 46  Bit Score: 43.62  E-value: 1.73e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1720399825 1903 YCqICRKGDNEELLLLCDGCDKGCHTYChrpkiTTIPDGD------WFCPAC 1948
Cdd:cd16039      1 YC-ICQKPDDGRWMIACDGCDEWYHFTC-----VNIPEADvelvdsFFCPPC 46
PHD_TIF1delta cd15625
PHD finger found in transcriptional intermediary factor 1 delta (TIF1delta); TIF1delta, also ...
1903-1948 1.84e-05

PHD finger found in transcriptional intermediary factor 1 delta (TIF1delta); TIF1delta, also termed tripartite motif-containing protein 66 (TRIM66), is a novel heterochromatin protein 1 (HP1)-interacting member of the transcriptional intermediary factor1 (TIF1) family expressed by elongating spermatids. Like other TIF1 proteins, TIF1delta displays a potent trichostatin A (TSA)-sensitive repression function; TSA is a specific inhibitor of histone deacetylases. Moreover, TIF1delta plays an important role in heterochromatin-mediated gene silencing during postmeiotic phases of spermatogenesis. It functions as a negative regulator of postmeiotic genes acting through HP1 isotype gamma (HP1gamma) complex formation and centromere association. TIF1delta contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), a plant homeodomain (PHD) finger, followed by a bromodomain in the C-terminal region.


Pssm-ID: 277095 [Multi-domain]  Cd Length: 49  Bit Score: 43.79  E-value: 1.84e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1720399825 1903 YCQICRKGDNeelLLLCDGCDKGCHTYCHRPKITTIPDGDWFCPAC 1948
Cdd:cd15625      4 FCAVCLNGGE---LLCCDRCPKVFHLSCHVPALLSFPVGEWVCTLC 46
PHD_TIF1beta cd15623
PHD finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also ...
1904-1948 2.13e-05

PHD finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also termed Kruppel-associated Box (KRAB)-associated protein 1 (KAP-1), or KRAB-interacting protein 1 (KRIP-1), or nuclear co-repressor KAP-1, or RING finger protein 96, or tripartite motif-containing protein 28 (TRIM28), or E3 SUMO-protein ligase TRIM28, acts as a nuclear co-repressor that plays a role in transcription and in DNA damage response. Upon DNA damage, the phosphorylation of KAP-1 on serine 824 by the ataxia telangiectasia-mutated (ATM) kinase enhances cell survival and facilitates chromatin relaxation and heterochromatic DNA repair. It also regulates CHD3 nucleosome remodeling during DNA double-strand break (DSB) response. Meanwhile, KAP-1 can be dephosphorylated by protein phosphatase PP4C in the DNA damage response. In addition, KAP-1 is a co-activator of the orphan nuclear receptor NGFI-B (or Nur77) and is involved in NGFI-B-dependent transcription. It is also a coiled-coil binding partner, substrate and activator of the c-Fes protein tyrosine kinase. TIF1-beta contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), which can interact with KRAB zinc finger proteins (KRAB-ZFPs), MDM2, MM1, C/EBPbeta, and mediates homo- and heterodimerization, a plant homeodomain (PHD) finger followed by a bromodomain in the C-terminal region, which interact with SETDB1, Mi-2alpha and other proteins to form complexes with histone deacetylase or methyltransferase activity.


Pssm-ID: 277093  Cd Length: 43  Bit Score: 43.25  E-value: 2.13e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1720399825 1904 CQICRKgdnEELLLLCDGCDKGCHTYCHRPKITTIPDGDWFCPAC 1948
Cdd:cd15623      2 CRVCQK---AGALVMCDQCEFCFHLDCHLPALQEVPGEDWKCLLC 43
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
848-1025 2.23e-05

Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 49.77  E-value: 2.23e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  848 RPPNVGSAEFLDNTDAKLLRKLQAQEIARQAAQIKLLRKLQKQEQARVAKEAKKQQAIMAaeEKRKQKEQMKIIKQQEKI 927
Cdd:COG4717    295 REKASLGKEAEELQALPALEELEEEELEELLAALGLPPDLSPEELLELLDRIEELQELLR--EAEELEEELQLEELEQEI 372
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  928 KRI---QQIRMEKELR--AQQILEEKELRRQQAVLlkHQELERHRLDME-----------RERRRQHVMLMKAMEARKKA 991
Cdd:COG4717    373 AALlaeAGVEDEEELRaaLEQAEEYQELKEELEEL--EEQLEELLGELEellealdeeelEEELEELEEELEELEEELEE 450
                          170       180       190
                   ....*....|....*....|....*....|....*.
gi 1720399825  992 --EEKERLKQEKrdeKRLNKERKLEQRRLELEMAKE 1025
Cdd:COG4717    451 lrEELAELEAEL---EQLEEDGELAELLQELEELKA 483
Bromodomain_1 cd05494
Bromodomain; uncharacterized subfamily. Bromodomains are found in many chromatin-associated ...
2035-2082 2.33e-05

Bromodomain; uncharacterized subfamily. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.


Pssm-ID: 99926 [Multi-domain]  Cd Length: 114  Bit Score: 45.51  E-value: 2.33e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1720399825 2035 DLALCSMILTEMETH---EDSWPFLLPVN--LKLVPGYKKVIKKPMDFSTIRE 2082
Cdd:cd05494      1 DYEALERVLRELKRHrrnEDAWPFLEPVNppRRGAPDYRDVIKRPMSFGTKVN 53
GBP_C cd16269
Guanylate-binding protein, C-terminal domain; Guanylate-binding protein (GBP), C-terminal ...
867-967 2.48e-05

Guanylate-binding protein, C-terminal domain; Guanylate-binding protein (GBP), C-terminal domain. Guanylate-binding proteins (GBPs) are synthesized after activation of the cell by interferons. The biochemical properties of GBPs are clearly different from those of Ras-like and heterotrimeric GTP-binding proteins. They bind guanine nucleotides with low affinity (micromolar range), are stable in their absence, and have a high turnover GTPase. In addition to binding GDP/GTP, they have the unique ability to bind GMP with equal affinity and hydrolyze GTP not only to GDP, but also to GMP. This C-terminal domain has been shown to mediate inhibition of endothelial cell proliferation by inflammatory cytokines.


Pssm-ID: 293879 [Multi-domain]  Cd Length: 291  Bit Score: 48.34  E-value: 2.48e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  867 RKLQAQEIARQAAQIKllRKLQKQEQARVAKEAKKQQAIMAAEEKRKQK--EQMKIIKQQEKIKRIQQIR--MEKELRAQ 942
Cdd:cd16269    191 QALTEKEKEIEAERAK--AEAAEQERKLLEEQQRELEQKLEDQERSYEEhlRQLKEKMEEERENLLKEQEraLESKLKEQ 268
                           90       100
                   ....*....|....*....|....*
gi 1720399825  943 QILEEKELrRQQAVLLKhQELERHR 967
Cdd:cd16269    269 EALLEEGF-KEQAELLQ-EEIRSLK 291
SMC_N pfam02463
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The ...
856-1019 2.50e-05

RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.


Pssm-ID: 426784 [Multi-domain]  Cd Length: 1161  Bit Score: 49.58  E-value: 2.50e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  856 EFLDNTDAKLLRKLQAQEIARQAAQIKLLRKLQKQEQARVAKEAKKQQAIMAAEEKRKQKEQMKIIKQQEKIKRIQQIRM 935
Cdd:pfam02463  861 EEITKEELLQELLLKEEELEEQKLKDELESKEEKEKEEKKELEEESQKLNLLEEKENEIEERIKEEAEILLKYEEEPEEL 940
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  936 ----EKELRAQQILEEKELRRQQAVLLKHQELERHRLDMERERRRQHvmlmkamEARKKAEEKERLKQEKRDEKRLNKER 1011
Cdd:pfam02463  941 lleeADEKEKEENNKEEEEERNKRLLLAKEELGKVNLMAIEEFEEKE-------ERYNKDELEKERLEEEKKKLIRAIIE 1013

                   ....*...
gi 1720399825 1012 KLEQRRLE 1019
Cdd:pfam02463 1014 ETCQRLKE 1021
RIB43A pfam05914
RIB43A; This family consists of several RIB43A-like eukaryotic proteins. Ciliary and flagellar ...
908-1008 2.63e-05

RIB43A; This family consists of several RIB43A-like eukaryotic proteins. Ciliary and flagellar microtubules contain a specialized set of protofilaments, termed ribbons, that are composed of tubulin and several associated proteins. RIB43A was first characterized in the unicellular biflagellate, Chlamydomonas reinhardtii although highly related sequences are present in several higher eukaryotes including humans. The function of this protein is unknown although the structure of RIB43A and its association with the specialized protofilament ribbons and with basal bodies is relevant to the proposed role of ribbons in forming and stabilising doublet and triplet microtubules and in organizing their three-dimensional structure. Human RIB43A homologs could represent a structural requirement in centriole replication in dividing cells.


Pssm-ID: 461780 [Multi-domain]  Cd Length: 372  Bit Score: 48.74  E-value: 2.63e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  908 AEEKRKQKEQMK--IIKQQEKikriQQIRMEKELRAQQILEEKELRRQQAVLlkhqELERhrldMERERRRQHVMLMKAM 985
Cdd:pfam05914  143 EERKKLQQEQMRewLEQQIEE----KKQAEEEEKHAELLYDQKRLERDRRAL----ELAK----LEEECRRAVNAATKNF 210
                           90       100
                   ....*....|....*....|...
gi 1720399825  986 EARKKAEEKERLKQEKRDEKRLN 1008
Cdd:pfam05914  211 NQALAAEQAERRRLEKRQEQEDN 233
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
835-1026 3.00e-05

Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 49.00  E-value: 3.00e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  835 RAREESRMKRRKGRPPNVGSAEFLDNTD--AKLLRKLQAQEIARQAAQIKLLRKLQKQ--EQARVAKEAKKQQAIMAAEE 910
Cdd:COG4717    317 EEEELEELLAALGLPPDLSPEELLELLDriEELQELLREAEELEEELQLEELEQEIAAllAEAGVEDEEELRAALEQAEE 396
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  911 KRKQKEQMKIIKQQekikrIQQIRmEKELRAQQILEEKELRRQQAVLLKHQELERHRLDMERERRRQHVMLMKAMEARKK 990
Cdd:COG4717    397 YQELKEELEELEEQ-----LEELL-GELEELLEALDEEELEEELEELEEELEELEEELEELREELAELEAELEQLEEDGE 470
                          170       180       190
                   ....*....|....*....|....*....|....*.
gi 1720399825  991 AEEKERLKQEKRDEKrlnkeRKLEQRRLELEMAKEL 1026
Cdd:COG4717    471 LAELLQELEELKAEL-----RELAEEWAALKLALEL 501
WSD pfam15613
Williams-Beuren syndrome DDT (WSD), D-TOX E motif; This family represents the combined ...
1682-1721 3.08e-05

Williams-Beuren syndrome DDT (WSD), D-TOX E motif; This family represents the combined alpha-helical module found in diverse eukaryotic chromatin proteins. Based on the Ioc3 structure, the N-terminus of this module is inferred to interact with nucleosomal linker DNA and the SLIDE domain of ISWI proteins. The resulting complex forms a protein ruler that measures out the spacing between two adjacent nucleosomes. The acidic residue from the GxD signature at the N-terminus is a major determinant of the interaction between the ISWI and WHIM motifs. The N-terminal portion also contacts the inter-nucleosomal linker DNA. The module shows a great domain architectural diversity and is often combined with other modified histone peptide recognizing and DNA binding domains, some of which discriminate methylated DNA. The WSD module constitutes the inter-nucleosomal linker DNA binding site in the major groove of DNA, and was first identified as WSD, the D-TOX E motif of plant homeodomains homologous with the mutant transcription factor causing Williams-Beuren syndrome in association with the DDT-domain.


Pssm-ID: 464775 [Multi-domain]  Cd Length: 69  Bit Score: 43.68  E-value: 3.08e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 1720399825 1682 EEMQFGWWRIID-PEDLKTLLKVLHLRGIREKALQKQIQKH 1721
Cdd:pfam15613   28 ESPSDGEWGVYSsKEQLDALIASLNPRGVRESALKEALEKI 68
MAP7 pfam05672
MAP7 (E-MAP-115) family; The organization of microtubules varies with the cell type and is ...
891-1043 3.18e-05

MAP7 (E-MAP-115) family; The organization of microtubules varies with the cell type and is presumably controlled by tissue-specific microtubule-associated proteins (MAPs). The 115-kDa epithelial MAP (E-MAP-115/MAP7) has been identified as a microtubule-stabilising protein predominantly expressed in cell lines of epithelial origin. The binding of this microtubule associated protein is nucleotide independent.


Pssm-ID: 461709 [Multi-domain]  Cd Length: 153  Bit Score: 46.19  E-value: 3.18e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  891 EQARVAKEAKKQQAimaaEEKRKQKEQMKIIKQQEKikriqqiRMEKELRAQQILEEKELRRQQAvllkhQELERHRLDM 970
Cdd:pfam05672   10 EEAARILAEKRRQA----REQREREEQERLEKEEEE-------RLRKEELRRRAEEERARREEEA-----RRLEEERRRE 73
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1720399825  971 ERERRRqhvmlmKAMEARKKAEEKERLKQEKRDEKRLNKERKL----EQRRLELEmakELKKPKEDMCLADQKPLPE 1043
Cdd:pfam05672   74 EEERQR------KAEEEAEEREQREQEEQERLQKQKEEAEAKAreeaERQRQERE---KIMQQEEQERLERKKRIEE 141
Caldesmon pfam02029
Caldesmon;
892-1040 3.24e-05

Caldesmon;


Pssm-ID: 460421 [Multi-domain]  Cd Length: 495  Bit Score: 48.71  E-value: 3.24e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  892 QARVAKEAKKQQA-IMAAEEKRKQKEQMKIIKQQEKIKRIQQIRMEKELRAQQI-LEEKELRRQQAVLLKHQ----ELER 965
Cdd:pfam02029  200 QKRGHPEVKSQNGeEEVTKLKVTTKRRQGGLSQSQEREEEAEVFLEAEQKLEELrRRRQEKESEEFEKLRQKqqeaELEL 279
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1720399825  966 HRLDMERERRRQhvmLMKAMEARKKAEEKERLKQEKRDEKRLNKErkLEQRRleLEMAKELKKPKEDMCLADQKP 1040
Cdd:pfam02029  280 EELKKKREERRK---LLEEEEQRRKQEEAERKLREEEEKRRMKEE--IERRR--AEAAEKRQKLPEDSSSEGKKP 347
Bromo_RACK7 cd05508
Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) ...
2054-2114 3.39e-05

Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) was identified as a potential tumor suppressor genes, it shares domain architecture with BS69/ZMYND11; both have been implicated in the regulation of cellular proliferation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99940  Cd Length: 99  Bit Score: 44.68  E-value: 3.39e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1720399825 2054 PFLLPVNLKLVPGYKKVIKKPMDFSTIREKLNNGQYPNFETFALDVRLVFDNCETFNEDDS 2114
Cdd:cd05508     22 PFLKPVDLEQFPDYAQYVFKPMDLSTLEKNVRKKAYGSTDAFLADAKWILHNAIIYNGGDH 82
Bromo_polybromo_II cd05517
Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which ...
2062-2130 3.49e-05

Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99948  Cd Length: 103  Bit Score: 44.74  E-value: 3.49e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1720399825 2062 KLVPGYKKVIKKPMDFSTIREKLNNGQYPNFETFALDVRLVFDNCETFNEDDSDIGRAGHSMRKYFEKK 2130
Cdd:cd05517     34 VLYPDYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKTFNEPGSQVYKDANAIKKIFTAK 102
PHD_PRKCBP1 cd15538
PHD finger found in protein kinase C-binding protein 1 (PRKCBP1); PRKCBP1, also termed ...
1903-1948 3.63e-05

PHD finger found in protein kinase C-binding protein 1 (PRKCBP1); PRKCBP1, also termed cutaneous T-cell lymphoma-associated antigen se14-3 (CTCL-associated antigen se14-3), or Rack7, or zinc finger MYND domain-containing protein 8 (ZMYND8), is a novel receptor for activated C-kinase (RACK)-like protein that may play an important role in the activation and regulation of PKC-beta I, and the PKC signaling cascade. It also has been identified as a formin homology-2-domain containing protein 1 (FHOD1)-binding protein that may be involved in FHOD1-regulated actin polymerization and transcription. Moreover, PRKCBP1 may function as a REST co-repressor 2 (RCOR2) interacting factor; the RCOR2/ZMYND8 complex which might be involved in the regulation of neural differentiation. PRKCBP1 contains a plant homeodomain (PHD) finger, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain.


Pssm-ID: 277013  Cd Length: 41  Bit Score: 42.70  E-value: 3.63e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1720399825 1903 YCQICRKGDNeelLLLCDGCDKGCHTYCHRPKITtiPDGDWFCPAC 1948
Cdd:cd15538      1 FCWRCHKEGQ---VLCCSLCPRVYHKKCLKLTSE--PDEDWVCPEC 41
Mitofilin pfam09731
Mitochondrial inner membrane protein; Mitofilin controls mitochondrial cristae morphology. ...
877-1023 3.97e-05

Mitochondrial inner membrane protein; Mitofilin controls mitochondrial cristae morphology. Mitofilin is enriched in the narrow space between the inner boundary and the outer membranes, where it forms a homotypic interaction and assembles into a large multimeric protein complex. The first 78 amino acids contain a typical amino-terminal-cleavable mitochondrial presequence rich in positive-charged and hydroxylated residues and a membrane anchor domain. In addition, it has three centrally located coiled coil domains.


Pssm-ID: 430783 [Multi-domain]  Cd Length: 618  Bit Score: 48.60  E-value: 3.97e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  877 QAAQIKLLRkLQKQEQARVAKEAKKQQA---------IMAAEEKRKQKEQMKIIKQQEKIKRIQQiRMEKELRAQqilee 947
Cdd:pfam09731  297 DQLSKKLAE-LKKREEKHIERALEKQKEeldklaeelSARLEEVRAADEAQLRLEFEREREEIRE-SYEEKLRTE----- 369
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1720399825  948 keLRRQqavllkHQELERHRLDMERERRRQhvmlmkaMEARKKAEEKERLKQEKrdEKRLNKERKLEQRRLELEMA 1023
Cdd:pfam09731  370 --LERQ------AEAHEEHLKDVLVEQEIE-------LQREFLQDIKEKVEEER--AGRLLKLNELLANLKGLEKA 428
PKK pfam12474
Polo kinase kinase; This domain family is found in eukaryotes, and is approximately 140 amino ...
914-1028 4.26e-05

Polo kinase kinase; This domain family is found in eukaryotes, and is approximately 140 amino acids in length. The family is found in association with pfam00069. Polo-like kinase 1 (Plx1) is essential during mitosis for the activation of Cdc25C, for spindle assembly, and for cyclin B degradation. This family is Polo kinase kinase (PKK) which phosphorylates Polo kinase and Polo-like kinase to activate them. PKK is a serine/threonine kinase.


Pssm-ID: 463600 [Multi-domain]  Cd Length: 139  Bit Score: 45.24  E-value: 4.26e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  914 QKEQMKIIKQQEkikRIQ-QIRMEKEL----RAQQILEEKeLRRQQAV----LLKHQELERH-RLDMERERRRQHVMLMK 983
Cdd:pfam12474    4 QKEQQKDRFEQE---RQQlKKRYEKELeqleRQQKQQIEK-LEQRQTQelrrLPKRIRAEQKkRLKMFRESLKQEKKELK 79
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1720399825  984 AMEAR-KKAEEKERLKQ-------EKRDEKRLNKERKLEQRRLELEMAKELKK 1028
Cdd:pfam12474   80 QEVEKlPKFQRKEAKRQrkeelelEQKHEELEFLQAQSEALERELQQLQNEKR 132
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
888-1052 4.35e-05

chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274009 [Multi-domain]  Cd Length: 1164  Bit Score: 48.91  E-value: 4.35e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  888 QKQEQAR-VAKEAKKQQAIMAAEEKRKQKEQMKIIKQQEKIKRIQQIRME-----KELRAQQILEEKELRRQQAVLLKHQ 961
Cdd:TIGR02169  795 EIQAELSkLEEEVSRIEARLREIEQKLNRLTLEKEYLEKEIQELQEQRIDlkeqiKSIEKEIENLNGKKEELEEELEELE 874
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  962 ----ELERHRLDMERERRRqhvmlmkaMEARKKAEEKERLKQE-KRDEKRLNKERKLEQRRLELEMAKELKKPKEdmclA 1036
Cdd:TIGR02169  875 aalrDLESRLGDLKKERDE--------LEAQLRELERKIEELEaQIEKKRKRLSELKAKLEALEEELSEIEDPKG----E 942
                          170
                   ....*....|....*.
gi 1720399825 1037 DQKPLPEWPRIPGLVL 1052
Cdd:TIGR02169  943 DEEIPEEELSLEDVQA 958
Myosin_tail_1 pfam01576
Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and ...
858-1032 4.37e-05

Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and four light chains it is a fundamental contractile protein found in all eukaryote cell types. This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then assemble into the macromolecular thick filament. The coiled-coil region provides the structural backbone the thick filament.


Pssm-ID: 460256 [Multi-domain]  Cd Length: 1081  Bit Score: 49.02  E-value: 4.37e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  858 LDNTDAKLL--RKLQAQEIARQAAQI-------KLLRKLQ-KQE------QARVAKEAKKQQAImaaeEKRKQK------ 915
Cdd:pfam01576  143 LEDQNSKLSkeRKLLEERISEFTSNLaeeeekaKSLSKLKnKHEamisdlEERLKKEEKGRQEL----EKAKRKlegest 218
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  916 ---EQMKIIKQQEKIKRIQQIRMEKELRAQQILEEKELRRQQAVLLKHQELERHRLDMERERRRQHVMLMKAMEARKK-A 991
Cdd:pfam01576  219 dlqEQIAELQAQIAELRAQLAKKEEELQAALARLEEETAQKNNALKKIRELEAQISELQEDLESERAARNKAEKQRRDlG 298
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|..
gi 1720399825  992 EEKERLKQEKRDE-KRLNKERKLEQRRlELEMAkELKKPKED 1032
Cdd:pfam01576  299 EELEALKTELEDTlDTTAAQQELRSKR-EQEVT-ELKKALEE 338
Borrelia_P83 pfam05262
Borrelia P83/100 protein; This family consists of several Borrelia P83/P100 antigen proteins.
866-1031 5.15e-05

Borrelia P83/100 protein; This family consists of several Borrelia P83/P100 antigen proteins.


Pssm-ID: 114011 [Multi-domain]  Cd Length: 489  Bit Score: 48.08  E-value: 5.15e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  866 LRKLQAQEIARQAAQIKLLRKLQKQEQARVAKEAKKQQAimAAEEKRKQKEQmkiiKQQEKIKriqqirMEKELRAQQIL 945
Cdd:pfam05262  203 LKERESQEDAKRAQQLKEELDKKQIDADKAQQKADFAQD--NADKQRDEVRQ----KQQEAKN------LPKPADTSSPK 270
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  946 EEKELRRQQAvllkhQELERHRLDMErerrrqhvmlmKAMEARKKAEEK--ERLKQEKRDEKRLNKERKLEQRRLELEMA 1023
Cdd:pfam05262  271 EDKQVAENQK-----REIEKAQIEIK-----------KNDEEALKAKDHkaFDLKQESKASEKEAEDKELEAQKKREPVA 334

                   ....*...
gi 1720399825 1024 KELKKPKE 1031
Cdd:pfam05262  335 EDLQKTKP 342
ARGLU pfam15346
Arginine and glutamate-rich 1; ARGLU, arginine and glutamate-rich 1 protein family, is ...
888-1039 5.93e-05

Arginine and glutamate-rich 1; ARGLU, arginine and glutamate-rich 1 protein family, is required for the oestrogen-dependent expression of ESR1 target genes. It functions in cooperation with MED1. The family of proteins is found in eukaryotes.


Pssm-ID: 405931 [Multi-domain]  Cd Length: 151  Bit Score: 45.43  E-value: 5.93e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  888 QKQEQARVAKEAKKQqaimaAEEKRKQKEQMKIIKQQEKIKRIQQIRMEkelRAQQILEEKELRrqqavllkhqELERHR 967
Cdd:pfam15346    1 KEAESKLLEEETARR-----VEEAVAKRVEEELEKRKDEIEAEVERRVE---EARKIMEKQVLE----------ELERER 62
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1720399825  968 LDMERERRRqhvmlmKAMEARKKAEEKERLKQEKRDE-----KRLNKER--KLEQRRLELEMAKELKKPKEDMCLADQK 1039
Cdd:pfam15346   63 EAELEEERR------KEEEERKKREELERILEENNRKieeaqRKEAEERlaMLEEQRRMKEERQRREKEEEEREKREQQ 135
GBP_C pfam02841
Guanylate-binding protein, C-terminal domain; Transcription of the anti-viral ...
881-1010 6.11e-05

Guanylate-binding protein, C-terminal domain; Transcription of the anti-viral guanylate-binding protein (GBP) is induced by interferon-gamma during macrophage induction. This family contains GBP1 and GPB2, both GTPases capable of binding GTP, GDP and GMP.


Pssm-ID: 460721 [Multi-domain]  Cd Length: 297  Bit Score: 47.28  E-value: 6.11e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  881 IKLLRKLQKQEQARVAKEAKKQQAIMAAEEKRKQKEQMKIikQQEKIKRIQQIRMEKELRAQQILEEKELRRQQAVLLKH 960
Cdd:pfam02841  172 VKAEEVLQEFLQSKEAVEEAILQTDQALTAKEKAIEAERA--KAEAAEAEQELLREKQKEEEQMMEAQERSYQEHVKQLI 249
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1720399825  961 QELERHRLDMERERRRqhvmlmkaMEARKKAEEKERLKQEKRDE-KRLNKE 1010
Cdd:pfam02841  250 EKMEAEREQLLAEQER--------MLEHKLQEQEELLKEGFKTEaESLQKE 292
PHD_PHF21B cd15524
PHD finger found in PHD finger protein 21B (PHF21B); PHF21B is a plant homeodomain (PHD) ...
1903-1948 6.32e-05

PHD finger found in PHD finger protein 21B (PHF21B); PHF21B is a plant homeodomain (PHD) finger-containing protein whose biological function remains unclear. It shows high sequence similarity with PHF21A, which is associated with LSD1, a lysine (K)-specific histone demethylase and inhibits LSD1-mediated histone demethylation in vitro. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins.


Pssm-ID: 276999 [Multi-domain]  Cd Length: 43  Bit Score: 42.19  E-value: 6.32e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1720399825 1903 YCQICRKGDNeelLLLCDGCDKGCHTYCHRPKITTIPDGDWFCPAC 1948
Cdd:cd15524      1 HCAACKRGGN---LQPCGTCPRAYHLDCLDPPLKTAPKGVWVCPKC 43
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
828-1024 6.44e-05

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 48.39  E-value: 6.44e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  828 PPNPDRPRAREESRMKRRKGRPPNVGSAEFLDNTDAK--LLRKLQAQEIARQAAQIKLLRKLQKQEQARVAKEAKKQQAI 905
Cdd:COG1196    578 PLDKIRARAALAAALARGAIGAAVDLVASDLREADARyyVLGDTLLGRTLVAARLEAALRRAVTLAGRLREVTLEGEGGS 657
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  906 MAAEEKRKQKEQMKIIKQQEKIKRIQQIRMEKELRAQQILEEKELRRQQAVLLKHQELERHRLDMERERRRQHVMLMKAM 985
Cdd:COG1196    658 AGGSLTGGSRRELLAALLEAEAELEELAERLAEEELELEEALLAEEEEERELAEAEEERLEEELEEEALEEQLEAEREEL 737
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|.
gi 1720399825  986 EARKKAEEKERLKQEKRDEKRLNKERKLEQR--RLELEMAK 1024
Cdd:COG1196    738 LEELLEEEELLEEEALEELPEPPDLEELEREleRLEREIEA 778
ERM_helical pfam20492
Ezrin/radixin/moesin, alpha-helical domain; The ERM family consists of three closely-related ...
866-970 7.69e-05

Ezrin/radixin/moesin, alpha-helical domain; The ERM family consists of three closely-related proteins, ezrin, radixin and moesin. Ezrin was first identified as a constituent of microvilli, radixin as a barbed, end-capping actin-modulating protein from isolated junctional fractions, and moesin as a heparin binding protein. A tumour suppressor molecule responsible for neurofibromatosis type 2 (NF2) is highly similar to ERM proteins and has been designated merlin (moesin-ezrin-radixin-like protein). ERM molecules contain 3 domains, an N-terminal globular domain, an extended alpha-helical domain and a charged C-terminal domain (pfam00769). Ezrin, radixin and merlin also contain a polyproline linker region between the helical and C-terminal domains. The N-terminal domain is highly conserved and is also found in merlin, band 4.1 proteins and members of the band 4.1 superfamily, designated the FERM domain. ERM proteins crosslink actin filaments with plasma membranes. They co-localize with CD44 at actin filament plasma membrane interaction sites, associating with CD44 via their N-terminal domains and with actin filaments via their C-terminal domains. This is the alpha-helical domain, which is involved in intramolecular masking of protein-protein interaction sites, regulating the activity of this proteins.


Pssm-ID: 466641 [Multi-domain]  Cd Length: 120  Bit Score: 44.14  E-value: 7.69e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  866 LRKLQAQ-EIARQAAQIKLLRKLQKQEQARVAKEAKK--QQAIMAAEEKRKQKEQMKIIKQQEKIKRIQQIRmEKELRAQ 942
Cdd:pfam20492   15 LKQYEEEtKKAQEELEESEETAEELEEERRQAEEEAErlEQKRQEAEEEKERLEESAEMEAEEKEQLEAELA-EAQEEIA 93
                           90       100
                   ....*....|....*....|....*...
gi 1720399825  943 QILEEKELRRQQAVLLKHqELERHRLDM 970
Cdd:pfam20492   94 RLEEEVERKEEEARRLQE-ELEEAREEE 120
COG4913 COG4913
Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];
863-1033 8.12e-05

Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];


Pssm-ID: 443941 [Multi-domain]  Cd Length: 1089  Bit Score: 47.99  E-value: 8.12e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  863 AKLLRKLQAQEIARQAAQ-------IKLLRKLQKQEQARVAK-EAKKQQAIMAAEEKRKQKEQMKIIKQQEKIKRIQQIr 934
Cdd:COG4913    265 AAARERLAELEYLRAALRlwfaqrrLELLEAELEELRAELARlEAELERLEARLDALREELDELEAQIRGNGGDRLEQL- 343
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  935 mEKELRAqqiLEEKELRRQQavllKHQELER--HRLDME--------RERRRQHVMLMKAMEARKKAEEKE------RLK 998
Cdd:COG4913    344 -EREIER---LERELEERER----RRARLEAllAALGLPlpasaeefAALRAEAAALLEALEEELEALEEAlaeaeaALR 415
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*
gi 1720399825  999 QEKRDEKRLNKERK-LEQRR---------LELEMAKELKKPKEDM 1033
Cdd:COG4913    416 DLRRELRELEAEIAsLERRKsniparllaLRDALAEALGLDEAEL 460
PRK11637 PRK11637
AmiB activator; Provisional
872-1017 8.41e-05

AmiB activator; Provisional


Pssm-ID: 236942 [Multi-domain]  Cd Length: 428  Bit Score: 47.38  E-value: 8.41e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  872 QEIARQAAQIKLLRKLQKQEQARVAKE---AKKQ------QAIMAAEE-KRKQKEQMKI----IKQQEKIKRIQQIRmeK 937
Cdd:PRK11637   103 KQIDELNASIAKLEQQQAAQERLLAAQldaAFRQgehtglQLILSGEEsQRGERILAYFgylnQARQETIAELKQTR--E 180
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  938 ELRAQ-QILEEKelRRQQAVLLKHQELERHRLDMERERRR--------------QHVMLMKAME-------ARKKAEEKE 995
Cdd:PRK11637   181 ELAAQkAELEEK--QSQQKTLLYEQQAQQQKLEQARNERKktltglesslqkdqQQLSELRANEsrlrdsiARAEREAKA 258
                          170       180
                   ....*....|....*....|..
gi 1720399825  996 RLKQEKRDEKRLNKERKLEQRR 1017
Cdd:PRK11637   259 RAEREAREAARVRDKQKQAKRK 280
ClassIIa_HDAC9_Gln-rich-N cd10163
Glutamine-rich N-terminal helical domain of HDAC9, a Class IIa histone deacetylase; This ...
895-981 8.61e-05

Glutamine-rich N-terminal helical domain of HDAC9, a Class IIa histone deacetylase; This family consists of the glutamine-rich domain of histone deacetylase 9 (HDAC9). It belongs to a superfamily that consists of the glutamine-rich N-terminal helical extension to certain Class IIa histone deacetylases (HDACs), including HDAC4, HDAC5 and HDCA9; it is missing from HDAC7. This domain confers responsiveness to calcium signals and mediates interactions with transcription factors and cofactors, and it is able to repress transcription independently of the HDAC C-terminal, zinc-dependent catalytic domain. It has many intra- and inter-helical interactions which are possibly involved in reversible assembly and disassembly of proteins. HDACs regulate diverse cellular processes through enzymatic deacetylation of histone as well as non-histone proteins, in particular deacetylating N(6)-acetyl-lysine residues.


Pssm-ID: 197399 [Multi-domain]  Cd Length: 90  Bit Score: 43.20  E-value: 8.61e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  895 VAKEAKKQQAIMAAEEKRKQKEQMKII---KQQEKIKRIQQIRMEKELRAQQilEEKELRRQQAVLLKHQELERHRLDME 971
Cdd:cd10163      3 TVREKQLQQELLLIQQQQQIQKQLLIAefqKQHENLTRQHQAQLQEHLKLQQ--ELLAMKQQQELLEKEQKLEQQRQEQE 80
                           90
                   ....*....|
gi 1720399825  972 RERRRQHVML 981
Cdd:cd10163     81 LERHRREQQL 90
PHD_BRPF cd15572
PHD finger found in bromodomain and PHD finger-containing (BRPF) proteins; The family of BRPF ...
1904-1953 9.25e-05

PHD finger found in bromodomain and PHD finger-containing (BRPF) proteins; The family of BRPF proteins includes BRPF1, BRD1/BRPF2, and BRPF3. They are scaffold proteins that form monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complexes with other regulatory subunits, such as inhibitor of growth 5 (ING5) and Esa1-associated factor 6 ortholog (EAF6). BRPF proteins have multiple domains, including a canonical Cys4HisCys3 plant homeodomain (PHD) zinc finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. PHD and ePHD fingers both bind to lysine 4 of histone H3 (K4H3), bromodomains interact with acetylated lysines on N-terminal tails of histones and other proteins, and PWWP domains show histone-binding and chromatin association properties. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277047 [Multi-domain]  Cd Length: 54  Bit Score: 41.83  E-value: 9.25e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1720399825 1904 CQICRKGD--NEELLLLCDGCDKGCHTYCHrpKITTIPDGDWFCPACISKAS 1953
Cdd:cd15572      4 CCICLDGEcqNSNVILFCDMCNLAVHQECY--GVPYIPEGQWLCRRCLQSPS 53
GBP_C pfam02841
Guanylate-binding protein, C-terminal domain; Transcription of the anti-viral ...
838-973 1.09e-04

Guanylate-binding protein, C-terminal domain; Transcription of the anti-viral guanylate-binding protein (GBP) is induced by interferon-gamma during macrophage induction. This family contains GBP1 and GPB2, both GTPases capable of binding GTP, GDP and GMP.


Pssm-ID: 460721 [Multi-domain]  Cd Length: 297  Bit Score: 46.51  E-value: 1.09e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  838 EESRMKRRKGrppnVGSAEFLDntdaKLLRKLQAQEIARQAAQIKLLRKLQKQEQARVAKEAKKQQAIMAAEEKRKQKEQ 917
Cdd:pfam02841  162 AKYNQVPRKG----VKAEEVLQ----EFLQSKEAVEEAILQTDQALTAKEKAIEAERAKAEAAEAEQELLREKQKEEEQM 233
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1720399825  918 M--KIIKQQEKIKRIQQiRMEKElRAQQILE-----EKELRRQQAVLlkHQELERHRLDMERE 973
Cdd:pfam02841  234 MeaQERSYQEHVKQLIE-KMEAE-REQLLAEqermlEHKLQEQEELL--KEGFKTEAESLQKE 292
CR6_interact pfam10147
Growth arrest and DNA-damage-inducible proteins-interacting protein 1; Members of this family ...
828-1005 1.10e-04

Growth arrest and DNA-damage-inducible proteins-interacting protein 1; Members of this family of proteins act as negative regulators of G1 to S cell cycle phase progression by inhibiting cyclin-dependent kinases. Inhibitory effects are additive with GADD45 proteins but occur also in the absence of GADD45 proteins. Furthermore, they act as a repressor of the orphan nuclear receptor NR4A1 by inhibiting AB domain-mediated transcriptional activity.


Pssm-ID: 431088 [Multi-domain]  Cd Length: 204  Bit Score: 45.61  E-value: 1.10e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  828 PPNPDRPRA-------REESRMKRRKGRPPNVGSAEFLDNTDAklLRKLQAQEIARQAAQIKLLRKLQKQEQARVAKEAK 900
Cdd:pfam10147   32 GVPPRRQPDswiqlteKYARKQFGRYGAKSGVNPKSLFPSAEQ--LEELEAEEREWYPSLAQMLESNRAQKAEKEARRQA 109
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  901 KQQAImaaEEKRKQKEQMKIIKQQEKIKRIQQIRMEKELRAqqileekelRRQQAVllkhQELERHRLDMERERrrqhvm 980
Cdd:pfam10147  110 REQEI---AKKMAKMPQWIADWNAQKAKREAEAQAAKERKE---------RLVAEA----REHFGFKVDPRDER------ 167
                          170       180
                   ....*....|....*....|....*
gi 1720399825  981 lMKAMEARKKAEEKERLKQEKRDEK 1005
Cdd:pfam10147  168 -FKEMLQQKEKEDKKKVKEAKRKEK 191
PHD_BRPF2 cd15677
PHD finger found in bromodomain and PHD finger-containing protein 2 (BRPF2) and similar ...
1904-1953 1.14e-04

PHD finger found in bromodomain and PHD finger-containing protein 2 (BRPF2) and similar proteins; BRPF2, also termed bromodomain-containing protein 1 (BRD1), or BR140-like protein, is encoded by BRL (BR140 Like gene). It is responsible for the bulk of the acetylation of H3K14 and forms a novel monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complex with HBO1 and ING4. The complex is required for full transcriptional activation of the erythroid-specific regulator genes essential for terminal differentiation and survival of erythroblasts in fetal liver. BRPF2 shows widespread expression and localizes to the nucleus within spermatocytes. It contains a cysteine rich region harboring a canonical Cys4HisCys3 plant homeodomain (PHD) finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277147 [Multi-domain]  Cd Length: 54  Bit Score: 41.54  E-value: 1.14e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1720399825 1904 CQICRKGD--NEELLLLCDGCDKGCHTYCHrpKITTIPDGDWFCPACISKAS 1953
Cdd:cd15677      4 CCICMDGEcqNSNVILFCDMCNLAVHQECY--GVPYIPEGQWLCRHCLQSRS 53
Activator_LAG-3 pfam11498
Transcriptional activator LAG-3; The C.elegans Notch pathway, involved in the control of ...
872-980 1.17e-04

Transcriptional activator LAG-3; The C.elegans Notch pathway, involved in the control of growth, differentiation and patterning in animal development, relies on either of the receptors GLP-1 or LIN-12. Both these receptors promote signalling by the recruitment of LAG-3 to target promoters, where it then acts as a transcriptional activator. LAG-3 works as a ternary complex together with the DNA binding protein, LAG-1. Its N-terminal region adopts an elongated kinked helix that is required for complex assembly.


Pssm-ID: 151935 [Multi-domain]  Cd Length: 476  Bit Score: 46.88  E-value: 1.17e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  872 QEIARQAAQIKLLRKLQKQEQARVAKEAKKQQAIMAAEEKRKQKE---QMKIIKQQEKIKRIQ---------QIRMEKEL 939
Cdd:pfam11498  320 QHIAQLAQQQNKMRLLQQQEMEMQRIEQQRQQQIMHQHQQQQQQEhqqQQMLLQQQQQMHQLQqhhqmngggQFATQAHQ 399
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 1720399825  940 RAQQILEEKELRRQQAVLLKHQELERHRLDMERERR--RQHVM 980
Cdd:pfam11498  400 HAAYLQQMQHMRLQEQIQHQQQQAQHHQQAQQQHQQpaQHGQM 442
flagell_FliJ TIGR02473
flagellar export protein FliJ; Members of this family are the FliJ protein found, in nearly ...
906-1023 1.28e-04

flagellar export protein FliJ; Members of this family are the FliJ protein found, in nearly every case, in the midst of other flagellar biosynthesis genes in bacgterial genomes. Typically the fliJ gene is found adjacent to the gene for the flagellum-specific ATPase FliI. Sequence scoring in the gray zone between trusted and noise cutoffs include both probable FliJ proteins and components of bacterial type III secretion systems.


Pssm-ID: 131526 [Multi-domain]  Cd Length: 141  Bit Score: 44.23  E-value: 1.28e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  906 MAAEEKRKQKEQMKiiKQQEKIKRIQQirmekelRAQQILEEKELRRQQAV--------LLKHQELERH--RLDMERERR 975
Cdd:TIGR02473   10 LREKEEEQAKLELA--KAQAEFERLET-------QLQQLIKYREEYEQQALekvgagtsALELSNYQRFirQLDQRIQQQ 80
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1720399825  976 RQHV-MLMKAMEARKK------AEEK--ERLKQEKRDEKRLNKERKlEQRRLElEMA 1023
Cdd:TIGR02473   81 QQELaLLQQEVEAKRErllearRELKalEKLKEKKQKEYRAEEAKR-EQKEMD-ELA 135
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
898-1025 1.39e-04

Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 47.07  E-value: 1.39e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  898 EAKK---QQAIMAAEEKRKQKEQMKIIKQQEKIKRIQQIRMeKELRAQQILEEKELRRQQAVLLKHQELERHRLDMERER 974
Cdd:COG4717     33 EAGKstlLAFIRAMLLERLEKEADELFKPQGRKPELNLKEL-KELEEELKEAEEKEEEYAELQEELEELEEELEELEAEL 111
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1720399825  975 ---RRQHVMLMKAMEARKKAEEKERLKQE------------KRDEKRLNKERKLEQRRLELEMAKE 1025
Cdd:COG4717    112 eelREELEKLEKLLQLLPLYQELEALEAElaelperleeleERLEELRELEEELEELEAELAELQE 177
TPH pfam13868
Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of ...
911-1027 1.41e-04

Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain.


Pssm-ID: 464007 [Multi-domain]  Cd Length: 341  Bit Score: 46.45  E-value: 1.41e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  911 KRKQKEQMKIIKQQekikrIQQIRMEKElRAQQIlEEKELRRQQAvllkHQELERHRLDMERERRRQHVMLMKAMEARK- 989
Cdd:pfam13868    1 LRENSDELRELNSK-----LLAAKCNKE-RDAQI-AEKKRIKAEE----KEEERRLDEMMEEERERALEEEEEKEEERKe 69
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 1720399825  990 -KAEEKERLKQ---EKRDEKRLNKERKLEQRRLELEMAKELK 1027
Cdd:pfam13868   70 eRKRYRQELEEqieEREQKRQEEYEEKLQEREQMDEIVERIQ 111
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
866-1031 1.43e-04

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 46.98  E-value: 1.43e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  866 LRKLQAQEIARQAAQIKLLRKLQKQEQARVA------KEAKKQQAIMAAEEKRKQKEQMKIIKQQEKIKRIQQIRMEKEL 939
Cdd:PRK03918   194 LIKEKEKELEEVLREINEISSELPELREELEklekevKELEELKEEIEELEKELESLEGSKRKLEEKIRELEERIEELKK 273
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  940 raqqilEEKELRRQQAVL-------LKHQELERHRLDMERERRRQHVML------MKAMEAR-KKAEEKERLKQE--KRD 1003
Cdd:PRK03918   274 ------EIEELEEKVKELkelkekaEEYIKLSEFYEEYLDELREIEKRLsrleeeINGIEERiKELEEKEERLEElkKKL 347
                          170       180
                   ....*....|....*....|....*...
gi 1720399825 1004 EKRLNKERKLEQRRLELEMAKELKKPKE 1031
Cdd:PRK03918   348 KELEKRLEELEERHELYEEAKAKKEELE 375
DDRGK pfam09756
DDRGK domain; This is a family of proteins of approximately 300 residues, found in plants and ...
885-959 1.43e-04

DDRGK domain; This is a family of proteins of approximately 300 residues, found in plants and vertebrates. They contain a highly conserved DDRGK motif.


Pssm-ID: 370664 [Multi-domain]  Cd Length: 188  Bit Score: 45.03  E-value: 1.43e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1720399825  885 RKLQKQEQARVA-KEAKKQQ--AIMAAEEKRKQKEQMKIIKQQEKIKRIQQIRMEKElRAQQILEEKELRRQQAVLLK 959
Cdd:pfam09756    1 KKLGAKKRAKLElKEAKRQQreAEEEEREEREKLEEKREEEYKEREEREEEAEKEKE-EEERKQEEEQERKEQEEYEK 77
PHD_TCF19_like cd15517
PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and ...
1904-1948 1.45e-04

PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and KDM5B, and other similar proteins; TCF-19 was identified as a putative trans-activating factor with expression beginning at the late G1-S boundary in dividing cells. It functions as a novel islet factor necessary for proliferation and survival in the INS-1 beta cell line. It plays an important role in susceptibility to both Type 1 Diabetes Mellitus (T1DM) and Type 2 Diabetes Mellitus (T2DM); it has been suggested that it may positively impact beta cell mass under conditions of beta cell stress and increased insulin demand. KDM5A was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interaction with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK, and BMAL1. KDM5B has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. Both KDM5A and KDM5B function as trimethylated histone H3 lysine 4 (H3K4me3) demethylases. This family also includes Caenorhabditis elegans Lysine-specific demethylase 7 homolog (ceKDM7A). ceKDM7A (also termed JmjC domain-containing protein 1.2, PHD finger protein 8 homolog, or PHF8 homolog) is a plant homeodomain (PHD)- and JmjC domain-containing protein that functions as a histone demethylase specific for H3K9me2 and H3K27me2. The binding of the PHD finger to H3K4me3 guides H3K9me2- and H3K27me2-specific demethylation by its catalytic JmjC domain in a trans-histone regulation mechanism. In addition, this family includes plant protein OBERON 1 and OBERON 2, Alfin1-like (AL) proteins, histone acetyltransferases (HATs) HAC, and AT-rich interactive domain-containing protein 4 (ARID4).


Pssm-ID: 276992 [Multi-domain]  Cd Length: 49  Bit Score: 41.38  E-value: 1.45e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1720399825 1904 CQICRK--GDNEELLLLCDGCDKGCHTYCHRPKITTIPDGD-WFCPAC 1948
Cdd:cd15517      2 CGICNLetAAVDELWVQCDGCDKWFHQFCLGLSNERYADEDkFKCPNC 49
COG4372 COG4372
Uncharacterized protein, contains DUF3084 domain [Function unknown];
863-1027 1.45e-04

Uncharacterized protein, contains DUF3084 domain [Function unknown];


Pssm-ID: 443500 [Multi-domain]  Cd Length: 370  Bit Score: 46.43  E-value: 1.45e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  863 AKLLRKLQAQEIARQAAQIKLLRKLQKQEQARVAKEAKKQQAIMAAEEKRKQKEQMKIIKQQEKIKRIQQIRMEKELRA- 941
Cdd:COG4372     48 EQLREELEQAREELEQLEEELEQARSELEQLEEELEELNEQLQAAQAELAQAQEELESLQEEAEELQEELEELQKERQDl 127
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  942 ---QQILEEKELRRQQAVLLKHQELErhRLDMERERRRQHV-MLMKAMEARKKAEEKERLKQEKRDEKR--LNKERKLEQ 1015
Cdd:COG4372    128 eqqRKQLEAQIAELQSEIAEREEELK--ELEEQLESLQEELaALEQELQALSEAEAEQALDELLKEANRnaEKEEELAEA 205
                          170
                   ....*....|..
gi 1720399825 1016 RRLELEMAKELK 1027
Cdd:COG4372    206 EKLIESLPRELA 217
HCR pfam07111
Alpha helical coiled-coil rod protein (HCR); This family consists of several mammalian alpha ...
862-1025 1.59e-04

Alpha helical coiled-coil rod protein (HCR); This family consists of several mammalian alpha helical coiled-coil rod HCR proteins. The function of HCR is unknown but it has been implicated in psoriasis in humans and is thought to affect keratinocyte proliferation.


Pssm-ID: 284517 [Multi-domain]  Cd Length: 749  Bit Score: 47.05  E-value: 1.59e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  862 DAKLLRKLQA--QEIARQAAQIKLLRKLQKQE--QARVAKEAKKQQAIMAAEE-----KRKQKEQMKIIKQQEKIKRIQQ 932
Cdd:pfam07111  476 DADLSLELEQlrEERNRLDAELQLSAHLIQQEvgRAREQGEAERQQLSEVAQQleqelQRAQESLASVGQQLEVARQGQQ 555
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  933 IRMEKELRAQQILEEKELRRQQAVLLKHQELE-RHRLDMERERRRQHvmlmkamEARKK-AEEKERLKQEKRDEKRlNKE 1010
Cdd:pfam07111  556 ESTEEAASLRQELTQQQEIYGQALQEKVAEVEtRLREQLSDTKRRLN-------EARREqAKAVVSLRQIQHRATQ-EKE 627
                          170
                   ....*....|....*
gi 1720399825 1011 RKLEQRRLELEMAKE 1025
Cdd:pfam07111  628 RNQELRRLQDEARKE 642
TolA COG3064
Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis];
868-1028 1.74e-04

Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442298 [Multi-domain]  Cd Length: 485  Bit Score: 46.57  E-value: 1.74e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  868 KLQAQEIARQAaqikllrklqkQEQARVAK-EAKKQQAIMAAEEKRKQKEqmkiikQQEKIKRIQQIRMEKELRAQQILE 946
Cdd:COG3064     43 RLAELEAKRQA-----------EEEAREAKaEAEQRAAELAAEAAKKLAE------AEKAAAEAEKKAAAEKAKAAKEAE 105
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  947 EKELRRQQAVLLKHQELERHRLDMERERRRqhvmlmKAMEARKKAEEKERLKQEKRDEKRLNKERKLEQRRLELEMAKEL 1026
Cdd:COG3064    106 AAAAAEKAAAAAEKEKAEEAKRKAEEEAKR------KAEEERKAAEAEAAAKAEAEAARAAAAAAAAAAAAAARAAAGAA 179

                   ..
gi 1720399825 1027 KK 1028
Cdd:COG3064    180 AA 181
PRK12704 PRK12704
phosphodiesterase; Provisional
863-1026 1.85e-04

phosphodiesterase; Provisional


Pssm-ID: 237177 [Multi-domain]  Cd Length: 520  Bit Score: 46.31  E-value: 1.85e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  863 AKLLRKLQAQEIARQAaqikllrklqKQEQARVAKEAKKQqaimaAEEKRKQKeqmkIIKQQEKIKRIQQiRMEKELRAQ 942
Cdd:PRK12704    21 GYFVRKKIAEAKIKEA----------EEEAKRILEEAKKE-----AEAIKKEA----LLEAKEEIHKLRN-EFEKELRER 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  943 qileEKELRRQQAVLLKHQElerhRLDmererrrqhvmlmKAMEARKKaEEKERLKQEKRDEKRLN--KERKLEQRRLEL 1020
Cdd:PRK12704    81 ----RNELQKLEKRLLQKEE----NLD-------------RKLELLEK-REEELEKKEKELEQKQQelEKKEEELEELIE 138

                   ....*.
gi 1720399825 1021 EMAKEL 1026
Cdd:PRK12704   139 EQLQEL 144
BAH_plant_2 cd04718
BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH ...
1925-1957 1.91e-04

BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.


Pssm-ID: 240069  Cd Length: 148  Bit Score: 43.73  E-value: 1.91e-04
                           10        20        30
                   ....*....|....*....|....*....|...
gi 1720399825 1925 GCHTYCHRPKITTIPDGDWFCPACISKASGQSI 1957
Cdd:cd04718      1 GFHLCCLRPPLKEVPEGDWICPFCEVEKSGQSA 33
NtpE COG1390
Archaeal/vacuolar-type H+-ATPase subunit E/Vma4 [Energy production and conversion]; Archaeal ...
919-1028 2.06e-04

Archaeal/vacuolar-type H+-ATPase subunit E/Vma4 [Energy production and conversion]; Archaeal/vacuolar-type H+-ATPase subunit E/Vma4 is part of the Pathway/BioSystem: A/V-type ATP synthase


Pssm-ID: 441000 [Multi-domain]  Cd Length: 196  Bit Score: 44.55  E-value: 2.06e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  919 KIIKQQEKikRIQQIRMEKELRAQQILEEKElrrQQAVLLKHQELERHRLDMERERRRQhvmLMKA-MEARKK-AEEKER 996
Cdd:COG1390     10 EILEEAEA--EAEEILEEAEEEAEKILEEAE---EEAEEIKEEILEKAEREAEREKRRI---ISSAeLEARKElLEAKEE 81
                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1720399825  997 LKQEKRDE--KRLNKERKlEQRRLEL--EMAKELKK 1028
Cdd:COG1390     82 LIEEVFEEalEKLKNLPK-DPEYKELlkKLLKEAAE 116
PHD_BRPF1 cd15676
PHD finger found in bromodomain and PHD finger-containing protein 1 (BRPF1) and similar ...
1904-1953 2.13e-04

PHD finger found in bromodomain and PHD finger-containing protein 1 (BRPF1) and similar proteins; BRPF1, also termed peregrin or protein Br140, is a multi-domain protein that binds histones, mediates monocytic leukemic zinc-finger protein (MOZ)-dependent histone acetylation, and is required for Hox gene expression and segmental identity. It is a close partner of the MOZ histone acetyltransferase (HAT) complex and a novel Trithorax group (TrxG) member with a central role during development. BRPF1 is primarily a nuclear protein that has a broad tissue distribution and is abundant in testes and spermatogonia. It contains a canonical Cys4HisCys3 plant homeodomain (PHD) zinc finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. PHD and ePHD fingers both bind to lysine 4 of histone H3 (K4H3), bromodomains interact with acetylated lysines on N-terminal tails of histones and other proteins, and PWWP domains show histone-binding and chromatin association properties. BRPF1 may be involved in chromatin remodeling. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277146 [Multi-domain]  Cd Length: 62  Bit Score: 41.19  E-value: 2.13e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1720399825 1904 CQICRKGD--NEELLLLCDGCDKGCHTYCHrpKITTIPDGDWFCPACISKAS 1953
Cdd:cd15676     10 CCICNDGEcqNSNVILFCDMCNLAVHQECY--GVPYIPEGQWLCRRCLQSPS 59
OmpH pfam03938
Outer membrane protein (OmpH-like); This family includes outer membrane proteins such as OmpH ...
872-959 2.51e-04

Outer membrane protein (OmpH-like); This family includes outer membrane proteins such as OmpH among others. Skp (OmpH) has been characterized as a molecular chaperone that interacts with unfolded proteins as they emerge in the periplasm from the Sec translocation machinery.


Pssm-ID: 461098 [Multi-domain]  Cd Length: 140  Bit Score: 43.33  E-value: 2.51e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  872 QEIARQAAQIK-LLRKLQKQEQARVAKEAKKQQAIMAAEEKRKQKEQMKIIKQQEKIKRIQQirMEKELRAQQILEEKEL 950
Cdd:pfam03938    8 QKILEESPEGKaAQAQLEKKFKKRQAELEAKQKELQKLYEELQKDGALLEEEREEKEQELQK--KEQELQQLQQKAQQEL 85

                   ....*....
gi 1720399825  951 RRQQAVLLK 959
Cdd:pfam03938   86 QKKQQELLQ 94
DUF4515 pfam14988
Domain of unknown function (DUF4515); This family of proteins is found in bacteria and ...
866-1028 2.65e-04

Domain of unknown function (DUF4515); This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 198 and 469 amino acids in length. There are two completely conserved L residues that may be functionally important.


Pssm-ID: 405647 [Multi-domain]  Cd Length: 206  Bit Score: 44.37  E-value: 2.65e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  866 LRKlQAQEIARQAAQIK--LLRKLQKQEQAR--VAKEAKKQQAIMAAEEKRKQKEQMKIIKQQEKIKRIQQIRMEKELRA 941
Cdd:pfam14988    9 LAK-KTEEKQKKIEKLWnqYVQECEEIERRRqeLASRYTQQTAELQTQLLQKEKEQASLKKELQALRPFAKLKESQEREI 87
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  942 QQILEEKE---------LRRQQAVLLK------HQELERHRLDMERERRRQHVMLMKAMEARKKAEEKERLKQEKRDEKR 1006
Cdd:pfam14988   88 QDLEEEKEkvraetaekDREAHLQFLKekalleKQLQELRILELGERATRELKRKAQALKLAAKQALSEFCRSIKRENRQ 167
                          170       180       190
                   ....*....|....*....|....*....|
gi 1720399825 1007 LNKE--------RKLEQRRLELEMAKELKK 1028
Cdd:pfam14988  168 LQKEllqliqetQALEAIKSKLENRKQRLK 197
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
870-1018 2.96e-04

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 46.20  E-value: 2.96e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  870 QAQEIARQAAQIKLLRklqkqeqarvAKEAKKQQAIMAAEEKRKQKEQMKIIKQQEKikriqqIRMEKELRAQQILEEKE 949
Cdd:TIGR02168  675 RRREIEELEEKIEELE----------EKIAELEKALAELRKELEELEEELEQLRKEL------EELSRQISALRKDLARL 738
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  950 LRRQQAVLLKHQELERHRLDMERERRRQHVMLMKAMEARKKAEEK------------ERLKQEKRDEKRLNKERKLEQRR 1017
Cdd:TIGR02168  739 EAEVEQLEERIAQLSKELTELEAEIEELEERLEEAEEELAEAEAEieeleaqieqlkEELKALREALDELRAELTLLNEE 818

                   .
gi 1720399825 1018 L 1018
Cdd:TIGR02168  819 A 819
Golgin_A5 pfam09787
Golgin subfamily A member 5; Members of this family of proteins are involved in maintaining ...
906-1021 3.72e-04

Golgin subfamily A member 5; Members of this family of proteins are involved in maintaining Golgi structure. They stimulate the formation of Golgi stacks and ribbons, and are involved in intra-Golgi retrograde transport. Two main interactions have been characterized: one with RAB1A that has been activated by GTP-binding and another with isoform CASP of CUTL1.


Pssm-ID: 462900 [Multi-domain]  Cd Length: 305  Bit Score: 44.75  E-value: 3.72e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  906 MAAEEKRKQKEQMKIIKQQEKIKrIQQIRME-KELRAQQILEEKELRRQQAVLLKHQELERH-RLDMERERRRQHvmlmk 983
Cdd:pfam09787   47 LELEELRQERDLLREEIQKLRGQ-IQQLRTElQELEAQQQEEAESSREQLQELEEQLATERSaRREAEAELERLQ----- 120
                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 1720399825  984 amearkkaEEKERLKQEKRDEKRLNKERkLEQRRLELE 1021
Cdd:pfam09787  121 --------EELRYLEEELRRSKATLQSR-IKDREAEIE 149
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
877-1033 4.04e-04

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 45.83  E-value: 4.04e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  877 QAAQIKLLRKLQKQEQARVAKEAKK-----QQAIMAAEEKRKQKEQMKIIKQQEKIKRIQQIRMEKELRAqqiLEEK--E 949
Cdd:PRK03918   187 RTENIEELIKEKEKELEEVLREINEisselPELREELEKLEKEVKELEELKEEIEELEKELESLEGSKRK---LEEKirE 263
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  950 LRRQQAvllkhqELERHRLDMERERRRQHVMLMKAMEARKKAEEKERLKQEKRD-EKRLNK--------ERKLEQRRLEL 1020
Cdd:PRK03918   264 LEERIE------ELKKEIEELEEKVKELKELKEKAEEYIKLSEFYEEYLDELREiEKRLSRleeeingiEERIKELEEKE 337
                          170
                   ....*....|...
gi 1720399825 1021 EMAKELKKPKEDM 1033
Cdd:PRK03918   338 ERLEELKKKLKEL 350
ClassIIa_HDAC4_Gln-rich-N cd10162
Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase; This ...
897-977 4.27e-04

Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase; This family consists of the glutamine-rich domain of histone deacetylase 4 (HDAC4). It belongs to a superfamily that consists of the glutamine-rich N-terminal helical extension to certain Class IIa histone deacetylases (HDACs), including HDAC4, HDAC5 and HDCA9; it is missing from HDAC7. This domain confers responsiveness to calcium signals and mediates interactions with transcription factors and cofactors, and it is able to repress transcription independently of the HDAC C-terminal, zinc-dependent catalytic domain. It has many intra- and inter-helical interactions which are possibly involved in reversible assembly and disassembly of proteins. HDACs regulate diverse cellular processes through enzymatic deacetylation of histone as well as non-histone proteins, in particular deacetylating N(6)-acetyl-lysine residues.


Pssm-ID: 197398 [Multi-domain]  Cd Length: 90  Bit Score: 41.34  E-value: 4.27e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  897 KEAKKQQAIMAAEEKRKQKEQMKII---KQQEKIKRIQQIRMEKELRAQQilEEKELRRQQAVLLKHQELERHRL--DME 971
Cdd:cd10162      5 REQQLQQELLALKQKQQIQRQLLIAefqRQHEQLSRQHEAQLHEHIKQQQ--ELLAMKHQQELLEHQRKLERHRQeqEME 82

                   ....*.
gi 1720399825  972 RERRRQ 977
Cdd:cd10162     83 KQQREQ 88
Bromo_Rsc1_2_I cd05521
Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
2065-2130 4.31e-04

Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99952  Cd Length: 106  Bit Score: 41.54  E-value: 4.31e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1720399825 2065 PGYKKVIKKPMDFSTIREKLNNgqYPNFETFALDVRLVFDNCETFNEDDSDIGRAGHSMRKYFEKK 2130
Cdd:cd05521     38 PDYYKIIKNPLSLNTVKKRLPH--YTNAQEFVNDLAQIPWNARLYNTKGSVIYKYALILEKYINDV 101
COG4372 COG4372
Uncharacterized protein, contains DUF3084 domain [Function unknown];
863-1028 4.33e-04

Uncharacterized protein, contains DUF3084 domain [Function unknown];


Pssm-ID: 443500 [Multi-domain]  Cd Length: 370  Bit Score: 44.89  E-value: 4.33e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  863 AKLLRKLQAQEIARQAAQIKLLRKLQKQEQARVAKEAKKQQAIMAAEEKRKQKEQMKIIKQQEKIKRIQQIRMEKELRAQ 942
Cdd:COG4372     27 AALSEQLRKALFELDKLQEELEQLREELEQAREELEQLEEELEQARSELEQLEEELEELNEQLQAAQAELAQAQEELESL 106
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  943 QiLEEKELRRQQAVLLKhqelERHRLDMERERRRQHVMLMKAMEARKKAEEKERLKQEKRDEKRLNKERKLEQRRLELEM 1022
Cdd:COG4372    107 Q-EEAEELQEELEELQK----ERQDLEQQRKQLEAQIAELQSEIAEREEELKELEEQLESLQEELAALEQELQALSEAEA 181

                   ....*.
gi 1720399825 1023 AKELKK 1028
Cdd:COG4372    182 EQALDE 187
FliJ pfam02050
Flagellar FliJ protein;
899-1018 4.99e-04

Flagellar FliJ protein;


Pssm-ID: 426581 [Multi-domain]  Cd Length: 123  Bit Score: 41.88  E-value: 4.99e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  899 AKKQQAIMAAEEKRKQKEQMKiikqQEKIKRIQQIrmEKELRAQQILEEKELRRQQAVLLKHQELERHRLDMERERRRQH 978
Cdd:pfam02050    8 AEAQRELQQAEEKLEELQQYR----AEYQQQLSGA--GQGISAAELRNYQAFISQLDEAIAQQQQELAQAEAQVEKAREE 81
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 1720399825  979 vmLMKAMEARKKAEekeRLKQEKRDEKRLnKERKLEQRRL 1018
Cdd:pfam02050   82 --WQEARQERKSLE---KLREREKKEERK-EQNRREQKQL 115
GBP_C cd16269
Guanylate-binding protein, C-terminal domain; Guanylate-binding protein (GBP), C-terminal ...
912-1027 5.22e-04

Guanylate-binding protein, C-terminal domain; Guanylate-binding protein (GBP), C-terminal domain. Guanylate-binding proteins (GBPs) are synthesized after activation of the cell by interferons. The biochemical properties of GBPs are clearly different from those of Ras-like and heterotrimeric GTP-binding proteins. They bind guanine nucleotides with low affinity (micromolar range), are stable in their absence, and have a high turnover GTPase. In addition to binding GDP/GTP, they have the unique ability to bind GMP with equal affinity and hydrolyze GTP not only to GDP, but also to GMP. This C-terminal domain has been shown to mediate inhibition of endothelial cell proliferation by inflammatory cytokines.


Pssm-ID: 293879 [Multi-domain]  Cd Length: 291  Bit Score: 44.49  E-value: 5.22e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  912 RKQKEQMKIIKQQEKIKRIQQIRMEKElRAQQILEEKELRRQQAVLlkhQELERHRLDMER---ERRRQHVMLMKaMEAR 988
Cdd:cd16269    177 QSKEAEAEAILQADQALTEKEKEIEAE-RAKAEAAEQERKLLEEQQ---RELEQKLEDQERsyeEHLRQLKEKME-EERE 251
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 1720399825  989 KKAEEKERLKQEK-RDEKRLNKERKLEQRRLELEMAKELK 1027
Cdd:cd16269    252 NLLKEQERALESKlKEQEALLEEGFKEQAELLQEEIRSLK 291
tolA PRK09510
cell envelope integrity inner membrane protein TolA; Provisional
907-1032 5.37e-04

cell envelope integrity inner membrane protein TolA; Provisional


Pssm-ID: 236545 [Multi-domain]  Cd Length: 387  Bit Score: 44.80  E-value: 5.37e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  907 AAEEKRKQKEQMKIIKQQEKIKRIQQIRMEKELRAQQILEEKELRRQQAVLLKHQELERHRLDMERERRRQHvmlMKAME 986
Cdd:PRK09510    60 VVEQYNRQQQQQKSAKRAEEQRKKKEQQQAEELQQKQAAEQERLKQLEKERLAAQEQKKQAEEAAKQAALKQ---KQAEE 136
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 1720399825  987 ARKKAEEKERLKQEKrDEKRLN---KERKLEQRRLELEMAKelKKPKED 1032
Cdd:PRK09510   137 AAAKAAAAAKAKAEA-EAKRAAaaaKKAAAEAKKKAEAEAA--KKAAAE 182
COG5141 COG5141
PHD zinc finger-containing protein [General function prediction only];
1903-1949 5.65e-04

PHD zinc finger-containing protein [General function prediction only];


Pssm-ID: 227470 [Multi-domain]  Cd Length: 669  Bit Score: 44.97  E-value: 5.65e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1720399825 1903 YCQICRK-----GDNEELLLLCDGCDKGCHTYCHrpKITTIPDGDWFCPACI 1949
Cdd:COG5141    192 FDDICTKctsthNENSNAIVFCDGCEICVHQSCY--GIQFLPEGFWLCRKCI 241
PRK12704 PRK12704
phosphodiesterase; Provisional
868-998 5.97e-04

phosphodiesterase; Provisional


Pssm-ID: 237177 [Multi-domain]  Cd Length: 520  Bit Score: 44.77  E-value: 5.97e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  868 KLQAQEIARQA---AQIKLLRKLQKQEQARVAKEAKKQQAimaaEEKRKQKEQMkIIKQQEKIKRIQQI--RMEKELRA- 941
Cdd:PRK12704    48 KKEAEAIKKEAlleAKEEIHKLRNEFEKELRERRNELQKL----EKRLLQKEEN-LDRKLELLEKREEEleKKEKELEQk 122
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1720399825  942 QQILEEKELRRQQAVLLKHQELE----------RHRL--DMERERRRQHVMLMKAMEARKKAEEKERLK 998
Cdd:PRK12704   123 QQELEKKEEELEELIEEQLQELErisgltaeeaKEILleKVEEEARHEAAVLIKEIEEEAKEEADKKAK 191
PHD_ATX3_4_5_like cd15495
PHD finger found in Arabidopsis thaliana histone-lysine N-methyltransferase arabidopsis ...
1904-1948 6.68e-04

PHD finger found in Arabidopsis thaliana histone-lysine N-methyltransferase arabidopsis trithorax-like protein ATX3, ATX4, ATX5, and similar proteins; The family includes A. thaliana ATX3 (also termed protein SET domain group 14, or trithorax-homolog protein 3), ATX4 (also termed protein SET domain group 16, or trithorax-homolog protein 4) and ATX5 (also termed protein SET domain group 29, or trithorax-homolog protein 5), which belong to the histone-lysine methyltransferase family. They show distinct phylogenetic origins from the ATX1 and ATX2 family. They are multi-domain containing proteins that consist of an N-terminal PWWP domain, a canonical Cys4HisCys3 plant homeodomain (PHD) finger, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a C-terminal SET domain; this model corresponds to the Cys4HisCys3 canonical PHD finger.


Pssm-ID: 276970 [Multi-domain]  Cd Length: 47  Bit Score: 39.28  E-value: 6.68e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1720399825 1904 CQICRKGDN--EELLLLCDGCDKGCHTYCHrpKITTI-PDGDWFCPAC 1948
Cdd:cd15495      2 CAVCNEGEDddNNPLITCNRCQISVHQKCY--GIREVdPDGSWVCRAC 47
YscO pfam07321
Type III secretion protein YscO; This family contains the bacterial type III secretion protein ...
859-977 6.76e-04

Type III secretion protein YscO; This family contains the bacterial type III secretion protein YscO, which is approximately 150 residues long. YscO has been shown to be required for high-level expression and secretion of the anti-host proteins V antigen and Yops in Yersinia pestis.


Pssm-ID: 399954 [Multi-domain]  Cd Length: 148  Bit Score: 42.00  E-value: 6.76e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  859 DNTDAKLLRKLQAQEIARQAAQiKLLRKLQKQEQARVAKE----AKKQQAIMAAEEKRKQKEQMKIIKQQEKI------K 928
Cdd:pfam07321   13 DRAEKAVKRQEQALAAARAAHQ-QAQASLQDYRAWRPQEEqrlyAEIQGKLVLLKELEKVKQQVALLRENEADlekqvaE 91
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 1720399825  929 RIQQIRMEKELRAQQILEEKELRRQQAVLLKHQELerHRLDMERERRRQ 977
Cdd:pfam07321   92 ARQQLEAEREALRQARQALAEARRAVEKFAELVRL--VQAEELRQQERQ 138
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
858-1033 7.11e-04

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 45.05  E-value: 7.11e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  858 LDNTDAKLLR-KLQAQEIARQAAQIK--------LLRKLQKQEQARVAKEAKKQQAIMAAEEKRKQKEQMKIIKQQEKIK 928
Cdd:TIGR02168  262 LQELEEKLEElRLEVSELEEEIEELQkelyalanEISRLEQQKQILRERLANLERQLEELEAQLEELESKLDELAEELAE 341
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  929 RIQQIRMEKELRAQQILEEKELRRQQavllkhQELERHR--LDMERERRRQHVMLMKA-----------MEARKK--AEE 993
Cdd:TIGR02168  342 LEEKLEELKEELESLEAELEELEAEL------EELESRLeeLEEQLETLRSKVAQLELqiaslnneierLEARLErlEDR 415
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....
gi 1720399825  994 KERLKQEKRD--EKRLNKERKLEQRRLEL--EMAKELKKPKEDM 1033
Cdd:TIGR02168  416 RERLQQEIEEllKKLEEAELKELQAELEEleEELEELQEELERL 459
PRK02224 PRK02224
DNA double-strand break repair Rad50 ATPase;
870-1021 7.55e-04

DNA double-strand break repair Rad50 ATPase;


Pssm-ID: 179385 [Multi-domain]  Cd Length: 880  Bit Score: 44.65  E-value: 7.55e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  870 QAQEIARQAAQIKLLRKlQKQEQARVAkEAKKQQAIMAAEEKRKQKEQMKIIKQQ-----EKIKRIQQIRMEKELRAQQI 944
Cdd:PRK02224   528 RRETIEEKRERAEELRE-RAAELEAEA-EEKREAAAEAEEEAEEAREEVAELNSKlaelkERIESLERIRTLLAAIADAE 605
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  945 LEEKELRRQQAVLLKHQELERHRLDMERERRRQ------HVMLMKAMEARKKAE-------EKERLKQEKRDE------- 1004
Cdd:PRK02224   606 DEIERLREKREALAELNDERRERLAEKRERKREleaefdEARIEEAREDKERAEeyleqveEKLDELREERDDlqaeiga 685
                          170       180
                   ....*....|....*....|....*.
gi 1720399825 1005 --------KRLNKERK-LEQRRLELE 1021
Cdd:PRK02224   686 veneleelEELRERREaLENRVEALE 711
CCDC47 pfam07946
PAT complex subunit CCDC47; This family represents CCDC47 proteins which are a component of ...
884-954 8.34e-04

PAT complex subunit CCDC47; This family represents CCDC47 proteins which are a component of the PAT complex, an endoplasmic reticulum (ER)-resident membrane multiprotein complex that facilitates multi-pass membrane proteins insertion into membranes. The PAT complex, formed by CCDC47 and Asterix proteins, acts as an intramembrane chaperone by directly interacting with nascent transmembrane domains (TMDs), releasing its substrates upon correct folding, and is needed for optimal biogenesis of multi-pass membrane proteins. CCDC47 is required to maintain the stability of Asterix. CCDC47 is associated with various membrane-associated processes and is component of a ribosome-associated ER translocon complex involved in multi-pass membrane protein transport into the ER membrane and biogenesis. It is also involved in the regulation of calcium ion homeostasis in the ER, being also required for proper protein degradation via the ERAD (ER-associated degradation) pathway.


Pssm-ID: 462322  Cd Length: 323  Bit Score: 43.71  E-value: 8.34e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1720399825  884 LRKLQKQEQARVAKEAKKQQAIMAAEEKRKQKEQMKiikqQEKIKRiqqirMEKElrAQQILEEKELRRQQ 954
Cdd:pfam07946  262 AKKTREEEIEKIKKAAEEERAEEAQEKKEEAKKKER----EEKLAK-----LSPE--EQRKYEEKERKKEQ 321
YscO pfam07321
Type III secretion protein YscO; This family contains the bacterial type III secretion protein ...
884-1025 8.66e-04

Type III secretion protein YscO; This family contains the bacterial type III secretion protein YscO, which is approximately 150 residues long. YscO has been shown to be required for high-level expression and secretion of the anti-host proteins V antigen and Yops in Yersinia pestis.


Pssm-ID: 399954 [Multi-domain]  Cd Length: 148  Bit Score: 42.00  E-value: 8.66e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  884 LRKLQKQEQARV---AKEAKKQQAIMAAEEKRKQKeqmkiikQQEKIKRIQQIRMEKELR-----AQQILEEKELRR--Q 953
Cdd:pfam07321    1 IRRLLRVKHLREdraEKAVKRQEQALAAARAAHQQ-------AQASLQDYRAWRPQEEQRlyaeiQGKLVLLKELEKvkQ 73
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  954 QAVLLKHQELE--------RHRLDMERERRRQhvMLMKAMEARKKAEEKERLKQEKRDEKRLNKERKLEQrrlELEMAKE 1025
Cdd:pfam07321   74 QVALLRENEADlekqvaeaRQQLEAEREALRQ--ARQALAEARRAVEKFAELVRLVQAEELRQQERQEEQ---ELEEFAE 148
ClassIIa_HDAC5_Gln-rich-N cd10164
Glutamine-rich N-terminal helical domain of HDAC5, a Class IIa histone deacetylase; This ...
895-1000 8.73e-04

Glutamine-rich N-terminal helical domain of HDAC5, a Class IIa histone deacetylase; This family consists of the glutamine-rich domain of histone deacetylase 5 (HDAC5). It belongs to a superfamily that consists of the glutamine-rich N-terminal helical extension to certain Class IIa histone deacetylases (HDACs), including HDAC4, HDAC5 and HDCA9; it is missing from HDAC7. This domain confers responsiveness to calcium signals and mediates interactions with transcription factors and cofactors, and it is able to repress transcription independently of the HDAC C-terminal, zinc-dependent catalytic domain. It has many intra- and inter-helical interactions which are possibly involved in reversible assembly and disassembly of proteins. HDACs regulate diverse cellular processes through enzymatic deacetylation of histone as well as non-histone proteins, in particular deacetylating N(6)-acetyl-lysine residues.


Pssm-ID: 197400 [Multi-domain]  Cd Length: 97  Bit Score: 40.58  E-value: 8.73e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  895 VAKEAKKQQAIMAAEEKRKQKEQM---KIIKQQEKIKRIQQIRMEKELRAQQilEEKELRRQQAVLL--KHQELERHRld 969
Cdd:cd10164      3 SLREQQLQQELLLLKQQQQLQKQLlfaEFQKQHEHLTRQHEVQLQKHLKVRA--ELFSEQQQQEILAakRQQELEQQR-- 78
                           90       100       110
                   ....*....|....*....|....*....|.
gi 1720399825  970 mERERRRQHVMlmkamearkkaeEKERLKQE 1000
Cdd:cd10164     79 -KREQQRQEEL------------EKQRLEQQ 96
ClassIIa_HDAC_Gln-rich-N cd10149
Glutamine-rich N-terminal helical domain of various Class IIa histone deacetylases (HDAC4, ...
944-1030 8.76e-04

Glutamine-rich N-terminal helical domain of various Class IIa histone deacetylases (HDAC4, HDAC5 and HDCA9); This superfamily consists of a glutamine-rich N-terminal helical extension to certain Class IIa histone deacetylases (HDACs), including HDAC4, HDAC5 and HDAC9; it is missing in HDAC7. It is referred to as the glutamine-rich domain, and confers responsiveness to calcium signals and mediates interactions with transcription factors and cofactors. This domain is able to repress transcription independently of the HDAC's C-terminal, zinc-dependent catalytic domain. It has many intra- and inter-helical interactions which are possibly involved in reversible assembly and disassembly of proteins. HDACs regulate diverse cellular processes through enzymatic deacetylation of histone as well as non-histone proteins, in particular deacetylating N(6)-acetyl-lysine residues.


Pssm-ID: 197397 [Multi-domain]  Cd Length: 90  Bit Score: 40.45  E-value: 8.76e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  944 ILEEKELRRQQAVLLKHQELERHRLDMERERRRQHVMLMKAMEARKKAEEKERLKQEKRDEKRLNKERKLEQRRLELEMA 1023
Cdd:cd10149      3 VLREQQLQQELLALKQQQQIQKQLLIAEFQKQHENLTRQHEAQLQEHIKQQQEMLAIKQQQELLEKQRKLEQQRQEQELE 82

                   ....*..
gi 1720399825 1024 KELKKPK 1030
Cdd:cd10149     83 KQRREQQ 89
rad50 TIGR00606
rad50; All proteins in this family for which functions are known are involvedin recombination, ...
844-1031 9.17e-04

rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).


Pssm-ID: 129694 [Multi-domain]  Cd Length: 1311  Bit Score: 44.65  E-value: 9.17e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  844 RRKGRPPNVGSAEFLDNTDAKL-LRKLQAQEIARQAAQIKL---------LRKLQKQEQARVAKEAKKQQAIMAAEEKRK 913
Cdd:TIGR00606  253 RLKEIEHNLSKIMKLDNEIKALkSRKKQMEKDNSELELKMEkvfqgtdeqLNDLYHNHQRTVREKERELVDCQRELEKLN 332
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  914 QKEQMKIIKQQEKIKRIQQIRMEKELRAQQILEEKELRRQQAVLLKHQELErHRLDMERERRRQHVMLMKAMEARKKA-- 991
Cdd:TIGR00606  333 KERRLLNQEKTELLVEQGRLQLQADRHQEHIRARDSLIQSLATRLELDGFE-RGPFSERQIKNFHTLVIERQEDEAKTaa 411
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*.
gi 1720399825  992 ------EEKERLKQEKRDEKRLnkERKLEQRRLELEMAKELKKPKE 1031
Cdd:TIGR00606  412 qlcadlQSKERLKQEQADEIRD--EKKGLGRTIELKKEILEKKQEE 455
GBP_C pfam02841
Guanylate-binding protein, C-terminal domain; Transcription of the anti-viral ...
935-1027 1.06e-03

Guanylate-binding protein, C-terminal domain; Transcription of the anti-viral guanylate-binding protein (GBP) is induced by interferon-gamma during macrophage induction. This family contains GBP1 and GPB2, both GTPases capable of binding GTP, GDP and GMP.


Pssm-ID: 460721 [Multi-domain]  Cd Length: 297  Bit Score: 43.43  E-value: 1.06e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  935 MEKELRAQQILEEkELRRQQAVLLKHQELERHRLDMERERRRQHV-MLMKAMEA--RKKAEEKERL--KQEKRDEKRLNK 1009
Cdd:pfam02841  202 KEKAIEAERAKAE-AAEAEQELLREKQKEEEQMMEAQERSYQEHVkQLIEKMEAerEQLLAEQERMleHKLQEQEELLKE 280
                           90
                   ....*....|....*...
gi 1720399825 1010 ERKLEQRRLELEMaKELK 1027
Cdd:pfam02841  281 GFKTEAESLQKEI-QDLK 297
PHD2_PHF14 cd15562
PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
1904-1948 1.10e-03

PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. It can interact with histones through its PHD fingers. The model corresponds to the second PHD finger.


Pssm-ID: 277037  Cd Length: 50  Bit Score: 38.93  E-value: 1.10e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1720399825 1904 CQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIPDGD----WFCPAC 1948
Cdd:cd15562      2 CGICKKSNDQHLLALCDTCKLYYHLGCLDPPLTRMPKKTknsgWQCSEC 50
EmrA COG1566
Multidrug resistance efflux pump EmrA [Defense mechanisms];
858-992 1.38e-03

Multidrug resistance efflux pump EmrA [Defense mechanisms];


Pssm-ID: 441174 [Multi-domain]  Cd Length: 331  Bit Score: 43.11  E-value: 1.38e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  858 LDNTDAKL-LRKLQAQeIARQAAQIKLLRKLQKQEQARVAKEAKKQQAIMAAEEKRKQKEQMKIIKQQEKIKRIQQIRME 936
Cdd:COG1566     76 LDPTDLQAaLAQAEAQ-LAAAEAQLARLEAELGAEAEIAAAEAQLAAAQAQLDLAQRELERYQALYKKGAVSQQELDEAR 154
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1720399825  937 KELR-AQQILEEKELRRQQAvllkhqeleRHRLDMERERRRQHVMLMKAMEARKKAE 992
Cdd:COG1566    155 AALDaAQAQLEAAQAQLAQA---------QAGLREEEELAAAQAQVAQAEAALAQAE 202
OmpH smart00935
Outer membrane protein (OmpH-like); This family includes outer membrane proteins such as OmpH ...
870-932 1.38e-03

Outer membrane protein (OmpH-like); This family includes outer membrane proteins such as OmpH among others. Skp (OmpH) has been characterized as a molecular chaperone that interacts with unfolded proteins as they emerge in the periplasm from the Sec translocation machinery.


Pssm-ID: 214922 [Multi-domain]  Cd Length: 140  Bit Score: 41.03  E-value: 1.38e-03
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1720399825   870 QAQEIARQAAQIK-LLRKLQKQ-----EQARVAKEAKKQQAIMAAEEKRKQKEQMKIIKQQEKIKRIQQ 932
Cdd:smart00935   30 RQAELEKLEKELQkLKEKLQKDaatlsEAAREKKEKELQKKVQEFQRKQQKLQQDLQKRQQEELQKILD 98
ATP-synt_Fo_b cd06503
F-type ATP synthase, membrane subunit b; Membrane subunit b is a component of the Fo complex ...
856-953 1.45e-03

F-type ATP synthase, membrane subunit b; Membrane subunit b is a component of the Fo complex of FoF1-ATP synthase. The F-type ATP synthases (FoF1-ATPase) consist of two structural domains: the F1 (assembly factor one) complex containing the soluble catalytic core, and the Fo (oligomycin sensitive factor) complex containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. F1 is composed of alpha (or A), beta (B), gamma (C), delta (D) and epsilon (E) subunits with a stoichiometry of 3:3:1:1:1, while Fo consists of the three subunits a, b, and c (1:2:10-14). An oligomeric ring of 10-14 c subunits (c-ring) make up the Fo rotor. The flux of protons through the ATPase channel (Fo) drives the rotation of the c-ring, which in turn is coupled to the rotation of the F1 complex gamma subunit rotor due to the permanent binding between the gamma and epsilon subunits of F1 and the c-ring of Fo. The F-ATP synthases are primarily found in the inner membranes of eukaryotic mitochondria, in the thylakoid membranes of chloroplasts or in the plasma membranes of bacteria. The F-ATP synthases are the primary producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). Alternatively, under conditions of low driving force, ATP synthases function as ATPases, thus generating a transmembrane proton or Na(+) gradient at the expense of energy derived from ATP hydrolysis. This group also includes F-ATP synthase that has also been found in the archaea Candidatus Methanoperedens.


Pssm-ID: 349951 [Multi-domain]  Cd Length: 132  Bit Score: 40.88  E-value: 1.45e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  856 EFLDNTDAKLLRKLQAQEIARQAAQikllrKLQKQEQARVAkEAKKQ-QAIMAAEEKRKQKEQMKIIKQ-QEKIKRI--- 930
Cdd:cd06503     26 KALDEREEKIAESLEEAEKAKEEAE-----ELLAEYEEKLA-EARAEaQEIIEEARKEAEKIKEEILAEaKEEAERIleq 99
                           90       100
                   ....*....|....*....|....*
gi 1720399825  931 --QQIRMEKElRAQqileeKELRRQ 953
Cdd:cd06503    100 akAEIEQEKE-KAL-----AELRKE 118
PspA_IM30 pfam04012
PspA/IM30 family; This family includes PspA a protein that suppresses sigma54-dependent ...
872-1039 1.46e-03

PspA/IM30 family; This family includes PspA a protein that suppresses sigma54-dependent transcription. The PspA protein, a negative regulator of the Escherichia coli phage shock psp operon, is produced when virulence factors are exported through secretins in many Gram-negative pathogenic bacteria and its homolog in plants, VIPP1, plays a critical role in thylakoid biogenesis, essential for photosynthesis. Activation of transcription by the enhancer-dependent bacterial sigma(54) containing RNA polymerase occurs through ATP hydrolysis-driven protein conformational changes enabled by activator proteins that belong to the large AAA(+) mechanochemical protein family. It has been shown that PspA directly and specifically acts upon and binds to the AAA(+) domain of the PspF transcription activator.


Pssm-ID: 461130 [Multi-domain]  Cd Length: 215  Bit Score: 42.36  E-value: 1.46e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  872 QEIARQAAQIKLLRKLQKQEQARVAK-EAKKQQAIMAAEEK--RKQKEQMKIIKQQ---EKIKRIQQIRMEKELRAQ-QI 944
Cdd:pfam04012   43 QALAQTIARQKQLERRLEQQTEQAKKlEEKAQAALTKGNEElaREALAEKKSLEKQaeaLETQLAQQRSAVEQLRKQlAA 122
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  945 LEEK--ELRRQQAVLLKHQELERHRLDMERERRRqhvmlMKAMEARKKAEEKERlKQEKRdEKRLNKERKLEQRR---LE 1019
Cdd:pfam04012  123 LETKiqQLKAKKNLLKARLKAAKAQEAVQTSLGS-----LSTSSATDSFERIEE-KIEER-EARADAAAELASAVdldAK 195
                          170       180
                   ....*....|....*....|
gi 1720399825 1020 LEMAKELKKPKEDMcLADQK 1039
Cdd:pfam04012  196 LEQAGIQMEVSEDV-LARLK 214
tolA_full TIGR02794
TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the ...
925-1032 1.59e-03

TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB. [Transport and binding proteins, Other, Cellular processes, Pathogenesis]


Pssm-ID: 274303 [Multi-domain]  Cd Length: 346  Bit Score: 42.91  E-value: 1.59e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  925 EKIKRIQQirMEKELRAQQILEEKELRRQQAVLLKHQELERHRLDMERERRRQHVMLMKAMEARKKAEEKER----LKQE 1000
Cdd:TIGR02794   50 QQANRIQQ--QKKPAAKKEQERQKKLEQQAEEAEKQRAAEQARQKELEQRAAAEKAAKQAEQAAKQAEEKQKqaeeAKAK 127
                           90       100       110
                   ....*....|....*....|....*....|..
gi 1720399825 1001 KRDEKRLNKERKLEQRRLElemakELKKPKED 1032
Cdd:TIGR02794  128 QAAEAKAKAEAEAERKAKE-----EAAKQAEE 154
COG4372 COG4372
Uncharacterized protein, contains DUF3084 domain [Function unknown];
867-1032 1.63e-03

Uncharacterized protein, contains DUF3084 domain [Function unknown];


Pssm-ID: 443500 [Multi-domain]  Cd Length: 370  Bit Score: 42.97  E-value: 1.63e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  867 RKLQA--QEIARQAAQIKLLRKLQKQEQARVAKEAKKQQAIMAAEEKRKQKEQMKIIKQQEKIKRIQQIRMEKELRAQQI 944
Cdd:COG4372     87 EQLQAaqAELAQAQEELESLQEEAEELQEELEELQKERQDLEQQRKQLEAQIAELQSEIAEREEELKELEEQLESLQEEL 166
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  945 LEEKELRRQQAVLLKHQELERHRLDMERERRRQHVMLMKAMEARKKAEEKERLKQEKRDEKRLNKERKLEQRRLELEMAK 1024
Cdd:COG4372    167 AALEQELQALSEAEAEQALDELLKEANRNAEKEEELAEAEKLIESLPRELAEELLEAKDSLEAKLGLALSALLDALELEE 246

                   ....*...
gi 1720399825 1025 ELKKPKED 1032
Cdd:COG4372    247 DKEELLEE 254
PHD_JADE2 cd15680
PHD finger found in protein Jade-2 and similar proteins; Jade-2, also termed PHD finger ...
1904-1948 1.68e-03

PHD finger found in protein Jade-2 and similar proteins; Jade-2, also termed PHD finger protein 15 (PHF15), is a plant homeodomain (PHD) zinc finger protein that is closely related to Jade-1, which functions as an essential regulator of multiple cell signaling pathways. Like Jade-1, Jade-2 is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and Eaf6 to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. Jade-2 contains a canonical Cys4HisCys3 PHD finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, both of which are zinc-binding motifs. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277150 [Multi-domain]  Cd Length: 46  Bit Score: 38.06  E-value: 1.68e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1720399825 1904 CQICR--KGDNEELLLLCDGCDKGCHTYCHrpKITTIPDGDWFCPAC 1948
Cdd:cd15680      2 CDVCRspEGEDGNEMVFCDKCNVCVHQACY--GILKVPTGSWLCRTC 46
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
868-1030 1.70e-03

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 43.51  E-value: 1.70e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  868 KLQAQEIARQAAQIKLLRKLQKqEQARVAKEAKKQQAIMAAEEKRKQKEQMKIIKQQEKIKRIQqirmEKELRAQQILEE 947
Cdd:PRK03918   272 KKEIEELEEKVKELKELKEKAE-EYIKLSEFYEEYLDELREIEKRLSRLEEEINGIEERIKELE----EKEERLEELKKK 346
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  948 -KELRRQQAVLLK-HQELERHRLDMER-ERRRQHVMLMKAMEARKKAEEKERLKQEKRDEKRLNKERK--LEQRRLELEM 1022
Cdd:PRK03918   347 lKELEKRLEELEErHELYEEAKAKKEElERLKKRLTGLTPEKLEKELEELEKAKEEIEEEISKITARIgeLKKEIKELKK 426

                   ....*....
gi 1720399825 1023 A-KELKKPK 1030
Cdd:PRK03918   427 AiEELKKAK 435
CCDC47 pfam07946
PAT complex subunit CCDC47; This family represents CCDC47 proteins which are a component of ...
963-1028 1.72e-03

PAT complex subunit CCDC47; This family represents CCDC47 proteins which are a component of the PAT complex, an endoplasmic reticulum (ER)-resident membrane multiprotein complex that facilitates multi-pass membrane proteins insertion into membranes. The PAT complex, formed by CCDC47 and Asterix proteins, acts as an intramembrane chaperone by directly interacting with nascent transmembrane domains (TMDs), releasing its substrates upon correct folding, and is needed for optimal biogenesis of multi-pass membrane proteins. CCDC47 is required to maintain the stability of Asterix. CCDC47 is associated with various membrane-associated processes and is component of a ribosome-associated ER translocon complex involved in multi-pass membrane protein transport into the ER membrane and biogenesis. It is also involved in the regulation of calcium ion homeostasis in the ER, being also required for proper protein degradation via the ERAD (ER-associated degradation) pathway.


Pssm-ID: 462322  Cd Length: 323  Bit Score: 42.94  E-value: 1.72e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1720399825  963 LERHRLDMERERRRQhvmlMKAMEARKKAEEKERLKQEKRDEKrLNKERKLEQRR-LELEMAKELKK 1028
Cdd:pfam07946  262 AKKTREEEIEKIKKA----AEEERAEEAQEKKEEAKKKEREEK-LAKLSPEEQRKyEEKERKKEQRK 323
YscO-like pfam16789
YscO-like protein; This family of proteins is similar to the type III secretion protein YscO. ...
925-1028 1.73e-03

YscO-like protein; This family of proteins is similar to the type III secretion protein YscO. The family includes Chlamydia trachomatis CT670 which is found in a type III secretion gene cluster. CT670 interacts with CT671, a putative YscP homolog and CT670 and CT671 may form a chaperone-effector pair.


Pssm-ID: 435583 [Multi-domain]  Cd Length: 160  Bit Score: 41.36  E-value: 1.73e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  925 EKIKRIQQIRMEkelRAQQILEEKELrrqqavLLKHQELERHRLDMERERRRQH--------------------VMLMKA 984
Cdd:pfam16789    6 EQVLDIKKKRVE---EAEKVVKDKKR------ALEKEKEKLAELEAERDKVRKHkkakmqqlrdemdrgttsdkILQMKR 76
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 1720399825  985 MEARKKAEEK-ERLKQEKRDEKRLNKERKLEQRRLELEMA-KELKK 1028
Cdd:pfam16789   77 YIKVVKERLKqEEKKVQDQKEQVRTAARNLEIAREELKKKrQEVEK 122
PHD5_NSD cd15568
PHD finger 5 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
1903-1946 1.78e-03

PHD finger 5 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The nuclear receptor binding SET domain (NSD) protein is a family of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1, that are critical in maintaining chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising to help suppress cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and they play non-redundant roles during development. NSD1 plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. NSD2 is involved in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). This model corresponds to the fifth PHD finger.


Pssm-ID: 277043 [Multi-domain]  Cd Length: 43  Bit Score: 38.08  E-value: 1.78e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1720399825 1903 YCQICRKGdneELLLLCDGcdKGCHTYCHRP--KITTIPDGDWFCP 1946
Cdd:cd15568      1 ECFRCGDG---GDLVLCDF--KGCPKVYHLSclGLEKPPGGKWICP 41
PRK08475 PRK08475
F0F1 ATP synthase subunit B; Validated
863-963 1.97e-03

F0F1 ATP synthase subunit B; Validated


Pssm-ID: 236272 [Multi-domain]  Cd Length: 167  Bit Score: 41.15  E-value: 1.97e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  863 AKLLRKLQAQEIARQAAQIKLLRKLQ--KQEQARVAKEAKKQQAIMAAE-EKRKQKEQMKIIKQQEKIKRIQQIRMEKEL 939
Cdd:PRK08475    59 SKRLEEIQEKLKESKEKKEDALKKLEeaKEKAELIVETAKKEAYILTQKiEKQTKDDIENLIKSFEELMEFEVRKMEREV 138
                           90       100
                   ....*....|....*....|....
gi 1720399825  940 rAQQILEekELRRQQAVLLKHQEL 963
Cdd:PRK08475   139 -VEEVLN--ELFESKKVSLNQQEY 159
hsdR PRK11448
type I restriction enzyme EcoKI subunit R; Provisional
847-976 2.07e-03

type I restriction enzyme EcoKI subunit R; Provisional


Pssm-ID: 236912 [Multi-domain]  Cd Length: 1123  Bit Score: 43.40  E-value: 2.07e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  847 GRPPNVGSAEFLDNTDAKLLRKLQAQEIARQAAQIKLLRKLQKQEQARVAKEAKKQQAI--MAAEEKRKQKEqmkiikQQ 924
Cdd:PRK11448   124 GKDWDFKPGPFVPPEDPENLLHALQQEVLTLKQQLELQAREKAQSQALAEAQQQELVALegLAAELEEKQQE------LE 197
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1720399825  925 EKIKRIQQIrmekelRAQQILEEKELRRQQAVllkhQELERHRLDmERERRR 976
Cdd:PRK11448   198 AQLEQLQEK------AAETSQERKQKRKEITD----QAAKRLELS-EEETRI 238
CALCOCO1 pfam07888
Calcium binding and coiled-coil domain (CALCOCO1) like; Proteins found in this family are ...
835-1021 2.07e-03

Calcium binding and coiled-coil domain (CALCOCO1) like; Proteins found in this family are similar to the coiled-coil transcriptional coactivator protein coexpressed by Mus musculus (CoCoA/CALCOCO1). This protein binds to a highly conserved N-terminal domain of p160 coactivators, such as GRIP1, and thus enhances transcriptional activation by a number of nuclear receptors. CALCOCO1 has a central coiled-coil region with three leucine zipper motifs, which is required for its interaction with GRIP1 and may regulate the autonomous transcriptional activation activity of the C-terminal region.


Pssm-ID: 462303 [Multi-domain]  Cd Length: 488  Bit Score: 42.96  E-value: 2.07e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  835 RAREESRMKRRKGRPPNVGSAEFLDNTDAKLLRKLQ-AQEIARQAAQ-IKLLRKLQKQEQARVAKEAKKQQAIMAAEEKR 912
Cdd:pfam07888   48 QAQEAANRQREKEKERYKRDREQWERQRRELESRVAeLKEELRQSREkHEELEEKYKELSASSEELSEEKDALLAQRAAH 127
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  913 KQKeqmkIIKQQEKIKRIQQIRMEKEL-------RAQQIL----EEKELRRQQAVLLKHQELERHRLDMERERRRQHV-- 979
Cdd:pfam07888  128 EAR----IRELEEDIKTLTQRVLERETelermkeRAKKAGaqrkEEEAERKQLQAKLQQTEEELRSLSKEFQELRNSLaq 203
                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1720399825  980 --------------MLMKAMEARKKAEEKERLKQEKRD-EKRLN-KERKLEQRRLELE 1021
Cdd:pfam07888  204 rdtqvlqlqdtittLTQKLTTAHRKEAENEALLEELRSlQERLNaSERKVEGLGEELS 261
Casc1_N pfam15927
Cancer susceptibility candidate 1 N-terminus; This presumed domain is functionally ...
987-1029 2.08e-03

Cancer susceptibility candidate 1 N-terminus; This presumed domain is functionally uncharacterized. This domain family is found in eukaryotes, and is approximately 200 amino acids in length. The family is found in association with pfam12366. There are two completely conserved residues (N and W) that may be functionally important.


Pssm-ID: 464947 [Multi-domain]  Cd Length: 201  Bit Score: 41.58  E-value: 2.08e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1720399825  987 ARKKAEEKERLKQEKRDEKRLNKERKLEQRRLELEMAKELKKP 1029
Cdd:pfam15927    1 ARLREEEEERLRAEEEEAERLEEERREEEEEERLAAEQDRRAE 43
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
884-1031 2.16e-03

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 43.13  E-value: 2.16e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  884 LRKLQKQEQARVAKEAKKQqaiMAAEEKRKQKEQMKIIKQQEKIKRIQQIRmeKELRAQqILEEKELRRQQAVLlkHQEL 963
Cdd:PRK03918   374 LERLKKRLTGLTPEKLEKE---LEELEKAKEEIEEEISKITARIGELKKEI--KELKKA-IEELKKAKGKCPVC--GREL 445
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1720399825  964 -ERHRLDMERERRRQhvmlMKAMEAR-KKAEEKER-LKQEKRD-EKRLNKERKLeqrRLELEMAKELKKPKE 1031
Cdd:PRK03918   446 tEEHRKELLEEYTAE----LKRIEKElKEIEEKERkLRKELRElEKVLKKESEL---IKLKELAEQLKELEE 510
rne PRK10811
ribonuclease E; Reviewed
828-977 2.17e-03

ribonuclease E; Reviewed


Pssm-ID: 236766 [Multi-domain]  Cd Length: 1068  Bit Score: 43.49  E-value: 2.17e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  828 PPNPDRPRAREESRMKRRKGRPPNVgsaefLDNTDAKLLRKLQAQEIARQAAQIKLLRKLQKQEQARVAKEAKKQQAIMA 907
Cdd:PRK10811   590 EQPAPKAEAKPERQQDRRKPRQNNR-----RDRNERRDTRDNRTRREGRENREENRRNRRQAQQQTAETRESQQAEVTEK 664
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  908 AEEKRKQKEQmkiiKQQEKIKRIQQirmekELRAQQiLEEKELRRQQAVLLKHQELERHRLDMERERRRQ 977
Cdd:PRK10811   665 ARTQDEQQQA----PRRERQRRRND-----EKRQAQ-QEAKALNVEEQSVQETEQEERVQQVQPRRKQRQ 724
PHD_BRPF3 cd15678
PHD finger found in bromodomain and PHD finger-containing protein 3 (BRPF3) and similar ...
1903-1953 2.20e-03

PHD finger found in bromodomain and PHD finger-containing protein 3 (BRPF3) and similar proteins; BRPF3 is a homolog of BRPF1 and BRPF2. It is a scaffold protein that forms a novel monocytic leukemic zinc finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complex with other regulatory subunits. BRPF3 contains a canonical Cys4HisCys3 plant homeodomain (PHD) finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277148 [Multi-domain]  Cd Length: 55  Bit Score: 38.08  E-value: 2.20e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1720399825 1903 YCQICRKGD--NEELLLLCDGCDKGCHTYCHrpKITTIPDGDWFCPACISKAS 1953
Cdd:cd15678      3 FCCVCLDDEchNSNVILFCDICNLAVHQECY--GVPYIPEGQWLCRCCLQSPS 53
RRP36 pfam06102
rRNA biogenesis protein RRP36; RRP36 is involved in the early processing steps of the pre-rRNA.
928-1017 2.38e-03

rRNA biogenesis protein RRP36; RRP36 is involved in the early processing steps of the pre-rRNA.


Pssm-ID: 461829 [Multi-domain]  Cd Length: 158  Bit Score: 40.62  E-value: 2.38e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  928 KRIQQIR-MEKELRAQQILEEKELRRQQAVLLKHQELERHRLDMERERRRQHVmlMKAMEAR---------KKAEEKERL 997
Cdd:pfam06102   57 YRKKEIEeLKKQLKKTKDPEEKEELKRTLQSMESRLKAKKRKDREREVLKEHK--KEEKEKVkqgkkpfylKKSEKKKLL 134
                           90       100
                   ....*....|....*....|..
gi 1720399825  998 KQEKRDEKRLNK--ERKLEQRR 1017
Cdd:pfam06102  135 LKEKFEELKKSGklDKAIEKKR 156
CwlO1 COG3883
Uncharacterized N-terminal coiled-coil domain of peptidoglycan hydrolase CwlO [Function ...
849-1025 2.40e-03

Uncharacterized N-terminal coiled-coil domain of peptidoglycan hydrolase CwlO [Function unknown];


Pssm-ID: 443091 [Multi-domain]  Cd Length: 379  Bit Score: 42.51  E-value: 2.40e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  849 PPNVGSAEFLDNTDAKLlRKLQAQEIARQAAqiklLRKLQKQEQARVAKEAKKQQAIMAAEEKRKQKEQmKIIKQQEKIK 928
Cdd:COG3883      9 PTPAFADPQIQAKQKEL-SELQAELEAAQAE----LDALQAELEELNEEYNELQAELEALQAEIDKLQA-EIAEAEAEIE 82
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  929 RiQQIRMEKELRAQQilEEKELRRQQAVLLKHQELER--HRLD-MERERRRQHVMLMKAMEARKKAEEKERLKQEKRDEK 1005
Cdd:COG3883     83 E-RREELGERARALY--RSGGSVSYLDVLLGSESFSDflDRLSaLSKIADADADLLEELKADKAELEAKKAELEAKLAEL 159
                          170       180
                   ....*....|....*....|
gi 1720399825 1006 RLNKErKLEQRRLELEMAKE 1025
Cdd:COG3883    160 EALKA-ELEAAKAELEAQQA 178
PTZ00266 PTZ00266
NIMA-related protein kinase; Provisional
891-986 2.43e-03

NIMA-related protein kinase; Provisional


Pssm-ID: 173502 [Multi-domain]  Cd Length: 1021  Bit Score: 43.19  E-value: 2.43e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  891 EQARVAKEAKKQQAIMAAEEKRKQKEQMKIIK----QQEKIKRIQQIRMEKELRAQQILEEKELRRQQAvllkhQELERH 966
Cdd:PTZ00266   436 ERARIEKENAHRKALEMKILEKKRIERLEREErerlERERMERIERERLERERLERERLERDRLERDRL-----DRLERE 510
                           90       100
                   ....*....|....*....|....
gi 1720399825  967 RLD-MER---ERRRQHVMLMKAME 986
Cdd:PTZ00266   511 RVDrLERdrlEKARRNSYFLKGME 534
WHIM1 pfam15612
WSTF, HB1, Itc1p, MBD9 motif 1; A conserved alpha helical motif that along with the WHIM2 and ...
1159-1199 2.65e-03

WSTF, HB1, Itc1p, MBD9 motif 1; A conserved alpha helical motif that along with the WHIM2 and WHIM3 motifs, and the DDT domain comprise an alpha helical module found in diverse eukaryotic chromatin proteins.Based on the Ioc3 structure, this module is inferred to interact with nucleosomal linker DNA and the SLIDE domain of ISWI proteins. The resulting complex forms a protein ruler that measures out the spacing between two adjacent nucleosomes. The conserved basic residue in WHIM1 is involved in packing with the DDT motif. The module shows a great domain architectural diversity and is often combined with other modified histone peptide recognising and DNA binding domains, some of which discriminate methylated DNA.


Pssm-ID: 464774 [Multi-domain]  Cd Length: 46  Bit Score: 37.48  E-value: 2.65e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 1720399825 1159 ELTESLKTKAFQAHTPAQKASILAFLVNELACSKSVVSEID 1199
Cdd:pfam15612    6 GLLETLKKGGYYELSPEEKLKILKALCDLLLSSSAIRDEIE 46
rad50 TIGR00606
rad50; All proteins in this family for which functions are known are involvedin recombination, ...
880-1025 2.79e-03

rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).


Pssm-ID: 129694 [Multi-domain]  Cd Length: 1311  Bit Score: 43.11  E-value: 2.79e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  880 QIKLLRKLQKQEQARVAKEAKKQQAIMAAEEKRKQKEQMKIIKQQEKIKRIQQIRMEKELRAQQILEEKELRRQQA---- 955
Cdd:TIGR00606  391 QIKNFHTLVIERQEDEAKTAAQLCADLQSKERLKQEQADEIRDEKKGLGRTIELKKEILEKKQEELKFVIKELQQLegss 470
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1720399825  956 --VLLKHQELERHRLDMERERRRQHVMLMKAMEARKKAEEKERLKQE-KRDEKRLNKERKLEQRRLELEMAKE 1025
Cdd:TIGR00606  471 drILELDQELRKAERELSKAEKNSLTETLKKEVKSLQNEKADLDRKLrKLDQEMEQLNHHTTTRTQMEMLTKD 543
DUF5384 pfam17358
Family of unknown function (DUF5384); This is a family of unknown function found in ...
931-1030 2.91e-03

Family of unknown function (DUF5384); This is a family of unknown function found in Proteobacteria.


Pssm-ID: 407453 [Multi-domain]  Cd Length: 145  Bit Score: 40.36  E-value: 2.91e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  931 QQIRMEKELRAQQILEEKELRRQQAvllkhqelERHRLDMERERRRQhvmlmkAMEARKKAEEKERLKQE-----KRDEK 1005
Cdd:pfam17358    2 QQGKEDRVAAERQAAYEREWEEEQA--------RAEAAAAAARRARA------AAAAAAAAAAKERAKAEaladkKRDQS 67
                           90       100
                   ....*....|....*....|....*
gi 1720399825 1006 RLNKERKLEQRRLELEMAKELKKPK 1030
Cdd:pfam17358   68 YEDELRALEIEERKLALAAQKARAK 92
PHD_PHF3_like cd15552
PHD finger found in PHD finger protein 3 (PHF3), and death-inducer obliterator variants Dido1, ...
1903-1948 2.92e-03

PHD finger found in PHD finger protein 3 (PHF3), and death-inducer obliterator variants Dido1, Dido2, and Dido3; PHF3 is a human homolog of yeast protein bypass of Ess1 (Bye1), a nuclear protein with a domain resembling the central domain in the transcription elongation factor TFIIS. It is ubiquitously expressed in normal tissues including brain, but its expression is significantly reduced or lost in glioblastomas. PHF3 contains an N-terminal plant homeodomain (PHD) finger, a central RNA polymerase II (Pol II)-binding TFIIS-like domain (TLD) domain, and a C-terminal Spen paralogue and orthologue C-terminal (SPOC) domain. This family also includes Dido gene encoding three alternative splicing variants (Dido1, 2, and 3), which have been implicated in a number of cellular processes such as apoptosis and chromosomal segregation, particularly in the hematopoietic system. Dido1 is important for maintaining embryonic stem (ES) cells and directly regulates the expression of pluripotency factors. It is the shortest isoform that contains only a highly conserved PHD finger responsible for the binding of histone H3 with a higher affinity for trimethylated lysine4 (H3K4me3). Gene Dido1 is a Bone morphogenetic protein (BMP) target gene and promotes BMP-induced melanoma progression. It also triggers apoptosis after nuclear translocation and caspase upregulation. Dido3 is the largest isoform and is ubiquitously expressed in all human tissues. It is dispensable for ES cell self-renewal and pluripotency, but is involved in the maintenance of stem cell genomic stability and tumorigenesis. Dido3 contains a PHD finger, a transcription elongation factor S-II subunit M (TFSIIM) domain, a SPOC module, and a long C-terminal region (CT) of unknown homology.


Pssm-ID: 277027  Cd Length: 50  Bit Score: 37.76  E-value: 2.92e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1720399825 1903 YCqICRKGDNEELLLLCDGCDKGCHTYC-----HRPKITTIPDGDWFCPAC 1948
Cdd:cd15552      1 YC-ICRKPHNNRFMICCDRCEEWFHGDCvgiteAQGKEMEENIEEYVCPKC 50
PHD_AF10_AF17 cd15574
PHD finger found in protein AF-10 and AF-17; This family includes protein AF-10 and AF-17. ...
1904-1948 3.01e-03

PHD finger found in protein AF-10 and AF-17; This family includes protein AF-10 and AF-17. AF-10, also termed ALL1 (acute lymphoblastic leukemia)-fused gene from chromosome 10 protein, is a transcription factor encoded by gene AF10, a translocation partner of the MLL (mixed-lineage leukemia) oncogene in leukemia. AF-10 has been implicated in the development of leukemia following chromosomal rearrangements between the AF10 gene and one of at least two other genes, MLL and CALM. It plays a key role in the survival of uncommitted hematopoietic cells. Moreover, AF-10 functions as a follistatin-related gene (FLRG)-interacting protein. The interaction with FLRG enhances AF10-dependent transcription. It interacts with the human counterpart of the yeast Dot1, hDOT1L, and may act as a bridge for the recruitment of hDOT1L to the genes targeted by MLL-AF10. It also interacts with the synovial sarcoma associated SYT protein and may play a role in synovial sarcomas and acute leukemias. AF-17, also termed ALL1-fused gene from chromosome 17 protein, is encoded by gene AF17 that has been identified in hematological malignancies as translocation partners of the mixed lineage leukemia gene MLL. It is a putative transcription factor that may play a role in multiple signaling pathways. It is involved in chromatin-mediated gene regulation mechanisms. It functions as a component of the multi-subunit Dot1 complex (Dotcom) and plays a role in the Wnt/Wingless signaling pathway. It also seems to be a downstream target of the beta-catenin/T-cell factor pathway, and participates in G2-M progression. Moreover, it may function as an important regulator of ENaC-mediated Na+ transport and thus blood pressure. Both AF-10 and AF-17 contain an N-terminal canonical Cys4HisCys3 plant homeodomain (PHD) finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. The PHD finger is involved in their homo-oligomerization. In the C-terminal region, they possess a leucine zipper domain and a glutamine-rich region. This family also includes ZFP-1, the Caenorhabditis elegans AF10 homolog. It was originally identified as a factor promoting RNAi interference in C. elegans. It also acts as a Dot1-interacting protein that opposes H2B ubiquitination to reduce polymerase II (Pol II) transcription. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277049 [Multi-domain]  Cd Length: 48  Bit Score: 37.49  E-value: 3.01e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1720399825 1904 CQIC--RKGDNEELLLLCDG--CDKGCHTYCHrpKITTIPDGDWFCPAC 1948
Cdd:cd15574      2 CCVCsdERGWAENPLVYCDGhgCNVAVHQACY--GIVQVPTGPWFCRKC 48
bMERB_dom pfam12130
Bivalent Mical/EHBP Rab binding domain; A variety of different effector proteins interact ...
917-1026 3.05e-03

Bivalent Mical/EHBP Rab binding domain; A variety of different effector proteins interact specifically with GTP-bound Rab proteins and mediate their versatile roles in membrane trafficking, including budding of vesicles from a donor membrane, directed transport through the cell and finally tethering and fusion with a target membrane. The 'bivalent Mical/EHBP Rab binding' (bMERB) domain is a Rab effector domain that is present in proteins of the Mical and EHBP families, both known to act in endosomal trafficking. The bMERB domain displays a preference for Rab8 family proteins (Rab8, 10, 13 and 15) and at least some of the bMERB domains contain two separate binding sites for Rab-proteins, allowing Micals and EHBPs to bind two Rabs simultaneously. The strong similarity between the two binding sites within one bMRB domain strongly suggests an evolutionarily development via duplication of a common ancestor supersecondary structure element. The bMERB domain has a completely alpha-helical fold consisting of a central helix and N- and C-terminal helices folding back on this central helix.


Pssm-ID: 463467 [Multi-domain]  Cd Length: 131  Bit Score: 39.80  E-value: 3.05e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  917 QMKII-KQQEKIKRiQQIRMEKELRAQ--------QILEEK--------ELRRQQA---VLLKHQELERHRLDMERERRR 976
Cdd:pfam12130    1 ELEEIeERQRELEE-RGVELEKALRGEmsgdeeeeQLLQEWfklvneknALVRRESelmYLAKEQDLEERQARLEQELRE 79
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  977 qhvmLMKAMEARK----KAEEKERLKQ-----EKRDEKRlnkeRKLEQRRL-ELEMAKEL 1026
Cdd:pfam12130   80 ----LMSKPDWLKteedKQREEELLEElveivEQRDALV----DSLEEDRLrEEEEDEEL 131
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
909-1043 3.13e-03

chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274009 [Multi-domain]  Cd Length: 1164  Bit Score: 42.75  E-value: 3.13e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  909 EEKRKQKEQMKIIKqqEKIKRIQQIrmEKELRAQQileeKELRRQQAVLLKHQELERhrldmERERRRQHVML--MKAME 986
Cdd:TIGR02169  170 RKKEKALEELEEVE--ENIERLDLI--IDEKRQQL----ERLRREREKAERYQALLK-----EKREYEGYELLkeKEALE 236
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1720399825  987 ARKKAEEKERLKQEKRDEKRlnkERKLEQRRLEL--------EMAKELKKPKEDMCLADQKPLPE 1043
Cdd:TIGR02169  237 RQKEAIERQLASLEEELEKL---TEEISELEKRLeeieqlleELNKKIKDLGEEEQLRVKEKIGE 298
fliJ PRK07720
flagellar biosynthesis chaperone FliJ;
897-1019 3.37e-03

flagellar biosynthesis chaperone FliJ;


Pssm-ID: 181091 [Multi-domain]  Cd Length: 146  Bit Score: 40.05  E-value: 3.37e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  897 KEAKKQQAIMAAEEKRKQKEQM-----KIIKQQEKIKRIQQIRMEKELRAQqileekELR-RQQAVLLKHQELE--RHRL 968
Cdd:PRK07720    14 KENEKEKALGEYEEAVSRFEQVaeklyELLKQKEDLEQAKEEKLQSGLSIQ------EIRhYQQFVTNLERTIDhyQLLV 87
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1720399825  969 DMERER--RRQHVMLMKAMEARKkaeeKERLKqEKRDEKRLNKERKLEQRRLE 1019
Cdd:PRK07720    88 MQAREQmnRKQQDLTEKNIEVKK----YEKMK-EKKQEMFALEEKAAEMKEMD 135
PHD_JADE1 cd15679
PHD finger found in protein Jade-1 and similar proteins; Jade-1, also termed PHD finger ...
1904-1948 3.70e-03

PHD finger found in protein Jade-1 and similar proteins; Jade-1, also termed PHD finger protein 17 (PHF17), is a novel binding partner of von Hippel-Lindau (VHL) tumor suppressor Pvhl, a key regulator of the cellular oxygen sensing pathway. It is highly expressed in renal proximal tubules. Jade-1 functions as an essential regulator of multiple cell signaling pathways. It may be involved in the serine/threonine kinase AKT/AKT1 pathway during renal cancer pathogenesis and normally prevents renal epithelial cell proliferation and transformation. It also acts as a pro-apoptotic and growth suppressive ubiquitin ligase to inhibit canonical Wnt downstream effector beta-catenin for proteasomal degradation, and as a transcription factor associated with histone acetyltransferase activity and with increased abundance of cyclin-dependent kinase inhibitor p21. Moreover, Jade-1 is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and Eaf6 to form a HBO1 complex, and plays a role in epithelial cell regeneration. It has also been identified as a novel component of the nephrocystin protein (NPHP) complex and interacts with the ciliary protein nephrocystin-4 (NPHP4). Jade-1 contains a canonical Cys4HisCys3 plant homeodomain (PHD) finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, both of which are zinc-binding motifs. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277149 [Multi-domain]  Cd Length: 46  Bit Score: 37.36  E-value: 3.70e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1720399825 1904 CQICRKGDNEE--LLLLCDGCDKGCHTYCHrpKITTIPDGDWFCPAC 1948
Cdd:cd15679      2 CDVCQSPDGEDgnEMVFCDKCNICVHQACY--GILKVPEGSWLCRTC 46
growth_prot_Scy NF041483
polarized growth protein Scy;
863-1032 3.77e-03

polarized growth protein Scy;


Pssm-ID: 469371 [Multi-domain]  Cd Length: 1293  Bit Score: 42.51  E-value: 3.77e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  863 AKLLRKlQAQE-IARQAAQIKLLRKlQKQEQArvakEAKKQQAIMAAEEKRKQKEQMKIIKQQEKIKRIQQIRMEKELR- 940
Cdd:NF041483   515 ATTLRR-QAEEtLERTRAEAERLRA-EAEEQA----EEVRAAAERAARELREETERAIAARQAEAAEELTRLHTEAEERl 588
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  941 --AQQIL-----EEKELRRQQAvllkhQELERHRLDM-------------ERERRRQHVMlMKAMEARKKAE-------- 992
Cdd:NF041483   589 taAEEALadaraEAERIRREAA-----EETERLRTEAaerirtlqaqaeqEAERLRTEAA-ADASAARAEGEnvavrlrs 662
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*
gi 1720399825  993 ----EKERLKQEKRDE-KRLNKERKLEQRRLELEMAKELKKPKED 1032
Cdd:NF041483   663 eaaaEAERLKSEAQESaDRVRAEAAAAAERVGTEAAEALAAAQEE 707
PspA COG1842
Phage shock protein A [Transcription, Signal transduction mechanisms];
881-1002 3.83e-03

Phage shock protein A [Transcription, Signal transduction mechanisms];


Pssm-ID: 441447 [Multi-domain]  Cd Length: 217  Bit Score: 40.96  E-value: 3.83e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  881 IKLLR-KLQKQEQARVakEAKKQQAIMAAEEKRkqkEQMKIIKQQEKIKRIQQirmekelRAQQILE--EKELRRqqAVL 957
Cdd:COG1842     25 EKMLDqAIRDMEEDLV--EARQALAQVIANQKR---LERQLEELEAEAEKWEE-------KARLALEkgREDLAR--EAL 90
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 1720399825  958 LKHQELERHRLDMERERRRQHVMLMKAMEARKKAEEK-ERLKQEKR 1002
Cdd:COG1842     91 ERKAELEAQAEALEAQLAQLEEQVEKLKEALRQLESKlEELKAKKD 136
GumC COG3206
Exopolysaccharide export protein/domain GumC/Wzc1 [Cell wall/membrane/envelope biogenesis];
863-955 3.85e-03

Exopolysaccharide export protein/domain GumC/Wzc1 [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442439 [Multi-domain]  Cd Length: 687  Bit Score: 42.31  E-value: 3.85e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  863 AKLLRKLQAQ--EIARQAAQIKLLRKLQKQEQARVAKEAKKQQAIMAAEEK--RKQKEQMKIIKQQEKIKRIQQIRMEKE 938
Cdd:COG3206    280 AELSARYTPNhpDVIALRAQIAALRAQLQQEAQRILASLEAELEALQAREAslQAQLAQLEARLAELPELEAELRRLERE 359
                           90
                   ....*....|....*...
gi 1720399825  939 L-RAQQILEEKELRRQQA 955
Cdd:COG3206    360 VeVARELYESLLQRLEEA 377
ClassIIa_HDAC4_Gln-rich-N cd10162
Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase; This ...
945-1030 3.92e-03

Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase; This family consists of the glutamine-rich domain of histone deacetylase 4 (HDAC4). It belongs to a superfamily that consists of the glutamine-rich N-terminal helical extension to certain Class IIa histone deacetylases (HDACs), including HDAC4, HDAC5 and HDCA9; it is missing from HDAC7. This domain confers responsiveness to calcium signals and mediates interactions with transcription factors and cofactors, and it is able to repress transcription independently of the HDAC C-terminal, zinc-dependent catalytic domain. It has many intra- and inter-helical interactions which are possibly involved in reversible assembly and disassembly of proteins. HDACs regulate diverse cellular processes through enzymatic deacetylation of histone as well as non-histone proteins, in particular deacetylating N(6)-acetyl-lysine residues.


Pssm-ID: 197398 [Multi-domain]  Cd Length: 90  Bit Score: 38.64  E-value: 3.92e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  945 LEEKELRRQQAVLLKHQELERHRLDMERERRRQHVMLMKAMEARKKAEEKERLKQEKRDEKRLNKERKLEQRRLELEMAK 1024
Cdd:cd10162      4 LREQQLQQELLALKQKQQIQRQLLIAEFQRQHEQLSRQHEAQLHEHIKQQQELLAMKHQQELLEHQRKLERHRQEQEMEK 83

                   ....*.
gi 1720399825 1025 ELKKPK 1030
Cdd:cd10162     84 QQREQK 89
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
855-1031 3.96e-03

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 42.36  E-value: 3.96e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  855 AEFLDNTDAKLlRKLQAQEIARQAAQIKLLRKLQ---KQEQARVAKEAKKQQAImaaeEKRKQKEQMKIIKQQEKIKRIQ 931
Cdd:PRK03918   502 AEQLKELEEKL-KKYNLEELEKKAEEYEKLKEKLiklKGEIKSLKKELEKLEEL----KKKLAELEKKLDELEEELAELL 576
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  932 QIRMEKELRAQQILEEKeLRRQQAVLLKHQELERHRLDMERERRRQHVMLMKAMEARKKAEEKERLKQEKRDE-----KR 1006
Cdd:PRK03918   577 KELEELGFESVEELEER-LKELEPFYNEYLELKDAEKELEREEKELKKLEEELDKAFEELAETEKRLEELRKEleeleKK 655
                          170       180
                   ....*....|....*....|....*
gi 1720399825 1007 LNKERKLEQRRLELEMAKELKKPKE 1031
Cdd:PRK03918   656 YSEEEYEELREEYLELSRELAGLRA 680
CALCOCO1 pfam07888
Calcium binding and coiled-coil domain (CALCOCO1) like; Proteins found in this family are ...
859-1016 4.29e-03

Calcium binding and coiled-coil domain (CALCOCO1) like; Proteins found in this family are similar to the coiled-coil transcriptional coactivator protein coexpressed by Mus musculus (CoCoA/CALCOCO1). This protein binds to a highly conserved N-terminal domain of p160 coactivators, such as GRIP1, and thus enhances transcriptional activation by a number of nuclear receptors. CALCOCO1 has a central coiled-coil region with three leucine zipper motifs, which is required for its interaction with GRIP1 and may regulate the autonomous transcriptional activation activity of the C-terminal region.


Pssm-ID: 462303 [Multi-domain]  Cd Length: 488  Bit Score: 42.19  E-value: 4.29e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  859 DNTDAKLLR-KLQAQEIARQAAQIKLLrklQKQEQARVAKEAKKQQAIMAAEEKRKQKEQMKIIKQQEkikRIQQIRMEK 937
Cdd:pfam07888  268 DRTQAELHQaRLQAAQLTLQLADASLA---LREGRARWAQERETLQQSAEADKDRIEKLSAELQRLEE---RLQEERMER 341
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1720399825  938 ELRAQQILEEKELRRQQAvllkhqelerhrldmeRERRRQHVMLMKAMEARKKaeEKERLKQEKRDekRLNKERKLEQR 1016
Cdd:pfam07888  342 EKLEVELGREKDCNRVQL----------------SESRRELQELKASLRVAQK--EKEQLQAEKQE--LLEYIRQLEQR 400
COG1340 COG1340
Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown];
864-1033 4.56e-03

Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown];


Pssm-ID: 440951 [Multi-domain]  Cd Length: 297  Bit Score: 41.43  E-value: 4.56e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  864 KLLRKLQAQEIARQAAQIKLLRKLQKQEQARVAKEAKKQQAIMAAEEKRKQK-EQMKIIKQQ---------EKIKRIQQI 933
Cdd:COG1340     18 EELREEIEELKEKRDELNEELKELAEKRDELNAQVKELREEAQELREKRDELnEKVKELKEErdelneklnELREELDEL 97
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  934 RMEKELRAQQILEEKELRRQQAVLLKHQELERHRLDMERERRRQHVMLMKAMEARKKAEEKERLKQEKRDEKRLNKERKL 1013
Cdd:COG1340     98 RKELAELNKAGGSIDKLRKEIERLEWRQQTEVLSPEEEKELVEKIKELEKELEKAKKALEKNEKLKELRAELKELRKEAE 177
                          170       180
                   ....*....|....*....|
gi 1720399825 1014 EQRRLELEMAKELKKPKEDM 1033
Cdd:COG1340    178 EIHKKIKELAEEAQELHEEM 197
DUF2368 pfam10166
Uncharacterized conserved protein (DUF2368); This family is conserved from nematodes to humans. ...
915-963 4.90e-03

Uncharacterized conserved protein (DUF2368); This family is conserved from nematodes to humans. The function is not known.


Pssm-ID: 431104  Cd Length: 134  Bit Score: 39.18  E-value: 4.90e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1720399825  915 KEQMKiiKQQEKIKRIQQIRMEKELRAQQILEEkelrRQQAV-LLKHQEL 963
Cdd:pfam10166   10 DENMK--KNQEFMLEMQRLQLERQLAMQNLMRE----RQMAMqIARSREL 53
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
860-942 5.17e-03

Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 443969 [Multi-domain]  Cd Length: 377  Bit Score: 41.67  E-value: 5.17e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  860 NTDAKLLRKLQAQEIARQAAQIKLLRKLQkQEQARVAKEAKKQQAIMAAEEKRKQKEQMKIIKQQEKIKRIQQI--RMEK 937
Cdd:COG4942    156 RADLAELAALRAELEAERAELEALLAELE-EERAALEALKAERQKLLARLEKELAELAAELAELQQEAEELEALiaRLEA 234

                   ....*
gi 1720399825  938 ELRAQ 942
Cdd:COG4942    235 EAAAA 239
ERM_helical pfam20492
Ezrin/radixin/moesin, alpha-helical domain; The ERM family consists of three closely-related ...
947-1033 5.28e-03

Ezrin/radixin/moesin, alpha-helical domain; The ERM family consists of three closely-related proteins, ezrin, radixin and moesin. Ezrin was first identified as a constituent of microvilli, radixin as a barbed, end-capping actin-modulating protein from isolated junctional fractions, and moesin as a heparin binding protein. A tumour suppressor molecule responsible for neurofibromatosis type 2 (NF2) is highly similar to ERM proteins and has been designated merlin (moesin-ezrin-radixin-like protein). ERM molecules contain 3 domains, an N-terminal globular domain, an extended alpha-helical domain and a charged C-terminal domain (pfam00769). Ezrin, radixin and merlin also contain a polyproline linker region between the helical and C-terminal domains. The N-terminal domain is highly conserved and is also found in merlin, band 4.1 proteins and members of the band 4.1 superfamily, designated the FERM domain. ERM proteins crosslink actin filaments with plasma membranes. They co-localize with CD44 at actin filament plasma membrane interaction sites, associating with CD44 via their N-terminal domains and with actin filaments via their C-terminal domains. This is the alpha-helical domain, which is involved in intramolecular masking of protein-protein interaction sites, regulating the activity of this proteins.


Pssm-ID: 466641 [Multi-domain]  Cd Length: 120  Bit Score: 38.75  E-value: 5.28e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  947 EKELRRQQAVLLKHQELERHRLDMERERRRQHVMLMKAMEARKKA-EEKERLKQEKRdekrlnkERKLEQRRLELEMAKE 1025
Cdd:pfam20492    2 EEAEREKQELEERLKQYEEETKKAQEELEESEETAEELEEERRQAeEEAERLEQKRQ-------EAEEEKERLEESAEME 74

                   ....*...
gi 1720399825 1026 LKKpKEDM 1033
Cdd:pfam20492   75 AEE-KEQL 81
DUF4200 pfam13863
Domain of unknown function (DUF4200); This family is found in eukaryotes. It is a coiled-coil ...
872-947 5.49e-03

Domain of unknown function (DUF4200); This family is found in eukaryotes. It is a coiled-coil domain of unknwon function.


Pssm-ID: 464003 [Multi-domain]  Cd Length: 119  Bit Score: 38.70  E-value: 5.49e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  872 QEIARQAAQIKL----LRKLQKQEQARVAK--------EAKKQQAIMAAEEKRKQKEQ--MKIIKQQEKIKRIQQI--RM 935
Cdd:pfam13863   20 EEIERLEELLKQreeeLEKKEQELKEDLIKfdkflkenDAKRRRALKKAEEETKLKKEkeKEIKKLTAQIEELKSEisKL 99
                           90
                   ....*....|..
gi 1720399825  936 EKELRAQQILEE 947
Cdd:pfam13863  100 EEKLEEYKPYED 111
CortBP2 pfam09727
Cortactin-binding protein-2; This entry is the first approximately 250 residues of ...
898-1039 5.77e-03

Cortactin-binding protein-2; This entry is the first approximately 250 residues of cortactin-binding protein 2. In addition to being a positional candidate for autism this protein is expressed at highest levels in the brain in humans. The human protein has six associated ankyrin repeat domains pfam00023 towards the C-terminus which act as protein-protein interaction domains.


Pssm-ID: 462860 [Multi-domain]  Cd Length: 187  Bit Score: 39.89  E-value: 5.77e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  898 EAKKQQAIMAAEEKRKQKEQMKIIKQQEKIKRIQQIRMekelraQQILEEKELRRQQAVllkhqelerHRLDMERERRRQ 977
Cdd:pfam09727   59 ELLRDQSQDEDVYEAMYEKPLAELEKLVEKQRETQRRM------LEQLAAAEKRHRRVI---------RELEEEKRKHAR 123
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  978 HV--------MLMKamearkkaeEKERLKQEkrdekrLNKERKlEQRRLELEMAKELKKPKEDmcLADQK 1039
Cdd:pfam09727  124 DTaqgddftyLLEK---------ERERLKQE------LEQEKA-QQKRLEKELKKLLEKLEEE--LSKQK 175
TolA COG3064
Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis];
870-1021 6.22e-03

Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442298 [Multi-domain]  Cd Length: 485  Bit Score: 41.56  E-value: 6.22e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  870 QAQEIARQAAQIKLLRKLQKQEQARVAKEAKKQ----------QAIMAAEEKRKQKEQMKIIKQQEKIKRIQQIRMEKEL 939
Cdd:COG3064     75 AAKKLAEAEKAAAEAEKKAAAEKAKAAKEAEAAaaaekaaaaaEKEKAEEAKRKAEEEAKRKAEEERKAAEAEAAAKAEA 154
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  940 RAQQILEEKELRRQQAVLLKHQELERHRLDMERERRRQHVMLMKAMEARKKAEEKERLKQEKRDEKRLNKERKLEQRRLE 1019
Cdd:COG3064    155 EAARAAAAAAAAAAAAAARAAAGAAAALVAAAAAAVEAADTAAAAAAALAAAAAAAAADAALLALAVAARAAAASREAAL 234

                   ..
gi 1720399825 1020 LE 1021
Cdd:COG3064    235 AA 236
UDM1_RNF168_RNF169-like cd22249
UDM1 (ubiquitin-dependent DSB recruitment module 1) found in RING finger proteins RNF168, ...
960-1026 6.42e-03

UDM1 (ubiquitin-dependent DSB recruitment module 1) found in RING finger proteins RNF168, RNF169 and similar proteins; This model represents the UDM1 (ubiquitin-dependent double-strand break [DSB] recruitment module 1) found in RING finger proteins, RNF168 and RNF169. RNF168 is an E3 ubiquitin-protein ligase that promotes non-canonical K27 ubiquitination to signal DNA damage. It functions, together with RNF8, as a DNA damage response (DDR) factor that promotes a series of ubiquitylation events on substrates such as H2A and H2AX. With H2AK13/15 ubiquitylation, it facilitates recruitment of repair factors p53-binding protein 1 (53BP1) or the RAP80-BRCA1 complex to sites of double-strand breaks (DSBs), and inhibits homologous recombination (HR) in cells deficient in the tumor suppressor BRCA1. RNF168 also promotes H2A neddylation, which antagonizes ubiquitylation of H2A and regulates DNA damage repair. In addition, RNF168 forms a functional complex with RAD6A or RAD6B during the DNA damage response. RNF169 is an uncharacterized E3 ubiquitin-protein ligase paralogous to RNF168. It functions as a negative regulator of the DNA damage signaling cascade. RNF169 recognizes polyubiquitin structures but does not itself contribute to double-strand break (DSB)-induced chromatin ubiquitylation. It contributes to the regulation of DSB repair pathway utilization via functionally competing with recruiting repair factors, 53BP1 and RAP80-BRCA1, for association with RNF168-modified chromatin, independent of its catalytic activity, limiting the magnitude of the RNF8/RNF168-dependent signaling response to DSBs. The UDM1 domain comprises LRM1 (LR motif 1), UMI (ubiquitin-interacting motif [UIM]- and MIU-related UBD) and MIU1 (motif interacting with ubiquitin 1). Mutations of Ub-interacting residues in UDM1 have little effect on the accumulation of RNF168 to DSB sites, suggesting that it may not be the main site of binding ubiquitylated and polyubiquitylated targets.


Pssm-ID: 409016 [Multi-domain]  Cd Length: 66  Bit Score: 37.25  E-value: 6.42e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1720399825  960 HQELERHRLDMERERRRQhvmlmKAMEARKKAEEKERLKQEkrdEKRLNKERKLEQRRLELEMAKEL 1026
Cdd:cd22249      8 REEYEAQLKKLEEERRKE-----REEEEKASEELIRKLQEE---EERQRKREREEQLKQDEELAKQL 66
HlpA COG2825
Periplasmic chaperone for outer membrane proteins, Skp family [Cell wall/membrane/envelope ...
868-953 7.05e-03

Periplasmic chaperone for outer membrane proteins, Skp family [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 442073 [Multi-domain]  Cd Length: 171  Bit Score: 39.43  E-value: 7.05e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  868 KLQAQEIARQAAQIKLLRKLQKQEQarvakEAKKQQAIMAAEEkrKQKEQMKIIKQQEKIKRIQQiRMEKELRAQQILEE 947
Cdd:COG2825     47 KLEKEFKKRQAELQKLEKELQALQE-----KLQKEAATLSEEE--RQKKERELQKKQQELQRKQQ-EAQQDLQKRQQELL 118

                   ....*.
gi 1720399825  948 KELRRQ 953
Cdd:COG2825    119 QPILEK 124
PHD_Cfp1 cd15553
PHD finger found in CXXC-type zinc finger protein 1 (Cfp1); Cfp1, also termed CpG-binding ...
1903-1948 7.94e-03

PHD finger found in CXXC-type zinc finger protein 1 (Cfp1); Cfp1, also termed CpG-binding protein, or PHD finger and CXXC domain-containing protein 1 (PCCX1), is a specificity factor that binds to unmethylated CpGs and links H3K4me3 with CpG islands (CGIs). It integrates both promoter CpG content and gene activity for accurate trimethylation of histone H3 Lys 4 (H3K4me3) deposition in embryonic stem cells. Moreover, Cfp1 is an essential component of the SETD1 histone H3K4 methyltransferase complex and functions as a critical regulator of histone methylation, cytosine methylation, cellular differentiation, and vertebrate development. Cfp1 contains a plant homeodomain (PHD) finger, a CXXC domain, and a CpG binding protein zinc finger C-terminal domain. Its CXXC domain selectively binds to non-methylated CpG islands, following by a preference for a guanosine nucleotide.


Pssm-ID: 277028  Cd Length: 46  Bit Score: 36.20  E-value: 7.94e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1720399825 1903 YCqICRKGDNEELLLLCDGCDKGCHTYC-----HRPKITTipdgDWFCPAC 1948
Cdd:cd15553      1 YC-ICRSSDISRFMIGCDNCEEWYHGDCiniteKEAKAIK----EWYCQQC 46
FliJ pfam02050
Flagellar FliJ protein;
864-1007 8.47e-03

Flagellar FliJ protein;


Pssm-ID: 426581 [Multi-domain]  Cd Length: 123  Bit Score: 38.42  E-value: 8.47e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  864 KLLRKLQAQEIARQAAQIKLLRKLQkqEQARVAKEAKKQQAIMAAEEKRKQKEQMKIIKQqekikRIQQIRmEKELRAQQ 943
Cdd:pfam02050    2 EAARELAEAQRELQQAEEKLEELQQ--YRAEYQQQLSGAGQGISAAELRNYQAFISQLDE-----AIAQQQ-QELAQAEA 73
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1720399825  944 ILEekelRRQQAVLLKHQELERHRLDMERERRrqhvmlmkamearkkaeeKERLKQEKRDEKRL 1007
Cdd:pfam02050   74 QVE----KAREEWQEARQERKSLEKLREREKK------------------EERKEQNRREQKQL 115
PKK pfam12474
Polo kinase kinase; This domain family is found in eukaryotes, and is approximately 140 amino ...
887-1028 8.95e-03

Polo kinase kinase; This domain family is found in eukaryotes, and is approximately 140 amino acids in length. The family is found in association with pfam00069. Polo-like kinase 1 (Plx1) is essential during mitosis for the activation of Cdc25C, for spindle assembly, and for cyclin B degradation. This family is Polo kinase kinase (PKK) which phosphorylates Polo kinase and Polo-like kinase to activate them. PKK is a serine/threonine kinase.


Pssm-ID: 463600 [Multi-domain]  Cd Length: 139  Bit Score: 38.70  E-value: 8.95e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  887 LQKQEQarvaKEAKKQQaiMAAEEKRKQKEQMKIIKQQ----EKIKRIQQIrmekELRAqqileekELRRQQAvllkhqE 962
Cdd:pfam12474    3 LQKEQQ----KDRFEQE--RQQLKKRYEKELEQLERQQkqqiEKLEQRQTQ----ELRR-------LPKRIRA------E 59
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1720399825  963 LERhRLDMERERRRQHVMLMKAMEAR-KKAEEKERLKQEKRDEKRLNKERKLEQRRLELE-MAKELKK 1028
Cdd:pfam12474   60 QKK-RLKMFRESLKQEKKELKQEVEKlPKFQRKEAKRQRKEELELEQKHEELEFLQAQSEaLERELQQ 126
PspA COG1842
Phage shock protein A [Transcription, Signal transduction mechanisms];
872-1030 9.27e-03

Phage shock protein A [Transcription, Signal transduction mechanisms];


Pssm-ID: 441447 [Multi-domain]  Cd Length: 217  Bit Score: 39.81  E-value: 9.27e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  872 QEIARQAA-QIKLLRKLQKQEqARVAK-EAKKQQAIMAAEEKRKQKEQMKIIKQQEKIKriqqiRMEKELRAQQILEEKe 949
Cdd:COG1842     44 QALAQVIAnQKRLERQLEELE-AEAEKwEEKARLALEKGREDLAREALERKAELEAQAE-----ALEAQLAQLEEQVEK- 116
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  950 LRRQqavllkHQELERHRLDMERERRrqhvmLMKAMEARKKAEEK--ERLKQEKRDE--KRLNK-ERKLEQRRLELEMAK 1024
Cdd:COG1842    117 LKEA------LRQLESKLEELKAKKD-----TLKARAKAAKAQEKvnEALSGIDSDDatSALERmEEKIEEMEARAEAAA 185

                   ....*.
gi 1720399825 1025 ELKKPK 1030
Cdd:COG1842    186 ELAAGD 191
COG4372 COG4372
Uncharacterized protein, contains DUF3084 domain [Function unknown];
866-1032 9.76e-03

Uncharacterized protein, contains DUF3084 domain [Function unknown];


Pssm-ID: 443500 [Multi-domain]  Cd Length: 370  Bit Score: 40.66  E-value: 9.76e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  866 LRKLQAQEIARQAAQIKLLRKLQKQEQARVAKEAKKQQAIMAAEEKRKQKEQM--KIIKQQEKIKRIQQIRMEKELRA-- 941
Cdd:COG4372    103 LESLQEEAEELQEELEELQKERQDLEQQRKQLEAQIAELQSEIAEREEELKELeeQLESLQEELAALEQELQALSEAEae 182
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  942 ---QQILEEKELRRQQAVLLKHQELERHRLDMERERRRQHVMLMKAMEARKKAEEKERLKQEKRDEKRLNKERKLEQRRL 1018
Cdd:COG4372    183 qalDELLKEANRNAEKEEELAEAEKLIESLPRELAEELLEAKDSLEAKLGLALSALLDALELEEDKEELLEEVILKEIEE 262
                          170
                   ....*....|....
gi 1720399825 1019 ELEMAKELKKPKED 1032
Cdd:COG4372    263 LELAILVEKDTEEE 276
FAM184 pfam15665
Family with sequence similarity 184, A and B; The function of FAM184 is not known.
885-1007 9.85e-03

Family with sequence similarity 184, A and B; The function of FAM184 is not known.


Pssm-ID: 464788 [Multi-domain]  Cd Length: 211  Bit Score: 39.64  E-value: 9.85e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399825  885 RKLQKQEQARVAKEAKKQQAIMAA-EEKRKQKEQMKIIKQQEKIKRIQQIRMEKELRAQQILeeKELRRQQAVLLKHQE- 962
Cdd:pfam15665   88 LKAEAEHRQRVVELSREVEEAKRAfEEKLESFEQLQAQFEQEKRKALEELRAKHRQEIQELL--TTQRAQSASSLAEQEk 165
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 1720399825  963 -LERHRLDMerERRRQHVMLMKAmEARKKAEEKE--RLKQEKRDEKRL 1007
Cdd:pfam15665  166 lEELHKAEL--ESLRKEVEDLRK-EKKKLAEEYEqkLSKAQAFYEREL 210
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH