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Conserved domains on  [gi|21071067|ref|NP_008882|]
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transcription initiation factor TFIID subunit 5 isoform 1 [Homo sapiens]

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];
456-740 7.11e-83

WD40 repeat [General function prediction only];


:

Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 270.24  E-value: 7.11e-83
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21071067 456 DCLPSICFYTFLNAYQGLTAVDVTDDSSLIAGGFADSTVRVWSV-TPKKLRSVKQASD--LSLI---DKE------SDDV 523
Cdd:COG2319 106 DLATGLLLRTLTGHTGAVRSVAFSPDGKTLASGSADGTVRLWDLaTGKLLRTLTGHSGavTSVAfspDGKllasgsDDGT 185

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21071067 524 LeRIMDEKTASELKILYGHSGPVYGASFSPDRNYLLSSSEDGTVRLWSLQTFTCLVGYKGHNYPVWDTQFSPYGYYFVSG 603
Cdd:COG2319 186 V-RLWDLATGKLLRTLTGHTGAVRSVAFSPDGKLLASGSADGTVRLWDLATGKLLRTLTGHSGSVRSVAFSPDGRLLASG 264

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21071067 604 GHDRVARLWATDHYQPLRIFAGHLADVNCTRFHPNSNYVATGSADRTVRLWDVLNGNCVRIFTGHKGPIHSLTFSPNGRF 683
Cdd:COG2319 265 SADGTVRLWDLATGELLRTLTGHSGGVNSVAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKT 344

                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 21071067 684 LATGATDGRVLLWDIGHGLMVGELKGHTDTVCSLRFSRDGEILASGSMDNTVRLWDA 740
Cdd:COG2319 345 LASGSDDGTVRLWDLATGELLRTLTGHTGAVTSVAFSPDGRTLASGSADGTVRLWDL 401
TFIID_NTD2 pfam04494
WD40 associated region in TFIID subunit, NTD2 domain; This region is an all-alpha domain ...
 208-337 4.79e-62

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: 204.65  E-value: 4.79e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21071067   208 QGDPTMYEEYYSGLKHFIECSLDCHRAELSQLFYPLFVHMYLELVYNQHENEAKSFFEKFHGDQECYYQDDLRVLSSLTK 287
Cdd:pfam04494   1 EGDPQKYERAYSLLRNWIESSLDIYKPELRRLLYPVFVHSYLDLVAKGHIEEAKEFFEKFRGDHEALHGDDLRKLAGITL 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 21071067   288 KEHMKGNETMLDFRTSKFVLRISRDSYQLLKRHLQEKQNNQIWNIVQEHL 337
Cdd:pfam04494  81 PEHLEENELAKLFRSNKYRIRLSRYSFDLLLRFLQENESSVILRIINEHL 130
 
Name Accession Description Interval E-value
WD40 COG2319
WD40 repeat [General function prediction only];
456-740 7.11e-83

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 270.24  E-value: 7.11e-83
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21071067 456 DCLPSICFYTFLNAYQGLTAVDVTDDSSLIAGGFADSTVRVWSV-TPKKLRSVKQASD--LSLI---DKE------SDDV 523
Cdd:COG2319 106 DLATGLLLRTLTGHTGAVRSVAFSPDGKTLASGSADGTVRLWDLaTGKLLRTLTGHSGavTSVAfspDGKllasgsDDGT 185

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21071067 524 LeRIMDEKTASELKILYGHSGPVYGASFSPDRNYLLSSSEDGTVRLWSLQTFTCLVGYKGHNYPVWDTQFSPYGYYFVSG 603
Cdd:COG2319 186 V-RLWDLATGKLLRTLTGHTGAVRSVAFSPDGKLLASGSADGTVRLWDLATGKLLRTLTGHSGSVRSVAFSPDGRLLASG 264

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21071067 604 GHDRVARLWATDHYQPLRIFAGHLADVNCTRFHPNSNYVATGSADRTVRLWDVLNGNCVRIFTGHKGPIHSLTFSPNGRF 683
Cdd:COG2319 265 SADGTVRLWDLATGELLRTLTGHSGGVNSVAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKT 344

                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 21071067 684 LATGATDGRVLLWDIGHGLMVGELKGHTDTVCSLRFSRDGEILASGSMDNTVRLWDA 740
Cdd:COG2319 345 LASGSDDGTVRLWDLATGELLRTLTGHTGAVTSVAFSPDGRTLASGSADGTVRLWDL 401
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 472-739 2.42e-76

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: 248.79  E-value: 2.42e-76
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21071067 472 GLTAVDVTDDSSLIAGGFADSTVRVWSVtpkklrsvkqasdlslidkesddvlerimdeKTASELKILYGHSGPVYGASF 551
Cdd:cd00200  11 GVTCVAFSPDGKLLATGSGDGTIKVWDL-------------------------------ETGELLRTLKGHTGPVRDVAA 59

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21071067 552 SPDRNYLLSSSEDGTVRLWSLQTFTCLVGYKGHNYPVWDTQFSPYGYYFVSGGHDRVARLWATDHYQPLRIFAGHLADVN 631
Cdd:cd00200  60 SADGTYLASGSSDKTIRLWDLETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVN 139

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21071067 632 CTRFHPNSNYVATGSADRTVRLWDVLNGNCVRIFTGHKGPIHSLTFSPNGRFLATGATDGRVLLWDIGHGLMVGELKGHT 711
Cdd:cd00200 140 SVAFSPDGTFVASSSQDGTIKLWDLRTGKCVATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGTLRGHE 219

                       250       260
                ....*....|....*....|....*...
gi 21071067 712 DTVCSLRFSRDGEILASGSMDNTVRLWD 739
Cdd:cd00200 220 NGVNSVAFSPDGYLLASGSEDGTIRVWD 247
TFIID_NTD2 pfam04494
WD40 associated region in TFIID subunit, NTD2 domain; This region is an all-alpha domain ...
 208-337 4.79e-62

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: 204.65  E-value: 4.79e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21071067   208 QGDPTMYEEYYSGLKHFIECSLDCHRAELSQLFYPLFVHMYLELVYNQHENEAKSFFEKFHGDQECYYQDDLRVLSSLTK 287
Cdd:pfam04494   1 EGDPQKYERAYSLLRNWIESSLDIYKPELRRLLYPVFVHSYLDLVAKGHIEEAKEFFEKFRGDHEALHGDDLRKLAGITL 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 21071067   288 KEHMKGNETMLDFRTSKFVLRISRDSYQLLKRHLQEKQNNQIWNIVQEHL 337
Cdd:pfam04494  81 PEHLEENELAKLFRSNKYRIRLSRYSFDLLLRFLQENESSVILRIINEHL 130
TAF5_NTD2 cd08044
TAF5_NTD2 is the second conserved N-terminal region of TATA Binding Protein (TBP) Associated ...
 211-343 7.06e-61

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: 201.65  E-value: 7.06e-61
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21071067 211 PTMYEEYYSGLKHFIECSLDCHRAELSQLFYPLFVHMYLELVYNQHENEAKSFFEKFHGDQECYYQDDLRVLSSLTKKEH 290
Cdd:cd08044   1 PNDYEQAYSKLRKWIESSLDIYKYELSQLLYPIFVHSYLDLVASGHLEEAKSFFERFSGDFEDSHSEDIKKLSSITTPEH 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|...
gi 21071067 291 MKGNETMLDFRTSKFVLRISRDSYQLLKRHLQEKQNNQIWNIVQEHLYIDIFD 343
Cdd:cd08044  81 LKENELAKLFRSNKYVIRMSRDAYSLLLRFLESWGGSLLLKILNEHIDIDVRD 133
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 658-697 1.19e-11

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: 59.63  E-value: 1.19e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 21071067    658 NGNCVRIFTGHKGPIHSLTFSPNGRFLATGATDGRVLLWD 697
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 pfam00400
WD domain, G-beta repeat;
659-697 1.02e-10

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 56.97  E-value: 1.02e-10
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 21071067   659 GNCVRIFTGHKGPIHSLTFSPNGRFLATGATDGRVLLWD 697
Cdd:pfam00400   1 GKLLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
PLN00181 PLN00181
protein SPA1-RELATED; Provisional
 642-761 8.14e-10

protein SPA1-RELATED; Provisional


Pssm-ID: 177776 [Multi-domain]  Cd Length: 793  Bit Score: 62.41  E-value: 8.14e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21071067  642 VATGSADRTVRLWDVLNGncVRIFT-GHKGPIHSLTF-SPNGRFLATGATDGRVLLWDIGH-GLMVGELKGHTDTVCSLR 718
Cdd:PLN00181 591 LASGSDDGSVKLWSINQG--VSIGTiKTKANICCVQFpSESGRSLAFGSADHKVYYYDLRNpKLPLCTMIGHSKTVSYVR 668

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 21071067  719 FSrDGEILASGSMDNTVRLWDAIKAFEDLETDDFTTATGHINL 761
Cdd:PLN00181 669 FV-DSSTLVSSSTDNTLKLWDLSMSISGINETPLHSFMGHTNV 710
 
Name Accession Description Interval E-value
WD40 COG2319
WD40 repeat [General function prediction only];
456-740 7.11e-83

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 270.24  E-value: 7.11e-83
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21071067 456 DCLPSICFYTFLNAYQGLTAVDVTDDSSLIAGGFADSTVRVWSV-TPKKLRSVKQASD--LSLI---DKE------SDDV 523
Cdd:COG2319 106 DLATGLLLRTLTGHTGAVRSVAFSPDGKTLASGSADGTVRLWDLaTGKLLRTLTGHSGavTSVAfspDGKllasgsDDGT 185

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21071067 524 LeRIMDEKTASELKILYGHSGPVYGASFSPDRNYLLSSSEDGTVRLWSLQTFTCLVGYKGHNYPVWDTQFSPYGYYFVSG 603
Cdd:COG2319 186 V-RLWDLATGKLLRTLTGHTGAVRSVAFSPDGKLLASGSADGTVRLWDLATGKLLRTLTGHSGSVRSVAFSPDGRLLASG 264

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21071067 604 GHDRVARLWATDHYQPLRIFAGHLADVNCTRFHPNSNYVATGSADRTVRLWDVLNGNCVRIFTGHKGPIHSLTFSPNGRF 683
Cdd:COG2319 265 SADGTVRLWDLATGELLRTLTGHSGGVNSVAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKT 344

                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 21071067 684 LATGATDGRVLLWDIGHGLMVGELKGHTDTVCSLRFSRDGEILASGSMDNTVRLWDA 740
Cdd:COG2319 345 LASGSDDGTVRLWDLATGELLRTLTGHTGAVTSVAFSPDGRTLASGSADGTVRLWDL 401
WD40 COG2319
WD40 repeat [General function prediction only];
465-740 1.77e-77

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 255.99  E-value: 1.77e-77
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21071067 465 TFLNAYQGLTAVDVTDDSSLIAGGFADSTVRVWSVTPKKLR-----------SVKQASDLSLIDKESDDVLERIMDEKTA 533
Cdd:COG2319  31 LLLGLAAAVASLAASPDGARLAAGAGDLTLLLLDAAAGALLatllghtaavlSVAFSPDGRLLASASADGTVRLWDLATG 110

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21071067 534 SELKILYGHSGPVYGASFSPDRNYLLSSSEDGTVRLWSLQTFTCLVGYKGHNYPVWDTQFSPYGYYFVSGGHDRVARLWA 613
Cdd:COG2319 111 LLLRTLTGHTGAVRSVAFSPDGKTLASGSADGTVRLWDLATGKLLRTLTGHSGAVTSVAFSPDGKLLASGSDDGTVRLWD 190

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21071067 614 TDHYQPLRIFAGHLADVNCTRFHPNSNYVATGSADRTVRLWDVLNGNCVRIFTGHKGPIHSLTFSPNGRFLATGATDGRV 693
Cdd:COG2319 191 LATGKLLRTLTGHTGAVRSVAFSPDGKLLASGSADGTVRLWDLATGKLLRTLTGHSGSVRSVAFSPDGRLLASGSADGTV 270

                       250       260       270       280
                ....*....|....*....|....*....|....*....|....*..
gi 21071067 694 LLWDIGHGLMVGELKGHTDTVCSLRFSRDGEILASGSMDNTVRLWDA 740
Cdd:COG2319 271 RLWDLATGELLRTLTGHSGGVNSVAFSPDGKLLASGSDDGTVRLWDL 317
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 472-739 2.42e-76

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: 248.79  E-value: 2.42e-76
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21071067 472 GLTAVDVTDDSSLIAGGFADSTVRVWSVtpkklrsvkqasdlslidkesddvlerimdeKTASELKILYGHSGPVYGASF 551
Cdd:cd00200  11 GVTCVAFSPDGKLLATGSGDGTIKVWDL-------------------------------ETGELLRTLKGHTGPVRDVAA 59

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21071067 552 SPDRNYLLSSSEDGTVRLWSLQTFTCLVGYKGHNYPVWDTQFSPYGYYFVSGGHDRVARLWATDHYQPLRIFAGHLADVN 631
Cdd:cd00200  60 SADGTYLASGSSDKTIRLWDLETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVN 139

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21071067 632 CTRFHPNSNYVATGSADRTVRLWDVLNGNCVRIFTGHKGPIHSLTFSPNGRFLATGATDGRVLLWDIGHGLMVGELKGHT 711
Cdd:cd00200 140 SVAFSPDGTFVASSSQDGTIKLWDLRTGKCVATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGTLRGHE 219

                       250       260
                ....*....|....*....|....*...
gi 21071067 712 DTVCSLRFSRDGEILASGSMDNTVRLWD 739
Cdd:cd00200 220 NGVNSVAFSPDGYLLASGSEDGTIRVWD 247
WD40 COG2319
WD40 repeat [General function prediction only];
471-740 1.24e-71

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 240.20  E-value: 1.24e-71
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21071067 471 QGLTAVDVTDDSSLIAGGFADSTVRVWSVTPKKLRSVKQASDLSLIDKESDDVLERIMDEKTASELKILYGHSGPVYGAS 550
Cdd:COG2319   6 GAALAAASADLALALLAAALGALLLLLLGLAAAVASLAASPDGARLAAGAGDLTLLLLDAAAGALLATLLGHTAAVLSVA 85

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21071067 551 FSPDRNYLLSSSEDGTVRLWSLQTFTCLVGYKGHNYPVWDTQFSPYGYYFVSGGHDRVARLWATDHYQPLRIFAGHLADV 630
Cdd:COG2319  86 FSPDGRLLASASADGTVRLWDLATGLLLRTLTGHTGAVRSVAFSPDGKTLASGSADGTVRLWDLATGKLLRTLTGHSGAV 165

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21071067 631 NCTRFHPNSNYVATGSADRTVRLWDVLNGNCVRIFTGHKGPIHSLTFSPNGRFLATGATDGRVLLWDIGHGLMVGELKGH 710
Cdd:COG2319 166 TSVAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKLLASGSADGTVRLWDLATGKLLRTLTGH 245

                       250       260       270
                ....*....|....*....|....*....|
gi 21071067 711 TDTVCSLRFSRDGEILASGSMDNTVRLWDA 740
Cdd:COG2319 246 SGSVRSVAFSPDGRLLASGSADGTVRLWDL 275
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 462-739 8.80e-70

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: 231.46  E-value: 8.80e-70
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21071067 462 CFYTFLNAYQGLTAVDVTDDSSLIAGGFADSTVRVWsvtpkklrsvkqasdlslidkesddvlerimDEKTASELKILYG 541
Cdd:cd00200  43 LLRTLKGHTGPVRDVAASADGTYLASGSSDKTIRLW-------------------------------DLETGECVRTLTG 91

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21071067 542 HSGPVYGASFSPDRNYLLSSSEDGTVRLWSLQTFTCLVGYKGHNYPVWDTQFSPYGYYFVSGGHDRVARLWATDHYQPLR 621
Cdd:cd00200  92 HTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDLRTGKCVA 171

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21071067 622 IFAGHLADVNCTRFHPNSNYVATGSADRTVRLWDVLNGNCVRIFTGHKGPIHSLTFSPNGRFLATGATDGRVLLWDIGHG 701
Cdd:cd00200 172 TLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGTLRGHENGVNSVAFSPDGYLLASGSEDGTIRVWDLRTG 251

                       250       260       270
                ....*....|....*....|....*....|....*...
gi 21071067 702 LMVGELKGHTDTVCSLRFSRDGEILASGSMDNTVRLWD 739
Cdd:cd00200 252 ECVQTLSGHTNSVTSLAWSPDGKRLASGSADGTIRIWD 289
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 535-796 6.18e-68

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: 226.45  E-value: 6.18e-68
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21071067 535 ELKILYGHSGPVYGASFSPDRNYLLSSSEDGTVRLWSLQTFTCLVGYKGHNYPVWDTQFSPYGYYFVSGGHDRVARLWAT 614
Cdd:cd00200   1 LRRTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASADGTYLASGSSDKTIRLWDL 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21071067 615 DHYQPLRIFAGHLADVNCTRFHPNSNYVATGSADRTVRLWDVLNGNCVRIFTGHKGPIHSLTFSPNGRFLATGATDGRVL 694
Cdd:cd00200  81 ETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIK 160

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21071067 695 LWDIGHGLMVGELKGHTDTVCSLRFSRDGEILASGSMDNTVRLWDaikafedletddftTATGHinlpensqelLLGTYM 774
Cdd:cd00200 161 LWDLRTGKCVATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWD--------------LSTGK----------CLGTLR 216

                       250       260
                ....*....|....*....|..
gi 21071067 775 TKSTPVVHLHFTRRNLVLAAGA 796
Cdd:cd00200 217 GHENGVNSVAFSPDGYLLASGS 238
TFIID_NTD2 pfam04494
WD40 associated region in TFIID subunit, NTD2 domain; This region is an all-alpha domain ...
 208-337 4.79e-62

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: 204.65  E-value: 4.79e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21071067   208 QGDPTMYEEYYSGLKHFIECSLDCHRAELSQLFYPLFVHMYLELVYNQHENEAKSFFEKFHGDQECYYQDDLRVLSSLTK 287
Cdd:pfam04494   1 EGDPQKYERAYSLLRNWIESSLDIYKPELRRLLYPVFVHSYLDLVAKGHIEEAKEFFEKFRGDHEALHGDDLRKLAGITL 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 21071067   288 KEHMKGNETMLDFRTSKFVLRISRDSYQLLKRHLQEKQNNQIWNIVQEHL 337
Cdd:pfam04494  81 PEHLEENELAKLFRSNKYRIRLSRYSFDLLLRFLQENESSVILRIINEHL 130
WD40 COG2319
WD40 repeat [General function prediction only];
510-740 2.95e-61

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 212.08  E-value: 2.95e-61
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21071067 510 ASDLSLIDKESDDVLERIMDEKTASELKILYGHSGPVYGASFSPDRNYLLSSSEDGTVRLWSLQTFTCLVGYKGHNYPVW 589
Cdd:COG2319   3 SADGAALAAASADLALALLAAALGALLLLLLGLAAAVASLAASPDGARLAAGAGDLTLLLLDAAAGALLATLLGHTAAVL 82

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21071067 590 DTQFSPYGYYFVSGGHDRVARLWATDHYQPLRIFAGHLADVNCTRFHPNSNYVATGSADRTVRLWDVLNGNCVRIFTGHK 669
Cdd:COG2319  83 SVAFSPDGRLLASASADGTVRLWDLATGLLLRTLTGHTGAVRSVAFSPDGKTLASGSADGTVRLWDLATGKLLRTLTGHS 162

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 21071067 670 GPIHSLTFSPNGRFLATGATDGRVLLWDIGHGLMVGELKGHTDTVCSLRFSRDGEILASGSMDNTVRLWDA 740
Cdd:COG2319 163 GAVTSVAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKLLASGSADGTVRLWDL 233
TAF5_NTD2 cd08044
TAF5_NTD2 is the second conserved N-terminal region of TATA Binding Protein (TBP) Associated ...
 211-343 7.06e-61

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: 201.65  E-value: 7.06e-61
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21071067 211 PTMYEEYYSGLKHFIECSLDCHRAELSQLFYPLFVHMYLELVYNQHENEAKSFFEKFHGDQECYYQDDLRVLSSLTKKEH 290
Cdd:cd08044   1 PNDYEQAYSKLRKWIESSLDIYKYELSQLLYPIFVHSYLDLVASGHLEEAKSFFERFSGDFEDSHSEDIKKLSSITTPEH 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|...
gi 21071067 291 MKGNETMLDFRTSKFVLRISRDSYQLLKRHLQEKQNNQIWNIVQEHLYIDIFD 343
Cdd:cd08044  81 LKENELAKLFRSNKYVIRMSRDAYSLLLRFLESWGGSLLLKILNEHIDIDVRD 133
WD40 COG2319
WD40 repeat [General function prediction only];
550-740 3.74e-45

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 167.40  E-value: 3.74e-45
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21071067 550 SFSPDRNYLLSSSEDGTVRLWSLQTFTCLVGYKGHNYPVWDTQFSPYGYYFVSGGHDRVARLWATDHYQPLRIFAGHLAD 629
Cdd:COG2319   1 ALSADGAALAAASADLALALLAAALGALLLLLLGLAAAVASLAASPDGARLAAGAGDLTLLLLDAAAGALLATLLGHTAA 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21071067 630 VNCTRFHPNSNYVATGSADRTVRLWDVLNGNCVRIFTGHKGPIHSLTFSPNGRFLATGATDGRVLLWDIGHGLMVGELKG 709
Cdd:COG2319  81 VLSVAFSPDGRLLASASADGTVRLWDLATGLLLRTLTGHTGAVRSVAFSPDGKTLASGSADGTVRLWDLATGKLLRTLTG 160

                       170       180       190
                ....*....|....*....|....*....|.
gi 21071067 710 HTDTVCSLRFSRDGEILASGSMDNTVRLWDA 740
Cdd:COG2319 161 HSGAVTSVAFSPDGKLLASGSDDGTVRLWDL 191
WD40 COG2319
WD40 repeat [General function prediction only];
472-574 6.87e-15

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 77.64  E-value: 6.87e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21071067 472 GLTAVDVTDDSSLIAGGFADSTVRVWSV-TPKKLRSVKQASD------LSLIDKE----SDDVLERIMDEKTASELKILY 540
Cdd:COG2319 290 GVNSVAFSPDGKLLASGSDDGTVRLWDLaTGKLLRTLTGHTGavrsvaFSPDGKTlasgSDDGTVRLWDLATGELLRTLT 369

                        90       100       110
                ....*....|....*....|....*....|....
gi 21071067 541 GHSGPVYGASFSPDRNYLLSSSEDGTVRLWSLQT 574
Cdd:COG2319 370 GHTGAVTSVAFSPDGRTLASGSADGTVRLWDLAT 403
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 658-697 1.19e-11

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: 59.63  E-value: 1.19e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 21071067    658 NGNCVRIFTGHKGPIHSLTFSPNGRFLATGATDGRVLLWD 697
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 704-739 8.59e-11

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: 57.32  E-value: 8.59e-11
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 21071067    704 VGELKGHTDTVCSLRFSRDGEILASGSMDNTVRLWD 739
Cdd:smart00320   5 LKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 618-655 9.20e-11

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: 57.32  E-value: 9.20e-11
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 21071067    618 QPLRIFAGHLADVNCTRFHPNSNYVATGSADRTVRLWD 655
Cdd:smart00320   3 ELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 pfam00400
WD domain, G-beta repeat;
659-697 1.02e-10

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 56.97  E-value: 1.02e-10
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 21071067   659 GNCVRIFTGHKGPIHSLTFSPNGRFLATGATDGRVLLWD 697
Cdd:pfam00400   1 GKLLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
WD40 pfam00400
WD domain, G-beta repeat;
704-739 1.54e-10

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 56.58  E-value: 1.54e-10
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 21071067   704 VGELKGHTDTVCSLRFSRDGEILASGSMDNTVRLWD 739
Cdd:pfam00400   4 LKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 532-571 2.22e-10

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: 56.17  E-value: 2.22e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 21071067    532 TASELKILYGHSGPVYGASFSPDRNYLLSSSEDGTVRLWS 571
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 pfam00400
WD domain, G-beta repeat;
618-655 2.82e-10

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 55.81  E-value: 2.82e-10
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 21071067   618 QPLRIFAGHLADVNCTRFHPNSNYVATGSADRTVRLWD 655
Cdd:pfam00400   2 KLLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
PLN00181 PLN00181
protein SPA1-RELATED; Provisional
 642-761 8.14e-10

protein SPA1-RELATED; Provisional


Pssm-ID: 177776 [Multi-domain]  Cd Length: 793  Bit Score: 62.41  E-value: 8.14e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21071067  642 VATGSADRTVRLWDVLNGncVRIFT-GHKGPIHSLTF-SPNGRFLATGATDGRVLLWDIGH-GLMVGELKGHTDTVCSLR 718
Cdd:PLN00181 591 LASGSDDGSVKLWSINQG--VSIGTiKTKANICCVQFpSESGRSLAFGSADHKVYYYDLRNpKLPLCTMIGHSKTVSYVR 668

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 21071067  719 FSrDGEILASGSMDNTVRLWDAIKAFEDLETDDFTTATGHINL 761
Cdd:PLN00181 669 FV-DSSTLVSSSTDNTLKLWDLSMSISGINETPLHSFMGHTNV 710
WD40 pfam00400
WD domain, G-beta repeat;
534-571 1.49e-09

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 53.89  E-value: 1.49e-09
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 21071067   534 SELKILYGHSGPVYGASFSPDRNYLLSSSEDGTVRLWS 571
Cdd:pfam00400   2 KLLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
PTZ00421 PTZ00421
coronin; Provisional
 531-742 1.06e-07

coronin; Provisional


Pssm-ID: 173611 [Multi-domain]  Cd Length: 493  Bit Score: 55.28  E-value: 1.06e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21071067  531 KTASELKILYGHSGPVYGASFSP-DRNYLLSSSEDGTVRLWSLQTftclvgyKGHNYPVWDtqfspygyyfvsgghdrva 609
Cdd:PTZ00421  63 KLASNPPILLGQEGPIIDVAFNPfDPQKLFTASEDGTIMGWGIPE-------EGLTQNISD------------------- 116

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21071067  610 rlwatdhyqPLRIFAGHLADVNCTRFHPNSNYV-ATGSADRTVRLWDVLNGNCVRIFTGHKGPIHSLTFSPNGRFLATGA 688
Cdd:PTZ00421 117 ---------PIVHLQGHTKKVGIVSFHPSAMNVlASAGADMVVNVWDVERGKAVEVIKCHSDQITSLEWNLDGSLLCTTS 187

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 21071067  689 TDGRVLLWDIGHGLMVGELKGHT-------------DTVCSLRFSRdgeilasgSMDNTVRLWDAIK 742
Cdd:PTZ00421 188 KDKKLNIIDPRDGTIVSSVEAHAsaksqrclwakrkDLIITLGCSK--------SQQRQIMLWDTRK 246
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 574-612 1.04e-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: 45.77  E-value: 1.04e-06
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 21071067    574 TFTCLVGYKGHNYPVWDTQFSPYGYYFVSGGHDRVARLW 612
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLW 39
WDR74 cd22857
WD repeat-containing protein 74; WDR74 (WD repeat-containing protein 74) from mammals and ...
 629-698 1.11e-05

WD repeat-containing protein 74; WDR74 (WD repeat-containing protein 74) from mammals and plants is an essential factor for ribosome assembly. In cooperation with the assembly factor NVL2, WDR74 participates in an early cleavage of the pre-rRNA processing pathway. NVL2 is a type II double ring, AAA-ATPase, that may mediate the release of WDR74 from nucleolar pre-60S particles. WDR74 has been implicated in tumorigenesis. In lung cancer, it regulates cell proliferation, cell cycle progression, chemoresistance and cell aggressiveness, by inducing nuclear beta-catenin accumulation and driving downstream Wnt-responsive genes expression. In melanoma, it promotes apoptosis resistance and aggressive behavior by regulating the RPL5-MDM2-p53 pathway. WDR74 contains an N-terminal seven-bladed beta-propeller WD40 domain that associates with the D1-AAA domain of the AAA-ATPase NVL2, and a flexible lysine-rich C-terminus that extends outward from the WD40 domain, and is required for nucleolar localization.


Pssm-ID: 439303 [Multi-domain]  Cd Length: 325  Bit Score: 48.38  E-value: 1.11e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21071067 629 DVNCTRFHPNSNYVATGSADRTVRLWDvLNGNCVRIFT---------GHKGPIH--SLTFSPNG--RFLATGATDGRVLL 695
Cdd:cd22857 128 NLLCMRVDPNENYFAFGGKEVELNVWD-LEEKPGKIWRaknvpndslGLRVPVWvtDLTFLSKDdhRKIVTGTGYHQVRL 206


                ...
gi 21071067 696 WDI 698
Cdd:cd22857 207 YDT 209
PTZ00420 PTZ00420
coronin; Provisional
 565-658 1.20e-05

coronin; Provisional


Pssm-ID: 240412 [Multi-domain]  Cd Length: 568  Bit Score: 48.79  E-value: 1.20e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21071067  565 GTVRLWSLQTFTCLVGYKGHNYPVWDTQFSP-YGYYFVSGGHDRVARLWATDH--------YQPLRIFAGHLADVNCTRF 635
Cdd:PTZ00420  54 GAIRLENQMRKPPVIKLKGHTSSILDLQFNPcFSEILASGSEDLTIRVWEIPHndesvkeiKDPQCILKGHKKKISIIDW 133

                         90       100
                 ....*....|....*....|....
gi 21071067  636 HPNSNYVATGSA-DRTVRLWDVLN 658
Cdd:PTZ00420 134 NPMNYYIMCSSGfDSFVNIWDIEN 157
WD40 pfam00400
WD domain, G-beta repeat;
575-612 1.67e-05

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 42.33  E-value: 1.67e-05
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 21071067   575 FTCLVGYKGHNYPVWDTQFSPYGYYFVSGGHDRVARLW 612
Cdd:pfam00400   1 GKLLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVW 38
PLN00181 PLN00181
protein SPA1-RELATED; Provisional
 552-696 2.12e-05

protein SPA1-RELATED; Provisional


Pssm-ID: 177776 [Multi-domain]  Cd Length: 793  Bit Score: 48.16  E-value: 2.12e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21071067  552 SPDRNYLLSSSEDGTVRLWSLQTFTClVGYKGHNYPVWDTQF-SPYGYYFVSGGHDRVARLWATDHYQ-PLRIFAGHLAD 629
Cdd:PLN00181 585 SADPTLLASGSDDGSVKLWSINQGVS-IGTIKTKANICCVQFpSESGRSLAFGSADHKVYYYDLRNPKlPLCTMIGHSKT 663

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 21071067  630 VNCTRFHPNSNYVATgSADRTVRLWDV------LNGNCVRIFTGHKGPIHSLTFSPNGRFLATGATDGRVLLW 696
Cdd:PLN00181 664 VSYVRFVDSSTLVSS-STDNTLKLWDLsmsisgINETPLHSFMGHTNVKNFVGLSVSDGYIATGSETNEVFVY 735
ANAPC4_WD40 pfam12894
Anaphase-promoting complex subunit 4 WD40 domain; Apc4 contains an N-terminal propeller-shaped ...
 657-717 1.93e-04

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: 41.11  E-value: 1.93e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 21071067   657 LNGNcvRIFTG----HKGPIHSLTFSPNGRFLATGATDGRVLLWDIGHGLMVGELKGHTDTVCSL 717
Cdd:pfam12894  24 LNWQ--RVWTLspdkEDLEVTSLAWRPDGKLLAVGYSDGTVRLLDAENGKIVHHFSAGSDLITCL 86
NBCH_WD40 pfam20426
Neurobeachin beta propeller domain; This entry represents the beta propeller domain found at ...
 701-743 6.40e-04

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: 42.75  E-value: 6.40e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 21071067   701 GLMVGELKGHTDTVCSLRFSRDGEILASGSMDNTVRLWDAIKA 743
Cdd:pfam20426 114 GRMVQSIRQHKDVVSCVAVTSDGSILATGSYDTTVMVWEVLRG 156
RAB3GAP2_N pfam14655
Rab3 GTPase-activating protein regulatory subunit N-terminus; This family includes the ...
 672-716 1.40e-03

Rab3 GTPase-activating protein regulatory subunit N-terminus; This family includes the N-terminus of the Rab3 GTPase-activating protein non-catalytic subunit. Rab3 GTPase-activating protein is a GTPase activating protein with specificity for Rab3 subfamily.


Pssm-ID: 464240  Cd Length: 416  Bit Score: 41.91  E-value: 1.40e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 21071067   672 IHSLTFSPNGRFLATgaTD--GRVLLWDIGHGLMVGELKGHTDTVCS 716
Cdd:pfam14655 312 GESITLSPSGRLAAV--TDslGRVLLLDVQAGVAVRLWKGYRDAQCG 356
ANAPC4_WD40 pfam12894
Anaphase-promoting complex subunit 4 WD40 domain; Apc4 contains an N-terminal propeller-shaped ...
 621-680 4.63e-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: 36.87  E-value: 4.63e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 21071067   621 RIFAGHLAD----VNCTRFHPNSNYVATGSADRTVRLWDVLNGNCVRIFTGHKGPIHSLTFSPN 680
Cdd:pfam12894  28 RVWTLSPDKedleVTSLAWRPDGKLLAVGYSDGTVRLLDAENGKIVHHFSAGSDLITCLGWGEN 91
ANAPC4_WD40 pfam12894
Anaphase-promoting complex subunit 4 WD40 domain; Apc4 contains an N-terminal propeller-shaped ...
 675-740 4.72e-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: 36.87  E-value: 4.72e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 21071067   675 LTFSPNGRFLATGATDGRVLLWDI-GHGLMVGELKGHTDTVCSLRFSRDGEILASGSMDNTVRLWDA 740
Cdd:pfam12894   1 MSWCPTMDLIALATEDGELLLHRLnWQRVWTLSPDKEDLEVTSLAWRPDGKLLAVGYSDGTVRLLDA 67
 
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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