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Conserved domains on  [gi|1729808|sp|P49846|]
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RecName: Full=Transcription initiation factor TFIID subunit 5; AltName: Full=TAFII-80; AltName: Full=Transcription initiation factor TFIID 85 kDa subunit; Short=p85

Protein Classification

TAF5 family protein( domain architecture ID 10169025)

TATA binding protein (TBP) associated factor 5 (TAF5) family protein, similar to TAF5 which is one of several TAFs that bind TBP and are involved in forming the transcription factor IID (TFIID) complex

Gene Ontology:  GO:0006357

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
WD40 COG2319
WD40 repeat [General function prediction only];
364-646 1.48e-80

WD40 repeat [General function prediction only];


:

Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 262.15  E-value: 1.48e-80
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808  364 QLPSAVFYTVLNSHQG-VTCAEISDDSTMLACGFGDSSVRIWSL-TPAKLRTLKD-ADSLREL----DKE-----SADIN 431
Cdd:COG2319 106 DLATGLLLRTLTGHTGaVRSVAFSPDGKTLASGSADGTVRLWDLaTGKLLRTLTGhSGAVTSVafspDGKllasgSDDGT 185

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808  432 VRMLDDRSGEVTRSLMGHTGPVYRCAFAPEMNLLLSCSEDSTIRLWSLLTWSCVVTYRGHVYPVWDVRFAPHGYYFVSCS 511
Cdd:COG2319 186 VRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKLLASGSADGTVRLWDLATGKLLRTLTGHSGSVRSVAFSPDGRLLASGS 265

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808  512 YDKTARLWATDSNQALRVFVGHLSDVDCVQFHPNSNYVATGSSDRTVRLWDNMTGQSVRLMTGHKGSVSSLAFSACGRYL 591
Cdd:COG2319 266 ADGTVRLWDLATGELLRTLTGHSGGVNSVAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKTL 345

                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|....*
gi 1729808  592 ASGSVDHNIIIWDLSNGSLVTTLLRHTSTVTTITFSRDGTVLAAAGLDNNLTLWD 646
Cdd:COG2319 346 ASGSDDGTVRLWDLATGELLRTLTGHTGAVTSVAFSPDGRTLASGSADGTVRLWD 400
TAF5_NTD2 cd08044
TAF5_NTD2 is the second conserved N-terminal region of TATA Binding Protein (TBP) Associated ...
 114-245 2.04e-44

TAF5_NTD2 is the second conserved N-terminal region of TATA Binding Protein (TBP) Associated Factor 5 (TAF5), involved in forming Transcription Factor IID (TFIID); The TATA Binding Protein (TBP) Associated Factor 5 (TAF5) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TAF5 contains three domains, two conserved sequence motifs at the N-terminal and one at the C-terminal region. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the preinitiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. In yeast and human cells, TAFs have been found as components of other complexes besides TFIID. TAF5 may play a major role in forming TFIID and its related complexes. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. TAF5 has a paralog gene (TAF5L) which has a redundant function. Several hypotheses are proposed for TAFs functions such as serving as activator-binding sites, core-promoter recognition or a role in essential catalytic activity. C-terminus of TAF5 contains six WD40 repeats that likely form a closed beta propeller structure and may be involved in protein-protein interaction. The first part of the TAF5 N-terminal (TAF5_NTD1) homodimerizes in the absence of other TAFs. The second conserved N-terminal part of TAF5 (TAF5_NTD2) has an alpha-helical domain. One study has shown that TAF5_NTD2 homodimerizes only at high concentration of calcium but not any other metals. No dimerization was observed in other structural studies of TAF_NTD2. Several TAFs interact via histone-fold (HFD) motifs; HFD is the interaction motif involved in heterodimerization of the core histones and their assembly into nucleosome octamer. However, TAF5 does not have a HFD motif.


:

Pssm-ID: 176269  Cd Length: 133  Bit Score: 155.43  E-value: 2.04e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808  114 QHYEQAYKELRTFVEDSLDIYKHELSMVLYPILVQIYFKILASGLREKAKEFIEKYKCDLDGYYIEGLFNLLLLSKPEEL 193
Cdd:cd08044   2 NDYEQAYSKLRKWIESSLDIYKYELSQLLYPIFVHSYLDLVASGHLEEAKSFFERFSGDFEDSHSEDIKKLSSITTPEHL 81

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|..
gi 1729808  194 LENDLVVAMEQDKFVIRMSRDSHSLFKRHIQDRRQEVVADIVSKYLHFDTYE 245
Cdd:cd08044  82 KENELAKLFRSNKYVIRMSRDAYSLLLRFLESWGGSLLLKILNEHIDIDVRD 133
 
Name Accession Description Interval E-value
WD40 COG2319
WD40 repeat [General function prediction only];
364-646 1.48e-80

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 262.15  E-value: 1.48e-80
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808  364 QLPSAVFYTVLNSHQG-VTCAEISDDSTMLACGFGDSSVRIWSL-TPAKLRTLKD-ADSLREL----DKE-----SADIN 431
Cdd:COG2319 106 DLATGLLLRTLTGHTGaVRSVAFSPDGKTLASGSADGTVRLWDLaTGKLLRTLTGhSGAVTSVafspDGKllasgSDDGT 185

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808  432 VRMLDDRSGEVTRSLMGHTGPVYRCAFAPEMNLLLSCSEDSTIRLWSLLTWSCVVTYRGHVYPVWDVRFAPHGYYFVSCS 511
Cdd:COG2319 186 VRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKLLASGSADGTVRLWDLATGKLLRTLTGHSGSVRSVAFSPDGRLLASGS 265

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808  512 YDKTARLWATDSNQALRVFVGHLSDVDCVQFHPNSNYVATGSSDRTVRLWDNMTGQSVRLMTGHKGSVSSLAFSACGRYL 591
Cdd:COG2319 266 ADGTVRLWDLATGELLRTLTGHSGGVNSVAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKTL 345

                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|....*
gi 1729808  592 ASGSVDHNIIIWDLSNGSLVTTLLRHTSTVTTITFSRDGTVLAAAGLDNNLTLWD 646
Cdd:COG2319 346 ASGSDDGTVRLWDLATGELLRTLTGHTGAVTSVAFSPDGRTLASGSADGTVRLWD 400
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 373-646 2.89e-73

WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.


Pssm-ID: 238121 [Multi-domain]  Cd Length: 289  Bit Score: 238.77  E-value: 2.89e-73
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808  373 VLNSHQG-VTCAEISDDSTMLACGFGDSSVRIWSL-TPAKLRTLKD-ADSLREL----DKE-----SADINVRMLDDRSG 440
Cdd:cd00200   4 TLKGHTGgVTCVAFSPDGKLLATGSGDGTIKVWDLeTGELLRTLKGhTGPVRDVaasaDGTylasgSSDKTIRLWDLETG 83

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808  441 EVTRSLMGHTGPVYRCAFAPEMNLLLSCSEDSTIRLWSLLTWSCVVTYRGHVYPVWDVRFAPHGYYFVSCSYDKTARLWA 520
Cdd:cd00200  84 ECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWD 163

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808  521 TDSNQALRVFVGHLSDVDCVQFHPNSNYVATGSSDRTVRLWDNMTGQSVRLMTGHKGSVSSLAFSACGRYLASGSVDHNI 600
Cdd:cd00200 164 LRTGKCVATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGTLRGHENGVNSVAFSPDGYLLASGSEDGTI 243

                       250       260       270       280
                ....*....|....*....|....*....|....*....|....*.
gi 1729808  601 IIWDLSNGSLVTTLLRHTSTVTTITFSRDGTVLAAAGLDNNLTLWD 646
Cdd:cd00200 244 RVWDLRTGECVQTLSGHTNSVTSLAWSPDGKRLASGSADGTIRIWD 289
TAF5_NTD2 cd08044
TAF5_NTD2 is the second conserved N-terminal region of TATA Binding Protein (TBP) Associated ...
 114-245 2.04e-44

TAF5_NTD2 is the second conserved N-terminal region of TATA Binding Protein (TBP) Associated Factor 5 (TAF5), involved in forming Transcription Factor IID (TFIID); The TATA Binding Protein (TBP) Associated Factor 5 (TAF5) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TAF5 contains three domains, two conserved sequence motifs at the N-terminal and one at the C-terminal region. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the preinitiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. In yeast and human cells, TAFs have been found as components of other complexes besides TFIID. TAF5 may play a major role in forming TFIID and its related complexes. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. TAF5 has a paralog gene (TAF5L) which has a redundant function. Several hypotheses are proposed for TAFs functions such as serving as activator-binding sites, core-promoter recognition or a role in essential catalytic activity. C-terminus of TAF5 contains six WD40 repeats that likely form a closed beta propeller structure and may be involved in protein-protein interaction. The first part of the TAF5 N-terminal (TAF5_NTD1) homodimerizes in the absence of other TAFs. The second conserved N-terminal part of TAF5 (TAF5_NTD2) has an alpha-helical domain. One study has shown that TAF5_NTD2 homodimerizes only at high concentration of calcium but not any other metals. No dimerization was observed in other structural studies of TAF_NTD2. Several TAFs interact via histone-fold (HFD) motifs; HFD is the interaction motif involved in heterodimerization of the core histones and their assembly into nucleosome octamer. However, TAF5 does not have a HFD motif.


Pssm-ID: 176269  Cd Length: 133  Bit Score: 155.43  E-value: 2.04e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808  114 QHYEQAYKELRTFVEDSLDIYKHELSMVLYPILVQIYFKILASGLREKAKEFIEKYKCDLDGYYIEGLFNLLLLSKPEEL 193
Cdd:cd08044   2 NDYEQAYSKLRKWIESSLDIYKYELSQLLYPIFVHSYLDLVASGHLEEAKSFFERFSGDFEDSHSEDIKKLSSITTPEHL 81

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|..
gi 1729808  194 LENDLVVAMEQDKFVIRMSRDSHSLFKRHIQDRRQEVVADIVSKYLHFDTYE 245
Cdd:cd08044  82 KENELAKLFRSNKYVIRMSRDAYSLLLRFLESWGGSLLLKILNEHIDIDVRD 133
TFIID_NTD2 pfam04494
WD40 associated region in TFIID subunit, NTD2 domain; This region is an all-alpha domain ...
 112-239 4.11e-37

WD40 associated region in TFIID subunit, NTD2 domain; This region is an all-alpha domain associated with the WD40 helical bundle of the TAF5 subunit of transcription factor TFIID. The domain has distant structural similarity to RNA polymerase II CTD interacting factors. It contains several conserved clefts that are likely to be critical for TFIID complex assembly. The TAF5 subunit is present twice in the TFIID complex and is critical for the function and assembly of the complex, and the NTD2 and N-terminal domain is crucial for homodimerization.


Pssm-ID: 461330  Cd Length: 130  Bit Score: 134.93  E-value: 4.11e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808    112 DAQHYEQAYKELRTFVEDSLDIYKHELSMVLYPILVQIYFKILASGLREKAKEFIEKYKCDLDGYYIEGLFNLLLLSKPE 191
Cdd:pfam04494   3 DPQKYERAYSLLRNWIESSLDIYKPELRRLLYPVFVHSYLDLVAKGHIEEAKEFFEKFRGDHEALHGDDLRKLAGITLPE 82

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1729808    192 ELLENDLVVAMEQDKFVIRMSRDSHSLFKRHIQDRRQEVVADIVSKYL 239
Cdd:pfam04494  83 HLEENELAKLFRSNKYRIRLSRYSFDLLLRFLQENESSVILRIINEHL 130
PLN00181 PLN00181
protein SPA1-RELATED; Provisional
 509-647 3.42e-12

protein SPA1-RELATED; Provisional


Pssm-ID: 177776 [Multi-domain]  Cd Length: 793  Bit Score: 69.73  E-value: 3.42e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808   509 SCSYDKTARLWATDSNQALRVFVGHLSDVDCVQFHP-NSNYVATGSSDRTVRLWDNMTGQSVRLMTGhKGSVSSLAF-SA 586
Cdd:PLN00181 550 SSNFEGVVQVWDVARSQLVTEMKEHEKRVWSIDYSSaDPTLLASGSDDGSVKLWSINQGVSIGTIKT-KANICCVQFpSE 628

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1729808   587 CGRYLASGSVDHNIIIWDLSNGSL-VTTLLRHTSTVTTITFSrDGTVLAAAGLDNNLTLWDF 647
Cdd:PLN00181 629 SGRSLAFGSADHKVYYYDLRNPKLpLCTMIGHSKTVSYVRFV-DSSTLVSSSTDNTLKLWDL 689
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 523-562 1.41e-09

WD40 repeats; Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.


Pssm-ID: 197651 [Multi-domain]  Cd Length: 40  Bit Score: 53.86  E-value: 1.41e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 1729808     523 SNQALRVFVGHLSDVDCVQFHPNSNYVATGSSDRTVRLWD 562
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 pfam00400
WD domain, G-beta repeat;
527-562 2.57e-09

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 53.12  E-value: 2.57e-09
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1729808    527 LRVFVGHLSDVDCVQFHPNSNYVATGSSDRTVRLWD 562
Cdd:pfam00400   4 LKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
 
Name Accession Description Interval E-value
WD40 COG2319
WD40 repeat [General function prediction only];
364-646 1.48e-80

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 262.15  E-value: 1.48e-80
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808  364 QLPSAVFYTVLNSHQG-VTCAEISDDSTMLACGFGDSSVRIWSL-TPAKLRTLKD-ADSLREL----DKE-----SADIN 431
Cdd:COG2319 106 DLATGLLLRTLTGHTGaVRSVAFSPDGKTLASGSADGTVRLWDLaTGKLLRTLTGhSGAVTSVafspDGKllasgSDDGT 185

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808  432 VRMLDDRSGEVTRSLMGHTGPVYRCAFAPEMNLLLSCSEDSTIRLWSLLTWSCVVTYRGHVYPVWDVRFAPHGYYFVSCS 511
Cdd:COG2319 186 VRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKLLASGSADGTVRLWDLATGKLLRTLTGHSGSVRSVAFSPDGRLLASGS 265

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808  512 YDKTARLWATDSNQALRVFVGHLSDVDCVQFHPNSNYVATGSSDRTVRLWDNMTGQSVRLMTGHKGSVSSLAFSACGRYL 591
Cdd:COG2319 266 ADGTVRLWDLATGELLRTLTGHSGGVNSVAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKTL 345

                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|....*
gi 1729808  592 ASGSVDHNIIIWDLSNGSLVTTLLRHTSTVTTITFSRDGTVLAAAGLDNNLTLWD 646
Cdd:COG2319 346 ASGSDDGTVRLWDLATGELLRTLTGHTGAVTSVAFSPDGRTLASGSADGTVRLWD 400
WD40 COG2319
WD40 repeat [General function prediction only];
350-646 9.00e-74

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 244.05  E-value: 9.00e-74
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808  350 ALREASKRLALSKDQLPSAVFYTVLNSHQGVTCAEISDDSTMLACGFGDSSVRIWSLTPAKLRTLKDADSL--------- 420
Cdd:COG2319  10 AAASADLALALLAAALGALLLLLLGLAAAVASLAASPDGARLAAGAGDLTLLLLDAAAGALLATLLGHTAAvlsvafspd 89

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808  421 -RELDKESADINVRMLDDRSGEVTRSLMGHTGPVYRCAFAPEMNLLLSCSEDSTIRLWSLLTWSCVVTYRGHVYPVWDVR 499
Cdd:COG2319  90 gRLLASASADGTVRLWDLATGLLLRTLTGHTGAVRSVAFSPDGKTLASGSADGTVRLWDLATGKLLRTLTGHSGAVTSVA 169

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808  500 FAPHGYYFVSCSYDKTARLWATDSNQALRVFVGHLSDVDCVQFHPNSNYVATGSSDRTVRLWDNMTGQSVRLMTGHKGSV 579
Cdd:COG2319 170 FSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKLLASGSADGTVRLWDLATGKLLRTLTGHSGSV 249

                       250       260       270       280       290       300
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1729808  580 SSLAFSACGRYLASGSVDHNIIIWDLSNGSLVTTLLRHTSTVTTITFSRDGTVLAAAGLDNNLTLWD 646
Cdd:COG2319 250 RSVAFSPDGRLLASGSADGTVRLWDLATGELLRTLTGHSGGVNSVAFSPDGKLLASGSDDGTVRLWD 316
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 373-646 2.89e-73

WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.


Pssm-ID: 238121 [Multi-domain]  Cd Length: 289  Bit Score: 238.77  E-value: 2.89e-73
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808  373 VLNSHQG-VTCAEISDDSTMLACGFGDSSVRIWSL-TPAKLRTLKD-ADSLREL----DKE-----SADINVRMLDDRSG 440
Cdd:cd00200   4 TLKGHTGgVTCVAFSPDGKLLATGSGDGTIKVWDLeTGELLRTLKGhTGPVRDVaasaDGTylasgSSDKTIRLWDLETG 83

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808  441 EVTRSLMGHTGPVYRCAFAPEMNLLLSCSEDSTIRLWSLLTWSCVVTYRGHVYPVWDVRFAPHGYYFVSCSYDKTARLWA 520
Cdd:cd00200  84 ECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWD 163

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808  521 TDSNQALRVFVGHLSDVDCVQFHPNSNYVATGSSDRTVRLWDNMTGQSVRLMTGHKGSVSSLAFSACGRYLASGSVDHNI 600
Cdd:cd00200 164 LRTGKCVATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGTLRGHENGVNSVAFSPDGYLLASGSEDGTI 243

                       250       260       270       280
                ....*....|....*....|....*....|....*....|....*.
gi 1729808  601 IIWDLSNGSLVTTLLRHTSTVTTITFSRDGTVLAAAGLDNNLTLWD 646
Cdd:cd00200 244 RVWDLRTGECVQTLSGHTNSVTSLAWSPDGKRLASGSADGTIRIWD 289
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 443-700 1.39e-67

WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.


Pssm-ID: 238121 [Multi-domain]  Cd Length: 289  Bit Score: 223.75  E-value: 1.39e-67
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808  443 TRSLMGHTGPVYRCAFAPEMNLLLSCSEDSTIRLWSLLTWSCVVTYRGHVYPVWDVRFAPHGYYFVSCSYDKTARLWATD 522
Cdd:cd00200   2 RRTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASADGTYLASGSSDKTIRLWDLE 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808  523 SNQALRVFVGHLSDVDCVQFHPNSNYVATGSSDRTVRLWDNMTGQSVRLMTGHKGSVSSLAFSACGRYLASGSVDHNIII 602
Cdd:cd00200  82 TGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKL 161

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808  603 WDLSNGSLVTTLLRHTSTVTTITFSRDGTVLAAAGLDNNLTLWDFHKVTedyisnhitvshhqdendedvyLMRTFPSKN 682
Cdd:cd00200 162 WDLRTGKCVATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGK----------------------CLGTLRGHE 219

                       250
                ....*....|....*...
gi 1729808  683 SPFVSLHFTRRNLLMCVG 700
Cdd:cd00200 220 NGVNSVAFSPDGYLLASG 237
WD40 COG2319
WD40 repeat [General function prediction only];
373-607 3.45e-63

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 215.93  E-value: 3.45e-63
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808  373 VLNSHQG-VTCAEISDDSTMLACGFGDSSVRIWSL-TPAKLRTLKD-ADSLREL----DKE-----SADINVRMLDDRSG 440
Cdd:COG2319 157 TLTGHSGaVTSVAFSPDGKLLASGSDDGTVRLWDLaTGKLLRTLTGhTGAVRSVafspDGKllasgSADGTVRLWDLATG 236

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808  441 EVTRSLMGHTGPVYRCAFAPEMNLLLSCSEDSTIRLWSLLTWSCVVTYRGHVYPVWDVRFAPHGYYFVSCSYDKTARLWA 520
Cdd:COG2319 237 KLLRTLTGHSGSVRSVAFSPDGRLLASGSADGTVRLWDLATGELLRTLTGHSGGVNSVAFSPDGKLLASGSDDGTVRLWD 316

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808  521 TDSNQALRVFVGHLSDVDCVQFHPNSNYVATGSSDRTVRLWDNMTGQSVRLMTGHKGSVSSLAFSACGRYLASGSVDHNI 600
Cdd:COG2319 317 LATGKLLRTLTGHTGAVRSVAFSPDGKTLASGSDDGTVRLWDLATGELLRTLTGHTGAVTSVAFSPDGRTLASGSADGTV 396


                ....*..
gi 1729808  601 IIWDLSN 607
Cdd:COG2319 397 RLWDLAT 403
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 484-647 7.57e-47

WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.


Pssm-ID: 238121 [Multi-domain]  Cd Length: 289  Bit Score: 167.90  E-value: 7.57e-47
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808  484 CVVTYRGHVYPVWDVRFAPHGYYFVSCSYDKTARLWATDSNQALRVFVGHLSDVDCVQFHPNSNYVATGSSDRTVRLWDN 563
Cdd:cd00200   1 LRRTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASADGTYLASGSSDKTIRLWDL 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808  564 MTGQSVRLMTGHKGSVSSLAFSACGRYLASGSVDHNIIIWDLSNGSLVTTLLRHTSTVTTITFSRDGTVLAAAGLDNNLT 643
Cdd:cd00200  81 ETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIK 160


                ....
gi 1729808  644 LWDF 647
Cdd:cd00200 161 LWDL 164
TAF5_NTD2 cd08044
TAF5_NTD2 is the second conserved N-terminal region of TATA Binding Protein (TBP) Associated ...
 114-245 2.04e-44

TAF5_NTD2 is the second conserved N-terminal region of TATA Binding Protein (TBP) Associated Factor 5 (TAF5), involved in forming Transcription Factor IID (TFIID); The TATA Binding Protein (TBP) Associated Factor 5 (TAF5) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TAF5 contains three domains, two conserved sequence motifs at the N-terminal and one at the C-terminal region. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the preinitiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. In yeast and human cells, TAFs have been found as components of other complexes besides TFIID. TAF5 may play a major role in forming TFIID and its related complexes. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. TAF5 has a paralog gene (TAF5L) which has a redundant function. Several hypotheses are proposed for TAFs functions such as serving as activator-binding sites, core-promoter recognition or a role in essential catalytic activity. C-terminus of TAF5 contains six WD40 repeats that likely form a closed beta propeller structure and may be involved in protein-protein interaction. The first part of the TAF5 N-terminal (TAF5_NTD1) homodimerizes in the absence of other TAFs. The second conserved N-terminal part of TAF5 (TAF5_NTD2) has an alpha-helical domain. One study has shown that TAF5_NTD2 homodimerizes only at high concentration of calcium but not any other metals. No dimerization was observed in other structural studies of TAF_NTD2. Several TAFs interact via histone-fold (HFD) motifs; HFD is the interaction motif involved in heterodimerization of the core histones and their assembly into nucleosome octamer. However, TAF5 does not have a HFD motif.


Pssm-ID: 176269  Cd Length: 133  Bit Score: 155.43  E-value: 2.04e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808  114 QHYEQAYKELRTFVEDSLDIYKHELSMVLYPILVQIYFKILASGLREKAKEFIEKYKCDLDGYYIEGLFNLLLLSKPEEL 193
Cdd:cd08044   2 NDYEQAYSKLRKWIESSLDIYKYELSQLLYPIFVHSYLDLVASGHLEEAKSFFERFSGDFEDSHSEDIKKLSSITTPEHL 81

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|..
gi 1729808  194 LENDLVVAMEQDKFVIRMSRDSHSLFKRHIQDRRQEVVADIVSKYLHFDTYE 245
Cdd:cd08044  82 KENELAKLFRSNKYVIRMSRDAYSLLLRFLESWGGSLLLKILNEHIDIDVRD 133
WD40 COG2319
WD40 repeat [General function prediction only];
457-646 1.83e-40

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 153.14  E-value: 1.83e-40
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808  457 AFAPEMNLLLSCSEDSTIRLWSLLTWSCVVTYRGHVYPVWDVRFAPHGYYFVSCSYDKTARLWATDSNQALRVFVGHLSD 536
Cdd:COG2319   1 ALSADGAALAAASADLALALLAAALGALLLLLLGLAAAVASLAASPDGARLAAGAGDLTLLLLDAAAGALLATLLGHTAA 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808  537 VDCVQFHPNSNYVATGSSDRTVRLWDNMTGQSVRLMTGHKGSVSSLAFSACGRYLASGSVDHNIIIWDLSNGSLVTTLLR 616
Cdd:COG2319  81 VLSVAFSPDGRLLASASADGTVRLWDLATGLLLRTLTGHTGAVRSVAFSPDGKTLASGSADGTVRLWDLATGKLLRTLTG 160

                       170       180       190
                ....*....|....*....|....*....|
gi 1729808  617 HTSTVTTITFSRDGTVLAAAGLDNNLTLWD 646
Cdd:COG2319 161 HSGAVTSVAFSPDGKLLASGSDDGTVRLWD 190
TFIID_NTD2 pfam04494
WD40 associated region in TFIID subunit, NTD2 domain; This region is an all-alpha domain ...
 112-239 4.11e-37

WD40 associated region in TFIID subunit, NTD2 domain; This region is an all-alpha domain associated with the WD40 helical bundle of the TAF5 subunit of transcription factor TFIID. The domain has distant structural similarity to RNA polymerase II CTD interacting factors. It contains several conserved clefts that are likely to be critical for TFIID complex assembly. The TAF5 subunit is present twice in the TFIID complex and is critical for the function and assembly of the complex, and the NTD2 and N-terminal domain is crucial for homodimerization.


Pssm-ID: 461330  Cd Length: 130  Bit Score: 134.93  E-value: 4.11e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808    112 DAQHYEQAYKELRTFVEDSLDIYKHELSMVLYPILVQIYFKILASGLREKAKEFIEKYKCDLDGYYIEGLFNLLLLSKPE 191
Cdd:pfam04494   3 DPQKYERAYSLLRNWIESSLDIYKPELRRLLYPVFVHSYLDLVAKGHIEEAKEFFEKFRGDHEALHGDDLRKLAGITLPE 82

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1729808    192 ELLENDLVVAMEQDKFVIRMSRDSHSLFKRHIQDRRQEVVADIVSKYL 239
Cdd:pfam04494  83 HLEENELAKLFRSNKYRIRLSRYSFDLLLRFLQENESSVILRIINEHL 130
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 568-667 2.05e-18

WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.


Pssm-ID: 238121 [Multi-domain]  Cd Length: 289  Bit Score: 86.23  E-value: 2.05e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808  568 SVRLMTGHKGSVSSLAFSACGRYLASGSVDHNIIIWDLSNGSLVTTLLRHTSTVTTITFSRDGTVLAAAGLDNNLTLWDF 647
Cdd:cd00200   1 LRRTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASADGTYLASGSSDKTIRLWDL 80

                        90       100
                ....*....|....*....|
gi 1729808  648 HKVTEdyisnHITVSHHQDE 667
Cdd:cd00200  81 ETGEC-----VRTLTGHTSY 95
PLN00181 PLN00181
protein SPA1-RELATED; Provisional
 509-647 3.42e-12

protein SPA1-RELATED; Provisional


Pssm-ID: 177776 [Multi-domain]  Cd Length: 793  Bit Score: 69.73  E-value: 3.42e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808   509 SCSYDKTARLWATDSNQALRVFVGHLSDVDCVQFHP-NSNYVATGSSDRTVRLWDNMTGQSVRLMTGhKGSVSSLAF-SA 586
Cdd:PLN00181 550 SSNFEGVVQVWDVARSQLVTEMKEHEKRVWSIDYSSaDPTLLASGSDDGSVKLWSINQGVSIGTIKT-KANICCVQFpSE 628

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1729808   587 CGRYLASGSVDHNIIIWDLSNGSL-VTTLLRHTSTVTTITFSrDGTVLAAAGLDNNLTLWDF 647
Cdd:PLN00181 629 SGRSLAFGSADHKVYYYDLRNPKLpLCTMIGHSKTVSYVRFV-DSSTLVSSSTDNTLKLWDL 689
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 523-562 1.41e-09

WD40 repeats; Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.


Pssm-ID: 197651 [Multi-domain]  Cd Length: 40  Bit Score: 53.86  E-value: 1.41e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 1729808     523 SNQALRVFVGHLSDVDCVQFHPNSNYVATGSSDRTVRLWD 562
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 pfam00400
WD domain, G-beta repeat;
527-562 2.57e-09

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 53.12  E-value: 2.57e-09
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1729808    527 LRVFVGHLSDVDCVQFHPNSNYVATGSSDRTVRLWD 562
Cdd:pfam00400   4 LKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 565-604 2.99e-09

WD40 repeats; Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.


Pssm-ID: 197651 [Multi-domain]  Cd Length: 40  Bit Score: 52.70  E-value: 2.99e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 1729808     565 TGQSVRLMTGHKGSVSSLAFSACGRYLASGSVDHNIIIWD 604
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 481-519 4.17e-09

WD40 repeats; Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.


Pssm-ID: 197651 [Multi-domain]  Cd Length: 40  Bit Score: 52.31  E-value: 4.17e-09
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 1729808     481 TWSCVVTYRGHVYPVWDVRFAPHGYYFVSCSYDKTARLW 519
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLW 39
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 439-478 4.21e-09

WD40 repeats; Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.


Pssm-ID: 197651 [Multi-domain]  Cd Length: 40  Bit Score: 52.31  E-value: 4.21e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 1729808     439 SGEVTRSLMGHTGPVYRCAFAPEMNLLLSCSEDSTIRLWS 478
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 pfam00400
WD domain, G-beta repeat;
566-604 1.47e-08

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 50.81  E-value: 1.47e-08
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1729808    566 GQSVRLMTGHKGSVSSLAFSACGRYLASGSVDHNIIIWD 604
Cdd:pfam00400   1 GKLLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
WD40 pfam00400
WD domain, G-beta repeat;
482-519 6.57e-08

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 48.88  E-value: 6.57e-08
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1729808    482 WSCVVTYRGHVYPVWDVRFAPHGYYFVSCSYDKTARLW 519
Cdd:pfam00400   1 GKLLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVW 38
WD40 pfam00400
WD domain, G-beta repeat;
440-478 7.61e-08

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 48.88  E-value: 7.61e-08
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1729808    440 GEVTRSLMGHTGPVYRCAFAPEMNLLLSCSEDSTIRLWS 478
Cdd:pfam00400   1 GKLLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 607-646 3.71e-06

WD40 repeats; Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.


Pssm-ID: 197651 [Multi-domain]  Cd Length: 40  Bit Score: 44.23  E-value: 3.71e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 1729808     607 NGSLVTTLLRHTSTVTTITFSRDGTVLAAAGLDNNLTLWD 646
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
PLN00181 PLN00181
protein SPA1-RELATED; Provisional
 467-649 4.97e-06

protein SPA1-RELATED; Provisional


Pssm-ID: 177776 [Multi-domain]  Cd Length: 793  Bit Score: 50.09  E-value: 4.97e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808   467 SCSEDSTIRLWSLLTWSCVVTYRGHVYPVWDVRFAPHG-YYFVSCSYDKTARLWATDSNqalrVFVGHL---SDVDCVQF 542
Cdd:PLN00181 550 SSNFEGVVQVWDVARSQLVTEMKEHEKRVWSIDYSSADpTLLASGSDDGSVKLWSINQG----VSIGTIktkANICCVQF 625

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808   543 HPNSN-YVATGSSDRTVRLWDnMTGQSVRL--MTGHKGSVSSLAFSACGRyLASGSVDHNIIIWDLS------NGSLVTT 613
Cdd:PLN00181 626 PSESGrSLAFGSADHKVYYYD-LRNPKLPLctMIGHSKTVSYVRFVDSST-LVSSSTDNTLKLWDLSmsisgiNETPLHS 703

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 1729808   614 LLRHTSTVTTITFS-RDGTVlaAAGLDNNlTLWDFHK 649
Cdd:PLN00181 704 FMGHTNVKNFVGLSvSDGYI--ATGSETN-EVFVYHK 737
PTZ00421 PTZ00421
coronin; Provisional
 532-622 1.03e-05

coronin; Provisional


Pssm-ID: 173611 [Multi-domain]  Cd Length: 493  Bit Score: 48.74  E-value: 1.03e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808   532 GHLSDVDCVQFHPNSNYV-ATGSSDRTVRLWDNMTGQSVRLMTGHKGSVSSLAFSACGRYLASGSVDHNIIIWDLSNGSL 610
Cdd:PTZ00421 123 GHTKKVGIVSFHPSAMNVlASAGADMVVNVWDVERGKAVEVIKCHSDQITSLEWNLDGSLLCTTSKDKKLNIIDPRDGTI 202

                         90
                 ....*....|..
gi 1729808   611 VTTLLRHTSTVT 622
Cdd:PTZ00421 203 VSSVEAHASAKS 214
WD40 pfam00400
WD domain, G-beta repeat;
608-646 1.31e-05

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 42.33  E-value: 1.31e-05
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1729808    608 GSLVTTLLRHTSTVTTITFSRDGTVLAAAGLDNNLTLWD 646
Cdd:pfam00400   1 GKLLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
PTZ00421 PTZ00421
coronin; Provisional
 529-646 2.03e-05

coronin; Provisional


Pssm-ID: 173611 [Multi-domain]  Cd Length: 493  Bit Score: 47.58  E-value: 2.03e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808   529 VFVGHLSDVDCVQFHP-NSNYVATGSSDRTVRLWD--------NMTGQSVRLmTGHKGSVSSLAF--SACGrYLASGSVD 597
Cdd:PTZ00421  70 ILLGQEGPIIDVAFNPfDPQKLFTASEDGTIMGWGipeegltqNISDPIVHL-QGHTKKVGIVSFhpSAMN-VLASAGAD 147

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 1729808   598 HNIIIWDLSNGSLVTTLLRHTSTVTTITFSRDGTVLAAAGLDNNLTLWD 646
Cdd:PTZ00421 148 MVVNVWDVERGKAVEVIKCHSDQITSLEWNLDGSLLCTTSKDKKLNIID 196
YncE COG3391
DNA-binding beta-propeller fold protein YncE [General function prediction only];
485-651 2.08e-05

DNA-binding beta-propeller fold protein YncE [General function prediction only];


Pssm-ID: 442618 [Multi-domain]  Cd Length: 237  Bit Score: 46.61  E-value: 2.08e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808  485 VVTYRGHVYPVWDVRFAPHG-YYFVSCSYDKTARLWATDSNQALRVF-VGhlSDVDCVQFHPNSNYV-ATGSSDRTVRLW 561
Cdd:COG3391  60 LGLGAAAVADADGADAGADGrRLYVANSGSGRVSVIDLATGKVVATIpVG--GGPRGLAVDPDGGRLyVADSGNGRVSVI 137

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808  562 DNMTGQSV-RLMTGhkGSVSSLAFSACGRYLASGSVDHN-----IIIWDLSNGSLVTTLLRHtSTVTTITFSRDGTVLAA 635
Cdd:COG3391 138 DTATGKVVaTIPVG--AGPHGIAVDPDGKRLYVANSGSNtvsviVSVIDTATGKVVATIPVG-GGPVGVAVSPDGRRLYV 214

                       170
                ....*....|....*.
gi 1729808  636 AGLDNNLTLWDFHKVT 651
Cdd:COG3391 215 ANRGSNTSNGGSNTVS 230
PTZ00420 PTZ00420
coronin; Provisional
 474-675 4.14e-05

coronin; Provisional


Pssm-ID: 240412 [Multi-domain]  Cd Length: 568  Bit Score: 46.87  E-value: 4.14e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808   474 IRLWSLLTWSCVVTYRGHVYPVWDVRFAP-HGYYFVSCSYDKTARLWATDSN--------QALRVFVGHLSDVDCVQFHP 544
Cdd:PTZ00420  56 IRLENQMRKPPVIKLKGHTSSILDLQFNPcFSEILASGSEDLTIRVWEIPHNdesvkeikDPQCILKGHKKKISIIDWNP 135

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808   545 NSNYVATGSS-DRTVRLWDnMTGQSVRLMTGHKGSVSSLAFSACGRYLASGSVDHNIIIWDLSNGSLVTTLLRHTSTVTT 623
Cdd:PTZ00420 136 MNYYIMCSSGfDSFVNIWD-IENEKRAFQINMPKKLSSLKWNIKGNLLSGTCVGKHMHIIDPRKQEIASSFHIHDGGKNT 214

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1729808   624 ITFSRDG------TVLAAAGLDNN---LTLWDFHKVTEDYISNHITVSH-----HQDENDEDVYLM 675
Cdd:PTZ00420 215 KNIWIDGlggddnYILSTGFSKNNmreMKLWDLKNTTSALVTMSIDNASaplipHYDESTGLIYLI 280
COG4946 COG4946
Uncharacterized N-terminal domain of tricorn protease, contains WD40 repeats [Function unknown] ...
 485-630 1.60e-04

Uncharacterized N-terminal domain of tricorn protease, contains WD40 repeats [Function unknown];


Pssm-ID: 443973 [Multi-domain]  Cd Length: 1072  Bit Score: 45.03  E-value: 1.60e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808   485 VVTYRGHVY--PVWD----------------VRFAPHG---YYF--VSCSYDktarLW---ATDSNQALRVFVGHLSDVD 538
Cdd:COG4946  317 AFEARGEVFtvPAEKgptrnltntpgvrerlPAWSPDGksiAYFsdASGEYE----LYiapADGSGEPKQLTLGDLGRVF 392

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808   539 CVQFHPNSNYVATgsSDRTVRLW--DNMTGQSVRLMTG-HKGSVSSLAFSACGRYLASGSVDHN----IIIWDLSNGSlV 611
Cdd:COG4946  393 NPVWSPDGKKIAF--TDNRGRLWvvDLASGKVRKVDTDgYGDGISDLAWSPDSKWLAYSKPGPNqlsqIFLYDVETGK-T 469

                        170
                 ....*....|....*....
gi 1729808   612 TTLLRHTSTVTTITFSRDG 630
Cdd:COG4946  470 VQLTDGRYDDGSPAFSPDG 488
PLN00181 PLN00181
protein SPA1-RELATED; Provisional
 386-479 3.01e-04

protein SPA1-RELATED; Provisional


Pssm-ID: 177776 [Multi-domain]  Cd Length: 793  Bit Score: 44.31  E-value: 3.01e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808   386 SDDSTMLACGFGDSSVRIWSLTPA-KLRTLKD----------ADSLRELDKESADINVRMLDDRSGEVTR-SLMGHTGPV 453
Cdd:PLN00181 585 SADPTLLASGSDDGSVKLWSINQGvSIGTIKTkaniccvqfpSESGRSLAFGSADHKVYYYDLRNPKLPLcTMIGHSKTV 664

                         90       100
                 ....*....|....*....|....*.
gi 1729808   454 YRCAFApEMNLLLSCSEDSTIRLWSL 479
Cdd:PLN00181 665 SYVRFV-DSSTLVSSSTDNTLKLWDL 689
NBCH_WD40 pfam20426
Neurobeachin beta propeller domain; This entry represents the beta propeller domain found at ...
 544-634 1.33e-03

Neurobeachin beta propeller domain; This entry represents the beta propeller domain found at the C-terminus of neurobeachin-like proteins.


Pssm-ID: 466575 [Multi-domain]  Cd Length: 350  Bit Score: 41.60  E-value: 1.33e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808    544 PNSNYVAT----GSSDRTVRLWDNMTGQSVRlmtGHKGSVSSLAFSACGRYLASGSVDHNIIIWDLSNGSLVTTLLRHTS 619
Cdd:pfam20426  91 PSENFLIScgnwENSFQVISLNDGRMVQSIR---QHKDVVSCVAVTSDGSILATGSYDTTVMVWEVLRGRSSEKRSRNTQ 167

                          90
                  ....*....|....*
gi 1729808    620 TvttiTFSRDGTVLA 634
Cdd:pfam20426 168 T----EFPRKDHVIA 178
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 373-405 2.21e-03

WD40 repeats; Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.


Pssm-ID: 197651 [Multi-domain]  Cd Length: 40  Bit Score: 36.14  E-value: 2.21e-03
                           10        20        30
                   ....*....|....*....|....*....|....
gi 1729808     373 VLNSHQG-VTCAEISDDSTMLACGFGDSSVRIWS 405
Cdd:smart00320   7 TLKGHTGpVTSVAFSPDGKYLASGSDDGTIKLWD 40
PTZ00421 PTZ00421
coronin; Provisional
 446-580 5.20e-03

coronin; Provisional


Pssm-ID: 173611 [Multi-domain]  Cd Length: 493  Bit Score: 39.88  E-value: 5.20e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729808   446 LMGHTGPVYRCAFAP-EMNLLLSCSEDSTIRLWSL----LTWSC---VVTYRGHVYPVWDVRFAPHGY-YFVSCSYDKTA 516
Cdd:PTZ00421  71 LLGQEGPIIDVAFNPfDPQKLFTASEDGTIMGWGIpeegLTQNIsdpIVHLQGHTKKVGIVSFHPSAMnVLASAGADMVV 150

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1729808   517 RLWATDSNQALRVFVGHLSDVDCVQFHPNSNYVATGSSDRTVRLWDNMTGQSVRLMTGHKGSVS 580
Cdd:PTZ00421 151 NVWDVERGKAVEVIKCHSDQITSLEWNLDGSLLCTTSKDKKLNIIDPRDGTIVSSVEAHASAKS 214
ANAPC4_WD40 pfam12894
Anaphase-promoting complex subunit 4 WD40 domain; Apc4 contains an N-terminal propeller-shaped ...
 574-627 6.04e-03

Anaphase-promoting complex subunit 4 WD40 domain; Apc4 contains an N-terminal propeller-shaped WD40 domain.The N-terminus of Afi1 serves to stabilize the union between Apc4 and Apc5, both of which lie towards the bottom-front of the APC,


Pssm-ID: 403945 [Multi-domain]  Cd Length: 91  Bit Score: 36.49  E-value: 6.04e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1729808    574 GHKGSVSSLAFSACGRYLASGSVDHNIIIWDLSNGSLVTTLLRHTSTVTTITFS 627
Cdd:pfam12894  36 KEDLEVTSLAWRPDGKLLAVGYSDGTVRLLDAENGKIVHHFSAGSDLITCLGWG 89
 
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.
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