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Conserved domains on  [gi|110665722|ref|NP_796316|]
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transcription initiation factor TFIID subunit 5 [Mus musculus]

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];
457-741 1.25e-83

WD40 repeat [General function prediction only];


:

Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 272.55  E-value: 1.25e-83
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 457 DCLPSICFYTFLNAYQGLTAVDVTDDSSLIAGGFADSTVRVWSV-TPKKLRSVKQASD--LSLI---DKE------SDDV 524
Cdd:COG2319  106 DLATGLLLRTLTGHTGAVRSVAFSPDGKTLASGSADGTVRLWDLaTGKLLRTLTGHSGavTSVAfspDGKllasgsDDGT 185

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 525 LeRIMDEKTASELKILYGHSGPVYGASFSPDRNYLLSSSEDGTVRLWSLQTFTCLVGYKGHNYPVWDTQFSPYGYYFVSG 604
Cdd:COG2319  186 V-RLWDLATGKLLRTLTGHTGAVRSVAFSPDGKLLASGSADGTVRLWDLATGKLLRTLTGHSGSVRSVAFSPDGRLLASG 264

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 605 GHDRVARLWATDHYQPLRIFAGHLADVNCTRFHPNSNYVATGSADRTVRLWDVLNGNCVRIFTGHKGPIHSLTFSPNGRF 684
Cdd:COG2319  265 SADGTVRLWDLATGELLRTLTGHSGGVNSVAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKT 344

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 110665722 685 LATGATDGRVLLWDIGHGLMVGELKGHTDTVCSLRFSRDGEILASGSMDNTVRLWDA 741
Cdd:COG2319  345 LASGSDDGTVRLWDLATGELLRTLTGHTGAVTSVAFSPDGRTLASGSADGTVRLWDL 401
TFIID_NTD2 pfam04494
WD40 associated region in TFIID subunit, NTD2 domain; This region is an all-alpha domain ...
 209-338 8.78e-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: 203.88  E-value: 8.78e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722  209 QGDPTMYEEYYSGLKHFIECSLDCHRAELSQLFYPLFVHMYLELVYNQHENEAKSFFEKFHGDQECYYQDDLRVLSSLTK 288
Cdd:pfam04494   1 EGDPQKYERAYSLLRNWIESSLDIYKPELRRLLYPVFVHSYLDLVAKGHIEEAKEFFEKFRGDHEALHGDDLRKLAGITL 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 110665722  289 KEHMKGNETMLDFRTSKFVLRISRDSYQLLKRHLQEKQNNQIWNIVQEHL 338
Cdd:pfam04494  81 PEHLEENELAKLFRSNKYRIRLSRYSFDLLLRFLQENESSVILRIINEHL 130
 
Name Accession Description Interval E-value
WD40 COG2319
WD40 repeat [General function prediction only];
457-741 1.25e-83

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 272.55  E-value: 1.25e-83
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 457 DCLPSICFYTFLNAYQGLTAVDVTDDSSLIAGGFADSTVRVWSV-TPKKLRSVKQASD--LSLI---DKE------SDDV 524
Cdd:COG2319  106 DLATGLLLRTLTGHTGAVRSVAFSPDGKTLASGSADGTVRLWDLaTGKLLRTLTGHSGavTSVAfspDGKllasgsDDGT 185

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 525 LeRIMDEKTASELKILYGHSGPVYGASFSPDRNYLLSSSEDGTVRLWSLQTFTCLVGYKGHNYPVWDTQFSPYGYYFVSG 604
Cdd:COG2319  186 V-RLWDLATGKLLRTLTGHTGAVRSVAFSPDGKLLASGSADGTVRLWDLATGKLLRTLTGHSGSVRSVAFSPDGRLLASG 264

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 605 GHDRVARLWATDHYQPLRIFAGHLADVNCTRFHPNSNYVATGSADRTVRLWDVLNGNCVRIFTGHKGPIHSLTFSPNGRF 684
Cdd:COG2319  265 SADGTVRLWDLATGELLRTLTGHSGGVNSVAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKT 344

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 110665722 685 LATGATDGRVLLWDIGHGLMVGELKGHTDTVCSLRFSRDGEILASGSMDNTVRLWDA 741
Cdd:COG2319  345 LASGSDDGTVRLWDLATGELLRTLTGHTGAVTSVAFSPDGRTLASGSADGTVRLWDL 401
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 473-743 2.08e-77

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: 251.87  E-value: 2.08e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 473 GLTAVDVTDDSSLIAGGFADSTVRVWSVtpkklrsvkqasdlslidkesddvlerimdeKTASELKILYGHSGPVYGASF 552
Cdd:cd00200   11 GVTCVAFSPDGKLLATGSGDGTIKVWDL-------------------------------ETGELLRTLKGHTGPVRDVAA 59

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 553 SPDRNYLLSSSEDGTVRLWSLQTFTCLVGYKGHNYPVWDTQFSPYGYYFVSGGHDRVARLWATDHYQPLRIFAGHLADVN 632
Cdd:cd00200   60 SADGTYLASGSSDKTIRLWDLETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVN 139

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 633 CTRFHPNSNYVATGSADRTVRLWDVLNGNCVRIFTGHKGPIHSLTFSPNGRFLATGATDGRVLLWDIGHGLMVGELKGHT 712
Cdd:cd00200  140 SVAFSPDGTFVASSSQDGTIKLWDLRTGKCVATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGTLRGHE 219

                        250       260       270
                 ....*....|....*....|....*....|.
gi 110665722 713 DTVCSLRFSRDGEILASGSMDNTVRLWDAVK 743
Cdd:cd00200  220 NGVNSVAFSPDGYLLASGSEDGTIRVWDLRT 250
TFIID_NTD2 pfam04494
WD40 associated region in TFIID subunit, NTD2 domain; This region is an all-alpha domain ...
 209-338 8.78e-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: 203.88  E-value: 8.78e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722  209 QGDPTMYEEYYSGLKHFIECSLDCHRAELSQLFYPLFVHMYLELVYNQHENEAKSFFEKFHGDQECYYQDDLRVLSSLTK 288
Cdd:pfam04494   1 EGDPQKYERAYSLLRNWIESSLDIYKPELRRLLYPVFVHSYLDLVAKGHIEEAKEFFEKFRGDHEALHGDDLRKLAGITL 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 110665722  289 KEHMKGNETMLDFRTSKFVLRISRDSYQLLKRHLQEKQNNQIWNIVQEHL 338
Cdd:pfam04494  81 PEHLEENELAKLFRSNKYRIRLSRYSFDLLLRFLQENESSVILRIINEHL 130
TAF5_NTD2 cd08044
TAF5_NTD2 is the second conserved N-terminal region of TATA Binding Protein (TBP) Associated ...
 212-344 1.33e-60

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: 200.88  E-value: 1.33e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 212 PTMYEEYYSGLKHFIECSLDCHRAELSQLFYPLFVHMYLELVYNQHENEAKSFFEKFHGDQECYYQDDLRVLSSLTKKEH 291
Cdd:cd08044    1 PNDYEQAYSKLRKWIESSLDIYKYELSQLLYPIFVHSYLDLVASGHLEEAKSFFERFSGDFEDSHSEDIKKLSSITTPEH 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 110665722 292 MKGNETMLDFRTSKFVLRISRDSYQLLKRHLQEKQNNQIWNIVQEHLYIDIFD 344
Cdd:cd08044   81 LKENELAKLFRSNKYVIRMSRDAYSLLLRFLESWGGSLLLKILNEHIDIDVRD 133
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 659-698 7.62e-12

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: 60.40  E-value: 7.62e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 110665722   659 NGNCVRIFTGHKGPIHSLTFSPNGRFLATGATDGRVLLWD 698
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 pfam00400
WD domain, G-beta repeat;
660-698 6.64e-11

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 57.74  E-value: 6.64e-11
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 110665722  660 GNCVRIFTGHKGPIHSLTFSPNGRFLATGATDGRVLLWD 698
Cdd:pfam00400   1 GKLLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
PLN00181 PLN00181
protein SPA1-RELATED; Provisional
 643-762 6.53e-10

protein SPA1-RELATED; Provisional


Pssm-ID: 177776 [Multi-domain]  Cd Length: 793  Bit Score: 62.80  E-value: 6.53e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 643 VATGSADRTVRLWDVLNGncVRIFT-GHKGPIHSLTF-SPNGRFLATGATDGRVLLWDIGH-GLMVGELKGHTDTVCSLR 719
Cdd:PLN00181 591 LASGSDDGSVKLWSINQG--VSIGTiKTKANICCVQFpSESGRSLAFGSADHKVYYYDLRNpKLPLCTMIGHSKTVSYVR 668

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 110665722 720 FSrDGEILASGSMDNTVRLWDAVKAFEDLETDDFTTATGHINL 762
Cdd:PLN00181 669 FV-DSSTLVSSSTDNTLKLWDLSMSISGINETPLHSFMGHTNV 710
 
Name Accession Description Interval E-value
WD40 COG2319
WD40 repeat [General function prediction only];
457-741 1.25e-83

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 272.55  E-value: 1.25e-83
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 457 DCLPSICFYTFLNAYQGLTAVDVTDDSSLIAGGFADSTVRVWSV-TPKKLRSVKQASD--LSLI---DKE------SDDV 524
Cdd:COG2319  106 DLATGLLLRTLTGHTGAVRSVAFSPDGKTLASGSADGTVRLWDLaTGKLLRTLTGHSGavTSVAfspDGKllasgsDDGT 185

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 525 LeRIMDEKTASELKILYGHSGPVYGASFSPDRNYLLSSSEDGTVRLWSLQTFTCLVGYKGHNYPVWDTQFSPYGYYFVSG 604
Cdd:COG2319  186 V-RLWDLATGKLLRTLTGHTGAVRSVAFSPDGKLLASGSADGTVRLWDLATGKLLRTLTGHSGSVRSVAFSPDGRLLASG 264

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 605 GHDRVARLWATDHYQPLRIFAGHLADVNCTRFHPNSNYVATGSADRTVRLWDVLNGNCVRIFTGHKGPIHSLTFSPNGRF 684
Cdd:COG2319  265 SADGTVRLWDLATGELLRTLTGHSGGVNSVAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKT 344

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 110665722 685 LATGATDGRVLLWDIGHGLMVGELKGHTDTVCSLRFSRDGEILASGSMDNTVRLWDA 741
Cdd:COG2319  345 LASGSDDGTVRLWDLATGELLRTLTGHTGAVTSVAFSPDGRTLASGSADGTVRLWDL 401
WD40 COG2319
WD40 repeat [General function prediction only];
466-741 3.64e-78

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 257.92  E-value: 3.64e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 466 TFLNAYQGLTAVDVTDDSSLIAGGFADSTVRVWSVTPKKLR-----------SVKQASDLSLIDKESDDVLERIMDEKTA 534
Cdd:COG2319   31 LLLGLAAAVASLAASPDGARLAAGAGDLTLLLLDAAAGALLatllghtaavlSVAFSPDGRLLASASADGTVRLWDLATG 110

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 535 SELKILYGHSGPVYGASFSPDRNYLLSSSEDGTVRLWSLQTFTCLVGYKGHNYPVWDTQFSPYGYYFVSGGHDRVARLWA 614
Cdd:COG2319  111 LLLRTLTGHTGAVRSVAFSPDGKTLASGSADGTVRLWDLATGKLLRTLTGHSGAVTSVAFSPDGKLLASGSDDGTVRLWD 190

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 615 TDHYQPLRIFAGHLADVNCTRFHPNSNYVATGSADRTVRLWDVLNGNCVRIFTGHKGPIHSLTFSPNGRFLATGATDGRV 694
Cdd:COG2319  191 LATGKLLRTLTGHTGAVRSVAFSPDGKLLASGSADGTVRLWDLATGKLLRTLTGHSGSVRSVAFSPDGRLLASGSADGTV 270

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*..
gi 110665722 695 LLWDIGHGLMVGELKGHTDTVCSLRFSRDGEILASGSMDNTVRLWDA 741
Cdd:COG2319  271 RLWDLATGELLRTLTGHSGGVNSVAFSPDGKLLASGSDDGTVRLWDL 317
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 473-743 2.08e-77

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: 251.87  E-value: 2.08e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 473 GLTAVDVTDDSSLIAGGFADSTVRVWSVtpkklrsvkqasdlslidkesddvlerimdeKTASELKILYGHSGPVYGASF 552
Cdd:cd00200   11 GVTCVAFSPDGKLLATGSGDGTIKVWDL-------------------------------ETGELLRTLKGHTGPVRDVAA 59

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 553 SPDRNYLLSSSEDGTVRLWSLQTFTCLVGYKGHNYPVWDTQFSPYGYYFVSGGHDRVARLWATDHYQPLRIFAGHLADVN 632
Cdd:cd00200   60 SADGTYLASGSSDKTIRLWDLETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVN 139

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 633 CTRFHPNSNYVATGSADRTVRLWDVLNGNCVRIFTGHKGPIHSLTFSPNGRFLATGATDGRVLLWDIGHGLMVGELKGHT 712
Cdd:cd00200  140 SVAFSPDGTFVASSSQDGTIKLWDLRTGKCVATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGTLRGHE 219

                        250       260       270
                 ....*....|....*....|....*....|.
gi 110665722 713 DTVCSLRFSRDGEILASGSMDNTVRLWDAVK 743
Cdd:cd00200  220 NGVNSVAFSPDGYLLASGSEDGTIRVWDLRT 250
WD40 COG2319
WD40 repeat [General function prediction only];
472-741 3.21e-72

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 242.12  E-value: 3.21e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 472 QGLTAVDVTDDSSLIAGGFADSTVRVWSVTPKKLRSVKQASDLSLIDKESDDVLERIMDEKTASELKILYGHSGPVYGAS 551
Cdd:COG2319    6 GAALAAASADLALALLAAALGALLLLLLGLAAAVASLAASPDGARLAAGAGDLTLLLLDAAAGALLATLLGHTAAVLSVA 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 552 FSPDRNYLLSSSEDGTVRLWSLQTFTCLVGYKGHNYPVWDTQFSPYGYYFVSGGHDRVARLWATDHYQPLRIFAGHLADV 631
Cdd:COG2319   86 FSPDGRLLASASADGTVRLWDLATGLLLRTLTGHTGAVRSVAFSPDGKTLASGSADGTVRLWDLATGKLLRTLTGHSGAV 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 632 NCTRFHPNSNYVATGSADRTVRLWDVLNGNCVRIFTGHKGPIHSLTFSPNGRFLATGATDGRVLLWDIGHGLMVGELKGH 711
Cdd:COG2319  166 TSVAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKLLASGSADGTVRLWDLATGKLLRTLTGH 245

                        250       260       270
                 ....*....|....*....|....*....|
gi 110665722 712 TDTVCSLRFSRDGEILASGSMDNTVRLWDA 741
Cdd:COG2319  246 SGSVRSVAFSPDGRLLASGSADGTVRLWDL 275
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 463-740 1.17e-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: 233.77  E-value: 1.17e-70
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 463 CFYTFLNAYQGLTAVDVTDDSSLIAGGFADSTVRVWsvtpkklrsvkqasdlslidkesddvlerimDEKTASELKILYG 542
Cdd:cd00200   43 LLRTLKGHTGPVRDVAASADGTYLASGSSDKTIRLW-------------------------------DLETGECVRTLTG 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 543 HSGPVYGASFSPDRNYLLSSSEDGTVRLWSLQTFTCLVGYKGHNYPVWDTQFSPYGYYFVSGGHDRVARLWATDHYQPLR 622
Cdd:cd00200   92 HTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDLRTGKCVA 171

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 623 IFAGHLADVNCTRFHPNSNYVATGSADRTVRLWDVLNGNCVRIFTGHKGPIHSLTFSPNGRFLATGATDGRVLLWDIGHG 702
Cdd:cd00200  172 TLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGTLRGHENGVNSVAFSPDGYLLASGSEDGTIRVWDLRTG 251

                        250       260       270
                 ....*....|....*....|....*....|....*...
gi 110665722 703 LMVGELKGHTDTVCSLRFSRDGEILASGSMDNTVRLWD 740
Cdd:cd00200  252 ECVQTLSGHTNSVTSLAWSPDGKRLASGSADGTIRIWD 289
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 536-797 8.93e-69

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: 228.76  E-value: 8.93e-69
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 536 ELKILYGHSGPVYGASFSPDRNYLLSSSEDGTVRLWSLQTFTCLVGYKGHNYPVWDTQFSPYGYYFVSGGHDRVARLWAT 615
Cdd:cd00200    1 LRRTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASADGTYLASGSSDKTIRLWDL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 616 DHYQPLRIFAGHLADVNCTRFHPNSNYVATGSADRTVRLWDVLNGNCVRIFTGHKGPIHSLTFSPNGRFLATGATDGRVL 695
Cdd:cd00200   81 ETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIK 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 696 LWDIGHGLMVGELKGHTDTVCSLRFSRDGEILASGSMDNTVRLWDavkafedletddftTATGHinlpensqelLLGTYM 775
Cdd:cd00200  161 LWDLRTGKCVATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWD--------------LSTGK----------CLGTLR 216

                        250       260
                 ....*....|....*....|..
gi 110665722 776 TKSTPVVHLHFTRRNLVLAAGA 797
Cdd:cd00200  217 GHENGVNSVAFSPDGYLLASGS 238
TFIID_NTD2 pfam04494
WD40 associated region in TFIID subunit, NTD2 domain; This region is an all-alpha domain ...
 209-338 8.78e-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: 203.88  E-value: 8.78e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722  209 QGDPTMYEEYYSGLKHFIECSLDCHRAELSQLFYPLFVHMYLELVYNQHENEAKSFFEKFHGDQECYYQDDLRVLSSLTK 288
Cdd:pfam04494   1 EGDPQKYERAYSLLRNWIESSLDIYKPELRRLLYPVFVHSYLDLVAKGHIEEAKEFFEKFRGDHEALHGDDLRKLAGITL 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 110665722  289 KEHMKGNETMLDFRTSKFVLRISRDSYQLLKRHLQEKQNNQIWNIVQEHL 338
Cdd:pfam04494  81 PEHLEENELAKLFRSNKYRIRLSRYSFDLLLRFLQENESSVILRIINEHL 130
WD40 COG2319
WD40 repeat [General function prediction only];
511-741 9.52e-62

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 213.62  E-value: 9.52e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 511 ASDLSLIDKESDDVLERIMDEKTASELKILYGHSGPVYGASFSPDRNYLLSSSEDGTVRLWSLQTFTCLVGYKGHNYPVW 590
Cdd:COG2319    3 SADGAALAAASADLALALLAAALGALLLLLLGLAAAVASLAASPDGARLAAGAGDLTLLLLDAAAGALLATLLGHTAAVL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 591 DTQFSPYGYYFVSGGHDRVARLWATDHYQPLRIFAGHLADVNCTRFHPNSNYVATGSADRTVRLWDVLNGNCVRIFTGHK 670
Cdd:COG2319   83 SVAFSPDGRLLASASADGTVRLWDLATGLLLRTLTGHTGAVRSVAFSPDGKTLASGSADGTVRLWDLATGKLLRTLTGHS 162

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 110665722 671 GPIHSLTFSPNGRFLATGATDGRVLLWDIGHGLMVGELKGHTDTVCSLRFSRDGEILASGSMDNTVRLWDA 741
Cdd:COG2319  163 GAVTSVAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKLLASGSADGTVRLWDL 233
TAF5_NTD2 cd08044
TAF5_NTD2 is the second conserved N-terminal region of TATA Binding Protein (TBP) Associated ...
 212-344 1.33e-60

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: 200.88  E-value: 1.33e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 212 PTMYEEYYSGLKHFIECSLDCHRAELSQLFYPLFVHMYLELVYNQHENEAKSFFEKFHGDQECYYQDDLRVLSSLTKKEH 291
Cdd:cd08044    1 PNDYEQAYSKLRKWIESSLDIYKYELSQLLYPIFVHSYLDLVASGHLEEAKSFFERFSGDFEDSHSEDIKKLSSITTPEH 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 110665722 292 MKGNETMLDFRTSKFVLRISRDSYQLLKRHLQEKQNNQIWNIVQEHLYIDIFD 344
Cdd:cd08044   81 LKENELAKLFRSNKYVIRMSRDAYSLLLRFLESWGGSLLLKILNEHIDIDVRD 133
WD40 COG2319
WD40 repeat [General function prediction only];
551-741 1.46e-45

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 168.55  E-value: 1.46e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 551 SFSPDRNYLLSSSEDGTVRLWSLQTFTCLVGYKGHNYPVWDTQFSPYGYYFVSGGHDRVARLWATDHYQPLRIFAGHLAD 630
Cdd:COG2319    1 ALSADGAALAAASADLALALLAAALGALLLLLLGLAAAVASLAASPDGARLAAGAGDLTLLLLDAAAGALLATLLGHTAA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 631 VNCTRFHPNSNYVATGSADRTVRLWDVLNGNCVRIFTGHKGPIHSLTFSPNGRFLATGATDGRVLLWDIGHGLMVGELKG 710
Cdd:COG2319   81 VLSVAFSPDGRLLASASADGTVRLWDLATGLLLRTLTGHTGAVRSVAFSPDGKTLASGSADGTVRLWDLATGKLLRTLTG 160

                        170       180       190
                 ....*....|....*....|....*....|.
gi 110665722 711 HTDTVCSLRFSRDGEILASGSMDNTVRLWDA 741
Cdd:COG2319  161 HSGAVTSVAFSPDGKLLASGSDDGTVRLWDL 191
WD40 COG2319
WD40 repeat [General function prediction only];
473-575 4.28e-15

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 78.03  E-value: 4.28e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 473 GLTAVDVTDDSSLIAGGFADSTVRVWSV-TPKKLRSVKQASD------LSLIDKE----SDDVLERIMDEKTASELKILY 541
Cdd:COG2319  290 GVNSVAFSPDGKLLASGSDDGTVRLWDLaTGKLLRTLTGHTGavrsvaFSPDGKTlasgSDDGTVRLWDLATGELLRTLT 369

                         90       100       110
                 ....*....|....*....|....*....|....
gi 110665722 542 GHSGPVYGASFSPDRNYLLSSSEDGTVRLWSLQT 575
Cdd:COG2319  370 GHTGAVTSVAFSPDGRTLASGSADGTVRLWDLAT 403
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 659-698 7.62e-12

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: 60.40  E-value: 7.62e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 110665722   659 NGNCVRIFTGHKGPIHSLTFSPNGRFLATGATDGRVLLWD 698
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 705-740 5.54e-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: 58.09  E-value: 5.54e-11
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 110665722   705 VGELKGHTDTVCSLRFSRDGEILASGSMDNTVRLWD 740
Cdd:smart00320   5 LKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 619-656 6.05e-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: 57.71  E-value: 6.05e-11
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 110665722   619 QPLRIFAGHLADVNCTRFHPNSNYVATGSADRTVRLWD 656
Cdd:smart00320   3 ELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 pfam00400
WD domain, G-beta repeat;
660-698 6.64e-11

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 57.74  E-value: 6.64e-11
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 110665722  660 GNCVRIFTGHKGPIHSLTFSPNGRFLATGATDGRVLLWD 698
Cdd:pfam00400   1 GKLLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
WD40 pfam00400
WD domain, G-beta repeat;
705-740 1.00e-10

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 56.97  E-value: 1.00e-10
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 110665722  705 VGELKGHTDTVCSLRFSRDGEILASGSMDNTVRLWD 740
Cdd:pfam00400   4 LKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 533-572 1.47e-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: 56.55  E-value: 1.47e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 110665722   533 TASELKILYGHSGPVYGASFSPDRNYLLSSSEDGTVRLWS 572
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 pfam00400
WD domain, G-beta repeat;
619-656 1.80e-10

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 56.58  E-value: 1.80e-10
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 110665722  619 QPLRIFAGHLADVNCTRFHPNSNYVATGSADRTVRLWD 656
Cdd:pfam00400   2 KLLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
PLN00181 PLN00181
protein SPA1-RELATED; Provisional
 643-762 6.53e-10

protein SPA1-RELATED; Provisional


Pssm-ID: 177776 [Multi-domain]  Cd Length: 793  Bit Score: 62.80  E-value: 6.53e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 643 VATGSADRTVRLWDVLNGncVRIFT-GHKGPIHSLTF-SPNGRFLATGATDGRVLLWDIGH-GLMVGELKGHTDTVCSLR 719
Cdd:PLN00181 591 LASGSDDGSVKLWSINQG--VSIGTiKTKANICCVQFpSESGRSLAFGSADHKVYYYDLRNpKLPLCTMIGHSKTVSYVR 668

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 110665722 720 FSrDGEILASGSMDNTVRLWDAVKAFEDLETDDFTTATGHINL 762
Cdd:PLN00181 669 FV-DSSTLVSSSTDNTLKLWDLSMSISGINETPLHSFMGHTNV 710
WD40 pfam00400
WD domain, G-beta repeat;
535-572 9.49e-10

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 54.27  E-value: 9.49e-10
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 110665722  535 SELKILYGHSGPVYGASFSPDRNYLLSSSEDGTVRLWS 572
Cdd:pfam00400   2 KLLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
PTZ00421 PTZ00421
coronin; Provisional
 532-743 9.22e-08

coronin; Provisional


Pssm-ID: 173611 [Multi-domain]  Cd Length: 493  Bit Score: 55.28  E-value: 9.22e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 532 KTASELKILYGHSGPVYGASFSP-DRNYLLSSSEDGTVRLWSLQTftclvgyKGHNYPVWDtqfspygyyfvsgghdrva 610
Cdd:PTZ00421  63 KLASNPPILLGQEGPIIDVAFNPfDPQKLFTASEDGTIMGWGIPE-------EGLTQNISD------------------- 116

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 611 rlwatdhyqPLRIFAGHLADVNCTRFHPNSNYV-ATGSADRTVRLWDVLNGNCVRIFTGHKGPIHSLTFSPNGRFLATGA 689
Cdd:PTZ00421 117 ---------PIVHLQGHTKKVGIVSFHPSAMNVlASAGADMVVNVWDVERGKAVEVIKCHSDQITSLEWNLDGSLLCTTS 187

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 110665722 690 TDGRVLLWDIGHGLMVGELKGHT-------------DTVCSLRFSRdgeilasgSMDNTVRLWDAVK 743
Cdd:PTZ00421 188 KDKKLNIIDPRDGTIVSSVEAHAsaksqrclwakrkDLIITLGCSK--------SQQRQIMLWDTRK 246
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 575-613 7.36e-07

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: 46.15  E-value: 7.36e-07
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 110665722   575 TFTCLVGYKGHNYPVWDTQFSPYGYYFVSGGHDRVARLW 613
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLW 39
WDR74 cd22857
WD repeat-containing protein 74; WDR74 (WD repeat-containing protein 74) from mammals and ...
 630-699 9.37e-06

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: 9.37e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 630 DVNCTRFHPNSNYVATGSADRTVRLWDvLNGNCVRIFT---------GHKGPIH--SLTFSPNG--RFLATGATDGRVLL 696
Cdd:cd22857  128 NLLCMRVDPNENYFAFGGKEVELNVWD-LEEKPGKIWRaknvpndslGLRVPVWvtDLTFLSKDdhRKIVTGTGYHQVRL 206


                 ...
gi 110665722 697 WDI 699
Cdd:cd22857  207 YDT 209
PTZ00420 PTZ00420
coronin; Provisional
 566-659 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 110665722 566 GTVRLWSLQTFTCLVGYKGHNYPVWDTQFSP-YGYYFVSGGHDRVARLWATDH--------YQPLRIFAGHLADVNCTRF 636
Cdd:PTZ00420  54 GAIRLENQMRKPPVIKLKGHTSSILDLQFNPcFSEILASGSEDLTIRVWEIPHndesvkeiKDPQCILKGHKKKISIIDW 133

                         90       100
                 ....*....|....*....|....
gi 110665722 637 HPNSNYVATGSA-DRTVRLWDVLN 659
Cdd:PTZ00420 134 NPMNYYIMCSSGfDSFVNIWDIEN 157
WD40 pfam00400
WD domain, G-beta repeat;
576-613 1.20e-05

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 42.72  E-value: 1.20e-05
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 110665722  576 FTCLVGYKGHNYPVWDTQFSPYGYYFVSGGHDRVARLW 613
Cdd:pfam00400   1 GKLLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVW 38
PLN00181 PLN00181
protein SPA1-RELATED; Provisional
 553-697 2.13e-05

protein SPA1-RELATED; Provisional


Pssm-ID: 177776 [Multi-domain]  Cd Length: 793  Bit Score: 48.16  E-value: 2.13e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 553 SPDRNYLLSSSEDGTVRLWSLQTFTClVGYKGHNYPVWDTQF-SPYGYYFVSGGHDRVARLWATDHYQ-PLRIFAGHLAD 630
Cdd:PLN00181 585 SADPTLLASGSDDGSVKLWSINQGVS-IGTIKTKANICCVQFpSESGRSLAFGSADHKVYYYDLRNPKlPLCTMIGHSKT 663

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 110665722 631 VNCTRFHPNSNYVATgSADRTVRLWDV------LNGNCVRIFTGHKGPIHSLTFSPNGRFLATGATDGRVLLW 697
Cdd:PLN00181 664 VSYVRFVDSSTLVSS-STDNTLKLWDLsmsisgINETPLHSFMGHTNVKNFVGLSVSDGYIATGSETNEVFVY 735
ANAPC4_WD40 pfam12894
Anaphase-promoting complex subunit 4 WD40 domain; Apc4 contains an N-terminal propeller-shaped ...
 658-718 1.94e-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: 1.94e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 110665722  658 LNGNcvRIFTG----HKGPIHSLTFSPNGRFLATGATDGRVLLWDIGHGLMVGELKGHTDTVCSL 718
Cdd:pfam12894  24 LNWQ--RVWTLspdkEDLEVTSLAWRPDGKLLAVGYSDGTVRLLDAENGKIVHHFSAGSDLITCL 86
NBCH_WD40 pfam20426
Neurobeachin beta propeller domain; This entry represents the beta propeller domain found at ...
 702-744 6.19e-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: 6.19e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 110665722  702 GLMVGELKGHTDTVCSLRFSRDGEILASGSMDNTVRLWDAVKA 744
Cdd:pfam20426 114 GRMVQSIRQHKDVVSCVAVTSDGSILATGSYDTTVMVWEVLRG 156
RAB3GAP2_N pfam14655
Rab3 GTPase-activating protein regulatory subunit N-terminus; This family includes the ...
 673-717 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 110665722  673 IHSLTFSPNGRFLATgaTD--GRVLLWDIGHGLMVGELKGHTDTVCS 717
Cdd:pfam14655 312 GESITLSPSGRLAAV--TDslGRVLLLDVQAGVAVRLWKGYRDAQCG 356
ANAPC4_WD40 pfam12894
Anaphase-promoting complex subunit 4 WD40 domain; Apc4 contains an N-terminal propeller-shaped ...
 676-744 1.91e-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: 38.03  E-value: 1.91e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722  676 LTFSPNGRFLATGATDGRVLLWDI-GHGLMVGELKGHTDTVCSLRFSRDGEILASGSMDNTVRLWDAVKA 744
Cdd:pfam12894   1 MSWCPTMDLIALATEDGELLLHRLnWQRVWTLSPDKEDLEVTSLAWRPDGKLLAVGYSDGTVRLLDAENG 70
ANAPC4_WD40 pfam12894
Anaphase-promoting complex subunit 4 WD40 domain; Apc4 contains an N-terminal propeller-shaped ...
 622-681 4.64e-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: 4.64e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 110665722  622 RIFAGHLAD----VNCTRFHPNSNYVATGSADRTVRLWDVLNGNCVRIFTGHKGPIHSLTFSPN 681
Cdd:pfam12894  28 RVWTLSPDKedleVTSLAWRPDGKLLAVGYSDGTVRLLDAENGKIVHHFSAGSDLITCLGWGEN 91
 
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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