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Conserved domains on  [gi|109090468|ref|XP_001113759|]
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PREDICTED: transcription initiation factor TFIID subunit 5 [Macaca mulatta]

Protein Classification

TAF5_NTD2 and WD40 domain-containing protein (domain architecture ID 10169025)

TAF5_NTD2 and WD40 domain-containing protein

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
472-739 5.59e-75

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  Cd Length: 289  Bit Score: 248.02  E-value: 5.59e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468 472 GLTAVDVTDDSSLIAGGFADSTVRVWSVtpkklrsvkqasdlslidkesddvlerimdeKTASELKILYGHSGPVYGASF 551
Cdd:cd00200   11 GVTCVAFSPDGKLLATGSGDGTIKVWDL-------------------------------ETGELLRTLKGHTGPVRDVAA 59
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468 552 SPDRNYLLSSSEDGTVRLWSLQTFTCLVGYKGHNYPVWDTQFSPYGYYFVSGGHDRVARLWATDHYQPLRIFAGHLADVN 631
Cdd:cd00200   60 SADGTYLASGSSDKTIRLWDLETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVN 139
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468 632 CTRFHPNSNYVATGSADRTVRLWDVLNGNCVRIFTGHKGPIHSLTFSPNGRFLATGATDGRVLLWDIGHGLMVGELKGHT 711
Cdd:cd00200  140 SVAFSPDGTFVASSSQDGTIKLWDLRTGKCVATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGTLRGHE 219
                        250       260
                 ....*....|....*....|....*...
gi 109090468 712 DTVCSLRFSRDGEILASGSMDNTVRLWD 739
Cdd:cd00200  220 NGVNSVAFSPDGYLLASGSEDGTIRVWD 247
TAF5_NTD2 cd08044
TAF5_NTD2 is the second conserved N-terminal region of TATA Binding Protein (TBP) Associated ...
211-343 4.05e-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: 201.27  E-value: 4.05e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468 211 PTMYEEYYSGLKHFIECSLDCHRAELSQLFYPLFVHMYLELVYNQHENEAKSFFEKFHGDQECYYQDDLRVLSSLTKKEH 290
Cdd:cd08044    1 PNDYEQAYSKLRKWIESSLDIYKYELSQLLYPIFVHSYLDLVASGHLEEAKSFFERFSGDFEDSHSEDIKKLSSITTPEH 80
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 109090468 291 MKGNETMLDFRTSKFVLRISRDSYQLLKRHLQEKQNNQIWNIVQEHLYIDIFD 343
Cdd:cd08044   81 LKENELAKLFRSNKYVIRMSRDAYSLLLRFLESWGGSLLLKILNEHIDIDVRD 133
 
Name Accession Description Interval E-value
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
472-739 5.59e-75

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  Cd Length: 289  Bit Score: 248.02  E-value: 5.59e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468 472 GLTAVDVTDDSSLIAGGFADSTVRVWSVtpkklrsvkqasdlslidkesddvlerimdeKTASELKILYGHSGPVYGASF 551
Cdd:cd00200   11 GVTCVAFSPDGKLLATGSGDGTIKVWDL-------------------------------ETGELLRTLKGHTGPVRDVAA 59
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468 552 SPDRNYLLSSSEDGTVRLWSLQTFTCLVGYKGHNYPVWDTQFSPYGYYFVSGGHDRVARLWATDHYQPLRIFAGHLADVN 631
Cdd:cd00200   60 SADGTYLASGSSDKTIRLWDLETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVN 139
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468 632 CTRFHPNSNYVATGSADRTVRLWDVLNGNCVRIFTGHKGPIHSLTFSPNGRFLATGATDGRVLLWDIGHGLMVGELKGHT 711
Cdd:cd00200  140 SVAFSPDGTFVASSSQDGTIKLWDLRTGKCVATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGTLRGHE 219
                        250       260
                 ....*....|....*....|....*...
gi 109090468 712 DTVCSLRFSRDGEILASGSMDNTVRLWD 739
Cdd:cd00200  220 NGVNSVAFSPDGYLLASGSEDGTIRVWD 247
TAF5_NTD2 cd08044
TAF5_NTD2 is the second conserved N-terminal region of TATA Binding Protein (TBP) Associated ...
211-343 4.05e-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: 201.27  E-value: 4.05e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468 211 PTMYEEYYSGLKHFIECSLDCHRAELSQLFYPLFVHMYLELVYNQHENEAKSFFEKFHGDQECYYQDDLRVLSSLTKKEH 290
Cdd:cd08044    1 PNDYEQAYSKLRKWIESSLDIYKYELSQLLYPIFVHSYLDLVASGHLEEAKSFFERFSGDFEDSHSEDIKKLSSITTPEH 80
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 109090468 291 MKGNETMLDFRTSKFVLRISRDSYQLLKRHLQEKQNNQIWNIVQEHLYIDIFD 343
Cdd:cd08044   81 LKENELAKLFRSNKYVIRMSRDAYSLLLRFLESWGGSLLLKILNEHIDIDVRD 133
TFIID_NTD2 pfam04494
WD40 associated region in TFIID subunit, NTD2 domain; This region is an all-alpha domain ...
211-337 1.97e-58

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 homodimerisation.


Pssm-ID: 309580  Cd Length: 127  Bit Score: 196.16  E-value: 1.97e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468  211 PTMYEEYYSGLKHFIECSLDCHRAELSQLFYPLFVHMYLELVYNQHENEAKSFFEKFHGDQECYYQDDLRVLSSLTKKEH 290
Cdd:pfam04494   1 PQKYERAYSLLRNWIDSSLDIYKPELSRLLYPVFVHSYLDLVSKGHIEEAKEFFERFRGDFEDLHGDDLRKLAGITLPEH 80
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 109090468  291 MKGNETMLDFRTSKFVLRISRDSYQLLKRHLQEKQNNQIWNIVQEHL 337
Cdd:pfam04494  81 LEENELAKLFRSNKYRIRLSRYSFSLLLRFLQENENSVILRILNEHL 127
WD40 COG2319
WD40 repeat [General function prediction only];
459-740 1.41e-50

WD40 repeat [General function prediction only];


Pssm-ID: 225201  Cd Length: 466  Bit Score: 185.29  E-value: 1.41e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468 459 PSICFYTFLNAYQGLTAVDVT-DDSSLIAGGFADSTVRVWSV-TPKKLRSVKQASD-----------LSLIDKESDDVLE 525
Cdd:COG2319  144 PGKLIRTLEGHSESVTSLAFSpDGKLLASGSSLDGTIKLWDLrTGKPLSTLAGHTDpvsslafspdgGLLIASGSSDGTI 223
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468 526 RIMDEKTASELKI-LYGHSGPVYGaSFSPDRNYLLSSSEDGTVRLWSLQTF-TCLVGYKGHNYPVWDTQFSPYGYYFVSG 603
Cdd:COG2319  224 RLWDLSTGKLLRStLSGHSDSVVS-SFSPDGSLLASGSSDGTIRLWDLRSSsSLLRTLSGHSSSVLSVAFSPDGKLLASG 302
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468 604 GHDRVARLWATDHYQPLRIFA--GHLADVNCTRFHPNSNYVATG-SADRTVRLWDVLNGNCVRIFTGHkGPIHSLTFSPN 680
Cdd:COG2319  303 SSDGTVRLWDLETGKLLSSLTlkGHEGPVSSLSFSPDGSLLVSGgSDDGTIRLWDLRTGKPLKTLEGH-SNVLSVSFSPD 381
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468 681 GRFLATGATDGRVLLWDIGHGLMVGELKGHTDTVCSLRFSRDGEILASGSMDNTVRLWDA 740
Cdd:COG2319  382 GRVVSSGSTDGTVRLWDLSTGSLLRNLDGHTSRVTSLDFSPDGKSLASGSSDNTIRLWDL 441
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
658-697 8.41e-11

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


Pssm-ID: 197651  Cd Length: 40  Bit Score: 59.63  E-value: 8.41e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 109090468   658 NGNCVRIFTGHKGPIHSLTFSPNGRFLATGATDGRVLLWD 697
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
PLN00181 PLN00181
protein SPA1-RELATED; Provisional
642-761 6.95e-10

protein SPA1-RELATED; Provisional


Pssm-ID: 177776  Cd Length: 793  Bit Score: 62.41  E-value: 6.95e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468 642 VATGSADRTVRLWDVLNGncVRIFT-GHKGPIHSLTF-SPNGRFLATGATDGRVLLWDIGH-GLMVGELKGHTDTVCSLR 718
Cdd:PLN00181 591 LASGSDDGSVKLWSINQG--VSIGTiKTKANICCVQFpSESGRSLAFGSADHKVYYYDLRNpKLPLCTMIGHSKTVSYVR 668
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 109090468 719 FSrDGEILASGSMDNTVRLWDAIKAFEDLETDDFTTATGHINL 761
Cdd:PLN00181 669 FV-DSSTLVSSSTDNTLKLWDLSMSISGINETPLHSFMGHTNV 710
WD40 pfam00400
WD domain, G-beta repeat;
618-655 1.24e-09

WD domain, G-beta repeat;


Pssm-ID: 306830  Cd Length: 39  Bit Score: 56.21  E-value: 1.24e-09
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 109090468  618 QPLRIFAGHLADVNCTRFHPNSNYVATGSADRTVRLWD 655
Cdd:pfam00400   2 KLLKTLKGHTSGVTSLAFSPDGKLLASGSDDGTVKLWD 39
 
Name Accession Description Interval E-value
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
472-739 5.59e-75

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  Cd Length: 289  Bit Score: 248.02  E-value: 5.59e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468 472 GLTAVDVTDDSSLIAGGFADSTVRVWSVtpkklrsvkqasdlslidkesddvlerimdeKTASELKILYGHSGPVYGASF 551
Cdd:cd00200   11 GVTCVAFSPDGKLLATGSGDGTIKVWDL-------------------------------ETGELLRTLKGHTGPVRDVAA 59
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468 552 SPDRNYLLSSSEDGTVRLWSLQTFTCLVGYKGHNYPVWDTQFSPYGYYFVSGGHDRVARLWATDHYQPLRIFAGHLADVN 631
Cdd:cd00200   60 SADGTYLASGSSDKTIRLWDLETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVN 139
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468 632 CTRFHPNSNYVATGSADRTVRLWDVLNGNCVRIFTGHKGPIHSLTFSPNGRFLATGATDGRVLLWDIGHGLMVGELKGHT 711
Cdd:cd00200  140 SVAFSPDGTFVASSSQDGTIKLWDLRTGKCVATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGTLRGHE 219
                        250       260
                 ....*....|....*....|....*...
gi 109090468 712 DTVCSLRFSRDGEILASGSMDNTVRLWD 739
Cdd:cd00200  220 NGVNSVAFSPDGYLLASGSEDGTIRVWD 247
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
462-739 1.37e-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  Cd Length: 289  Bit Score: 230.68  E-value: 1.37e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468 462 CFYTFLNAYQGLTAVDVTDDSSLIAGGFADSTVRVWsvtpkklrsvkqasdlslidkesddvlerimDEKTASELKILYG 541
Cdd:cd00200   43 LLRTLKGHTGPVRDVAASADGTYLASGSSDKTIRLW-------------------------------DLETGECVRTLTG 91
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468 542 HSGPVYGASFSPDRNYLLSSSEDGTVRLWSLQTFTCLVGYKGHNYPVWDTQFSPYGYYFVSGGHDRVARLWATDHYQPLR 621
Cdd:cd00200   92 HTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDLRTGKCVA 171
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468 622 IFAGHLADVNCTRFHPNSNYVATGSADRTVRLWDVLNGNCVRIFTGHKGPIHSLTFSPNGRFLATGATDGRVLLWDIGHG 701
Cdd:cd00200  172 TLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGTLRGHENGVNSVAFSPDGYLLASGSEDGTIRVWDLRTG 251
                        250       260       270
                 ....*....|....*....|....*....|....*...
gi 109090468 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 9.12e-67

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


Pssm-ID: 238121  Cd Length: 289  Bit Score: 225.68  E-value: 9.12e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468 535 ELKILYGHSGPVYGASFSPDRNYLLSSSEDGTVRLWSLQTFTCLVGYKGHNYPVWDTQFSPYGYYFVSGGHDRVARLWAT 614
Cdd:cd00200    1 LRRTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASADGTYLASGSSDKTIRLWDL 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468 615 DHYQPLRIFAGHLADVNCTRFHPNSNYVATGSADRTVRLWDVLNGNCVRIFTGHKGPIHSLTFSPNGRFLATGATDGRVL 694
Cdd:cd00200   81 ETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIK 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468 695 LWDIGHGLMVGELKGHTDTVCSLRFSRDGEILASGSMDNTVRLWDaikafedletddftTATGHinlpensqelLLGTYM 774
Cdd:cd00200  161 LWDLRTGKCVATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWD--------------LSTGK----------CLGTLR 216
                        250       260
                 ....*....|....*....|..
gi 109090468 775 TKSTPVVHLHFTRRNLVLAAGA 796
Cdd:cd00200  217 GHENGVNSVAFSPDGYLLASGS 238
TAF5_NTD2 cd08044
TAF5_NTD2 is the second conserved N-terminal region of TATA Binding Protein (TBP) Associated ...
211-343 4.05e-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: 201.27  E-value: 4.05e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468 211 PTMYEEYYSGLKHFIECSLDCHRAELSQLFYPLFVHMYLELVYNQHENEAKSFFEKFHGDQECYYQDDLRVLSSLTKKEH 290
Cdd:cd08044    1 PNDYEQAYSKLRKWIESSLDIYKYELSQLLYPIFVHSYLDLVASGHLEEAKSFFERFSGDFEDSHSEDIKKLSSITTPEH 80
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 109090468 291 MKGNETMLDFRTSKFVLRISRDSYQLLKRHLQEKQNNQIWNIVQEHLYIDIFD 343
Cdd:cd08044   81 LKENELAKLFRSNKYVIRMSRDAYSLLLRFLESWGGSLLLKILNEHIDIDVRD 133
TFIID_NTD2 pfam04494
WD40 associated region in TFIID subunit, NTD2 domain; This region is an all-alpha domain ...
211-337 1.97e-58

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 homodimerisation.


Pssm-ID: 309580  Cd Length: 127  Bit Score: 196.16  E-value: 1.97e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468  211 PTMYEEYYSGLKHFIECSLDCHRAELSQLFYPLFVHMYLELVYNQHENEAKSFFEKFHGDQECYYQDDLRVLSSLTKKEH 290
Cdd:pfam04494   1 PQKYERAYSLLRNWIDSSLDIYKPELSRLLYPVFVHSYLDLVSKGHIEEAKEFFERFRGDFEDLHGDDLRKLAGITLPEH 80
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 109090468  291 MKGNETMLDFRTSKFVLRISRDSYQLLKRHLQEKQNNQIWNIVQEHL 337
Cdd:pfam04494  81 LEENELAKLFRSNKYRIRLSRYSFSLLLRFLQENENSVILRILNEHL 127
WD40 COG2319
WD40 repeat [General function prediction only];
459-740 1.41e-50

WD40 repeat [General function prediction only];


Pssm-ID: 225201  Cd Length: 466  Bit Score: 185.29  E-value: 1.41e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468 459 PSICFYTFLNAYQGLTAVDVT-DDSSLIAGGFADSTVRVWSV-TPKKLRSVKQASD-----------LSLIDKESDDVLE 525
Cdd:COG2319  144 PGKLIRTLEGHSESVTSLAFSpDGKLLASGSSLDGTIKLWDLrTGKPLSTLAGHTDpvsslafspdgGLLIASGSSDGTI 223
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468 526 RIMDEKTASELKI-LYGHSGPVYGaSFSPDRNYLLSSSEDGTVRLWSLQTF-TCLVGYKGHNYPVWDTQFSPYGYYFVSG 603
Cdd:COG2319  224 RLWDLSTGKLLRStLSGHSDSVVS-SFSPDGSLLASGSSDGTIRLWDLRSSsSLLRTLSGHSSSVLSVAFSPDGKLLASG 302
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468 604 GHDRVARLWATDHYQPLRIFA--GHLADVNCTRFHPNSNYVATG-SADRTVRLWDVLNGNCVRIFTGHkGPIHSLTFSPN 680
Cdd:COG2319  303 SSDGTVRLWDLETGKLLSSLTlkGHEGPVSSLSFSPDGSLLVSGgSDDGTIRLWDLRTGKPLKTLEGH-SNVLSVSFSPD 381
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468 681 GRFLATGATDGRVLLWDIGHGLMVGELKGHTDTVCSLRFSRDGEILASGSMDNTVRLWDA 740
Cdd:COG2319  382 GRVVSSGSTDGTVRLWDLSTGSLLRNLDGHTSRVTSLDFSPDGKSLASGSSDNTIRLWDL 441
WD40 COG2319
WD40 repeat [General function prediction only];
472-798 7.13e-47

WD40 repeat [General function prediction only];


Pssm-ID: 225201  Cd Length: 466  Bit Score: 174.51  E-value: 7.13e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468 472 GLTAVDVTDDSSLIAGGFADSTVRVWSVTPKKL-------RSVKQASDLSLIDKESDDVLE---------RIMDEKTASE 535
Cdd:COG2319   67 SITSIAFSPDGELLLSGSSDGTIKLWDLDNGEKlikslegLHDSSVSKLALSSPDGNSILLasssldgtvKLWDLSTPGK 146
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468 536 -LKILYGHSGPVYGASFSPDRNYLLSSSE-DGTVRLWSLQTFTCLVGYKGHNYPVWDTQFSPYG-YYFVSGGHDRVARLW 612
Cdd:COG2319  147 lIRTLEGHSESVTSLAFSPDGKLLASGSSlDGTIKLWDLRTGKPLSTLAGHTDPVSSLAFSPDGgLLIASGSSDGTIRLW 226
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468 613 ATDHYQPLRI-FAGHLaDVNCTRFHPNSNYVATGSADRTVRLWDVLNG-NCVRIFTGHKGPIHSLTFSPNGRFLATGATD 690
Cdd:COG2319  227 DLSTGKLLRStLSGHS-DSVVSSFSPDGSLLASGSSDGTIRLWDLRSSsSLLRTLSGHSSSVLSVAFSPDGKLLASGSSD 305
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468 691 GRVLLWDIGHG--LMVGELKGHTDTVCSLRFSRDGEILASG-SMDNTVRLWDAIKAFEDLETDDFTTAT----------- 756
Cdd:COG2319  306 GTVRLWDLETGklLSSLTLKGHEGPVSSLSFSPDGSLLVSGgSDDGTIRLWDLRTGKPLKTLEGHSNVLsvsfspdgrvv 385
                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....*...
gi 109090468 757 ------GHINLPENSQELLLGTYMTKSTPVVHLHFTRRNLVLAAGAYS 798
Cdd:COG2319  386 ssgstdGTVRLWDLSTGSLLRNLDGHTSRVTSLDFSPDGKSLASGSSD 433
WD40 COG2319
WD40 repeat [General function prediction only];
498-751 8.00e-40

WD40 repeat [General function prediction only];


Pssm-ID: 225201  Cd Length: 466  Bit Score: 154.09  E-value: 8.00e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468 498 SVTPKKLRSVKQASDLSLIDKESDDVLERIMDEKTASELKILYGHSGPVYGASFSPDRNYLLSSSEDGTVRLWSLQTFTC 577
Cdd:COG2319   20 ELGPSLNSLSLLSLGSSESGILLLALLSDSLVSLPDLSSLLLRGHEDSITSIAFSPDGELLLSGSSDGTIKLWDLDNGEK 99
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468 578 LVG--YKGHNYPVWDTQF-SPYGYYFVS--GGHDRVARLWA-TDHYQPLRIFAGHLADVNCTRFHPNSNYVATGS-ADRT 650
Cdd:COG2319  100 LIKslEGLHDSSVSKLALsSPDGNSILLasSSLDGTVKLWDlSTPGKLIRTLEGHSESVTSLAFSPDGKLLASGSsLDGT 179
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468 651 VRLWDVLNGNCVRIFTGHKGPIHSLTFSPNGRF-LATGATDGRVLLWDIGHG-LMVGELKGHTDTVCSLrFSRDGEILAS 728
Cdd:COG2319  180 IKLWDLRTGKPLSTLAGHTDPVSSLAFSPDGGLlIASGSSDGTIRLWDLSTGkLLRSTLSGHSDSVVSS-FSPDGSLLAS 258
                        250       260
                 ....*....|....*....|...
gi 109090468 729 GSMDNTVRLWDAIKAFEDLETDD 751
Cdd:COG2319  259 GSSDGTIRLWDLRSSSSLLRTLS 281
WD40 COG2319
WD40 repeat [General function prediction only];
456-693 9.90e-27

WD40 repeat [General function prediction only];


Pssm-ID: 225201  Cd Length: 466  Bit Score: 114.42  E-value: 9.90e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468 456 DCLPSICFYTFLNAYQGLTAVDVTDDSSLIAGGFADSTVRVWSVTPKK------------LRSVKQASDLSLIDKESDDV 523
Cdd:COG2319  227 DLSTGKLLRSTLSGHSDSVVSSFSPDGSLLASGSSDGTIRLWDLRSSSsllrtlsghsssVLSVAFSPDGKLLASGSSDG 306
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468 524 LERIMDEKTASELKIL--YGHSGPVYGASFSPDRNYLLSS-SEDGTVRLWSLQTFTCLVGYKGHNyPVWDTQFSPYGYYF 600
Cdd:COG2319  307 TVRLWDLETGKLLSSLtlKGHEGPVSSLSFSPDGSLLVSGgSDDGTIRLWDLRTGKPLKTLEGHS-NVLSVSFSPDGRVV 385
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468 601 VSGGHDRVARLWATDHYQPLRIFAGHLADVNCTRFHPNSNYVATGSADRTVRLWDVlngncvriftghKGPIHSLTFSPN 680
Cdd:COG2319  386 SSGSTDGTVRLWDLSTGSLLRNLDGHTSRVTSLDFSPDGKSLASGSSDNTIRLWDL------------KTSLKSVSFSPD 453
                        250
                 ....*....|...
gi 109090468 681 GRFLATGATDGRV 693
Cdd:COG2319  454 GKVLASKSSDLSV 466
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
658-697 8.41e-11

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


Pssm-ID: 197651  Cd Length: 40  Bit Score: 59.63  E-value: 8.41e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 109090468   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 5.92e-10

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


Pssm-ID: 197651  Cd Length: 40  Bit Score: 57.32  E-value: 5.92e-10
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 109090468   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 6.21e-10

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


Pssm-ID: 197651  Cd Length: 40  Bit Score: 57.32  E-value: 6.21e-10
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 109090468   618 QPLRIFAGHLADVNCTRFHPNSNYVATGSADRTVRLWD 655
Cdd:smart00320   3 ELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
PLN00181 PLN00181
protein SPA1-RELATED; Provisional
642-761 6.95e-10

protein SPA1-RELATED; Provisional


Pssm-ID: 177776  Cd Length: 793  Bit Score: 62.41  E-value: 6.95e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468 642 VATGSADRTVRLWDVLNGncVRIFT-GHKGPIHSLTF-SPNGRFLATGATDGRVLLWDIGH-GLMVGELKGHTDTVCSLR 718
Cdd:PLN00181 591 LASGSDDGSVKLWSINQG--VSIGTiKTKANICCVQFpSESGRSLAFGSADHKVYYYDLRNpKLPLCTMIGHSKTVSYVR 668
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 109090468 719 FSrDGEILASGSMDNTVRLWDAIKAFEDLETDDFTTATGHINL 761
Cdd:PLN00181 669 FV-DSSTLVSSSTDNTLKLWDLSMSISGINETPLHSFMGHTNV 710
WD40 pfam00400
WD domain, G-beta repeat;
618-655 1.24e-09

WD domain, G-beta repeat;


Pssm-ID: 306830  Cd Length: 39  Bit Score: 56.21  E-value: 1.24e-09
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 109090468  618 QPLRIFAGHLADVNCTRFHPNSNYVATGSADRTVRLWD 655
Cdd:pfam00400   2 KLLKTLKGHTSGVTSLAFSPDGKLLASGSDDGTVKLWD 39
WD40 pfam00400
WD domain, G-beta repeat;
704-739 1.30e-09

WD domain, G-beta repeat;


Pssm-ID: 306830  Cd Length: 39  Bit Score: 56.21  E-value: 1.30e-09
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 109090468  704 VGELKGHTDTVCSLRFSRDGEILASGSMDNTVRLWD 739
Cdd:pfam00400   4 LKTLKGHTSGVTSLAFSPDGKLLASGSDDGTVKLWD 39
WD40 pfam00400
WD domain, G-beta repeat;
659-697 1.33e-09

WD domain, G-beta repeat;


Pssm-ID: 306830  Cd Length: 39  Bit Score: 56.21  E-value: 1.33e-09
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 109090468  659 GNCVRIFTGHKGPIHSLTFSPNGRFLATGATDGRVLLWD 697
Cdd:pfam00400   1 GKLLKTLKGHTSGVTSLAFSPDGKLLASGSDDGTVKLWD 39
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
532-571 1.47e-09

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


Pssm-ID: 197651  Cd Length: 40  Bit Score: 56.17  E-value: 1.47e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 109090468   532 TASELKILYGHSGPVYGASFSPDRNYLLSSSEDGTVRLWS 571
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 pfam00400
WD domain, G-beta repeat;
534-571 2.10e-08

WD domain, G-beta repeat;


Pssm-ID: 306830  Cd Length: 39  Bit Score: 52.75  E-value: 2.10e-08
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 109090468  534 SELKILYGHSGPVYGASFSPDRNYLLSSSEDGTVRLWS 571
Cdd:pfam00400   2 KLLKTLKGHTSGVTSLAFSPDGKLLASGSDDGTVKLWD 39
PTZ00421 PTZ00421
coronin; Provisional
531-742 9.18e-08

coronin; Provisional


Pssm-ID: 173611  Cd Length: 493  Bit Score: 55.28  E-value: 9.18e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468 531 KTASELKILYGHSGPVYGASFSP-DRNYLLSSSEDGTVRLWSLQTftclvgyKGHNYPVWDtqfspygyyfvsgghdrva 609
Cdd:PTZ00421  63 KLASNPPILLGQEGPIIDVAFNPfDPQKLFTASEDGTIMGWGIPE-------EGLTQNISD------------------- 116
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468 610 rlwatdhyqPLRIFAGHLADVNCTRFHPNSNYV-ATGSADRTVRLWDVLNGNCVRIFTGHKGPIHSLTFSPNGRFLATGA 688
Cdd:PTZ00421 117 ---------PIVHLQGHTKKVGIVSFHPSAMNVlASAGADMVVNVWDVERGKAVEVIKCHSDQITSLEWNLDGSLLCTTS 187
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 109090468 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 5.60e-06

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


Pssm-ID: 197651  Cd Length: 40  Bit Score: 45.77  E-value: 5.60e-06
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 109090468   574 TFTCLVGYKGHNYPVWDTQFSPYGYYFVSGGHDRVARLW 612
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLW 39
PTZ00420 PTZ00420
coronin; Provisional
565-658 1.02e-05

coronin; Provisional


Pssm-ID: 240412  Cd Length: 568  Bit Score: 48.79  E-value: 1.02e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468 565 GTVRLWSLQTFTCLVGYKGHNYPVWDTQFSP-YGYYFVSGGHDRVARLWATDH--------YQPLRIFAGHLADVNCTRF 635
Cdd:PTZ00420  54 GAIRLENQMRKPPVIKLKGHTSSILDLQFNPcFSEILASGSEDLTIRVWEIPHndesvkeiKDPQCILKGHKKKISIIDW 133
                         90       100
                 ....*....|....*....|....
gi 109090468 636 HPNSNYVATGSA-DRTVRLWDVLN 658
Cdd:PTZ00420 134 NPMNYYIMCSSGfDSFVNIWDIEN 157
PLN00181 PLN00181
protein SPA1-RELATED; Provisional
552-696 1.81e-05

protein SPA1-RELATED; Provisional


Pssm-ID: 177776  Cd Length: 793  Bit Score: 48.16  E-value: 1.81e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468 552 SPDRNYLLSSSEDGTVRLWSLQTFTClVGYKGHNYPVWDTQF-SPYGYYFVSGGHDRVARLWATDHYQ-PLRIFAGHLAD 629
Cdd:PLN00181 585 SADPTLLASGSDDGSVKLWSINQGVS-IGTIKTKANICCVQFpSESGRSLAFGSADHKVYYYDLRNPKlPLCTMIGHSKT 663
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 109090468 630 VNCTRFHPNSNYVATgSADRTVRLWDV------LNGNCVRIFTGHKGPIHSLTFSPNGRFLATGATDGRVLLW 696
Cdd:PLN00181 664 VSYVRFVDSSTLVSS-STDNTLKLWDLsmsisgINETPLHSFMGHTNVKNFVGLSVSDGYIATGSETNEVFVY 735
WD40 pfam00400
WD domain, G-beta repeat;
575-612 8.59e-05

WD domain, G-beta repeat;


Pssm-ID: 306830  Cd Length: 39  Bit Score: 42.35  E-value: 8.59e-05
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 109090468  575 FTCLVGYKGHNYPVWDTQFSPYGYYFVSGGHDRVARLW 612
Cdd:pfam00400   1 GKLLKTLKGHTSGVTSLAFSPDGKLLASGSDDGTVKLW 38
ANAPC4_WD40 pfam12894
Anaphase-promoting complex subunit 4 WD40 domain; Apc4 contains an N-terminal propeller-shaped ...
657-722 1.79e-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: 315554  Cd Length: 91  Bit Score: 41.88  E-value: 1.79e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468  657 LNGNcvRIFTG----HKGPIHSLTFSPNGRFLATGATDGRVLLWDIGHGLMVGELKGHTDTVCSLRFSRD 722
Cdd:pfam12894  24 LNWQ--RVWTLsppkEDLEVTSLAWRPDGKLLAVGYSDGTVRLLDAENGKIVHSFSAGSDLITCLGWGEN 91
TolB COG0823
Periplasmic component of the Tol biopolymer transport system [Intracellular trafficking, ...
465-684 1.54e-03

Periplasmic component of the Tol biopolymer transport system [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 223893  Cd Length: 425  Bit Score: 41.67  E-value: 1.54e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468 465 TFLNAYQGLTAVDVTDDSSLIaggfadSTVRVWSVTPKKLRSVKQASDLSLIdkesddvleRIMDEKTASELKILyGHSG 544
Cdd:COG0823  175 LALGDYDGYNQQKLTDSGSLI------LTPAWSPDGKKLAYVSFELGGCPRI---------YYLDLNTGKRPVIL-NFNG 238
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109090468 545 PVYGASFSPDRNYL-LSSSEDGTVRLW----SLQTFTCLVGYKGHNypvWDTQFSPYG--YYFVS--GGHDRVARLwATD 615
Cdd:COG0823  239 NNGAPAFSPDGSKLaFSSSRDGSPDIYlmdlDGKNLPRLTNGFGIN---TSPSWSPDGskIVFTSdrGGRPQIYLY-DLE 314
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 109090468 616 HYQPLRIFAGHLADVNcTRFHPNSNYVATGSADRTVR---LWDVLNGNCVRIFTgHKGPIHSLTFSPNGRFL 684
Cdd:COG0823  315 GSQVTRLTFSGGGNSN-PVWSPDGDKIVFESSSGGQWdidKNDLASGGKIRILT-STYLNESPSWAPNGRMI 384
RAB3GAP2_N pfam14655
Rab3 GTPase-activating protein regulatory subunit N-terminus; This family includes the ...
672-716 2.40e-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: 317100  Cd Length: 415  Bit Score: 40.74  E-value: 2.40e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 109090468  672 IHSLTFSPNGRFLATgaTD--GRVLLWDIGHGLMVGELKGHTDTVCS 716
Cdd:pfam14655 311 GESITLSPSGTLAAV--TDslGRVLLLDVQAGVVVRMWKGYRDAQCG 355
ANAPC4_WD40 pfam12894
Anaphase-promoting complex subunit 4 WD40 domain; Apc4 contains an N-terminal propeller-shaped ...
630-680 7.81e-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: 315554  Cd Length: 91  Bit Score: 36.87  E-value: 7.81e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 109090468  630 VNCTRFHPNSNYVATGSADRTVRLWDVLNGNCVRIFTGHKGPIHSLTFSPN 680
Cdd:pfam12894  41 VTSLAWRPDGKLLAVGYSDGTVRLLDAENGKIVHSFSAGSDLITCLGWGEN 91
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.16
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
  • Marchler-Bauer A et al. (2015), "CDD: NCBI's conserved domain database.", Nucleic Acids Res.43(D)222-6.
  • Marchler-Bauer A et al. (2011), "CDD: a Conserved Domain Database for the functional annotation of proteins.", Nucleic Acids Res.39(D)225-9.
  • Marchler-Bauer A, Bryant SH (2004), "CD-Search: protein domain annotations on the fly.", Nucleic Acids Res.32(W)327-331.
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