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Conserved domains on  [gi|110665722|ref|NP_796316.2|]
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transcription initiation factor TFIID subunit 5

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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 ...
473-743 1.05e-76

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


:

Pssm-ID: 238121 [Multi-domain]  Cd Length: 289  Bit Score: 251.87  E-value: 1.05e-76
                         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
TAF5_NTD2 cd08044
TAF5_NTD2 is the second conserved N-terminal region of TATA Binding Protein (TBP) Associated ...
212-344 2.53e-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: 2.53e-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];
460-741 3.75e-52

WD40 repeat [General function prediction only];


:

Pssm-ID: 225201 [Multi-domain]  Cd Length: 466  Bit Score: 188.76  E-value: 3.75e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 460 PSICFYTFLNAYQGLTAVDVT-DDSSLIAGGFADSTVRVWSV-TPKKLRSVKQASD-----------LSLIDKESDDVLE 526
Cdd:COG2319  144 PGKLIRTLEGHSESVTSLAFSpDGKLLASGSSLDGTIKLWDLrTGKPLSTLAGHTDpvsslafspdgGLLIASGSSDGTI 223
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 527 RIMDEKTASELKI-LYGHSGPVYGaSFSPDRNYLLSSSEDGTVRLWSLQTF-TCLVGYKGHNYPVWDTQFSPYGYYFVSG 604
Cdd:COG2319  224 RLWDLSTGKLLRStLSGHSDSVVS-SFSPDGSLLASGSSDGTIRLWDLRSSsSLLRTLSGHSSSVLSVAFSPDGKLLASG 302
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 605 GHDRVARLWATDHYQPLRIFA--GHLADVNCTRFHPNSNYVATG-SADRTVRLWDVLNGNCVRIFTGHkGPIHSLTFSPN 681
Cdd:COG2319  303 SSDGTVRLWDLETGKLLSSLTlkGHEGPVSSLSFSPDGSLLVSGgSDDGTIRLWDLRTGKPLKTLEGH-SNVLSVSFSPD 381
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 682 GRFLATGATDGRVLLWDIGHGLMVGELKGHTDTVCSLRFSRDGEILASGSMDNTVRLWDA 741
Cdd:COG2319  382 GRVVSSGSTDGTVRLWDLSTGSLLRNLDGHTSRVTSLDFSPDGKSLASGSSDNTIRLWDL 441
 
Name Accession Description Interval E-value
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
473-743 1.05e-76

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


Pssm-ID: 238121 [Multi-domain]  Cd Length: 289  Bit Score: 251.87  E-value: 1.05e-76
                         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
TAF5_NTD2 cd08044
TAF5_NTD2 is the second conserved N-terminal region of TATA Binding Protein (TBP) Associated ...
212-344 2.53e-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: 2.53e-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
TFIID_90kDa pfam04494
WD40 associated region in TFIID subunit; This region, possibly a domain is found in subunits ...
212-339 2.94e-49

WD40 associated region in TFIID subunit; This region, possibly a domain is found in subunits of transcription factor TFIID. The function of this region is unknown.


Pssm-ID: 252629  Cd Length: 131  Bit Score: 170.08  E-value: 2.94e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722  212 PTMYEEYYSGLKHFIECSLDCHRAELSQLFYPLFVHMYLELVYNQHENEAKSFFEKFHGDQECYYQDDLRVLSSLTKKEH 291
Cdd:pfam04494   1 PQQYERAYALLRNWIESSLDIYKPELSRLLYPLFVHSYLDLVAKGHPSEARAFFDKFHGDFEQLHGEDIEKLRGISLPEH 80
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 110665722  292 MKGNETMLDFRTSKFVLRISRDSYQLLKRHLQEKQNNQ---IWNIVQEHLY 339
Cdd:pfam04494  81 IKENELAKAFRDNKYRIRLSRYSFSLLLRFLEENENVGgslLLRILNQHLQ 131
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
659-698 2.00e-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: 60.40  E-value: 2.00e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 110665722   659 NGNCVRIFTGHKGPIHSLTFSPNGRFLATGATDGRVLLWD 698
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 pfam00400
WD domain, G-beta repeat;
705-740 2.07e-11

WD domain, G-beta repeat;


Pssm-ID: 249832  Cd Length: 39  Bit Score: 60.45  E-value: 2.07e-11
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 110665722  705 VGELKGHTDTVCSLRFSRDGEILASGSMDNTVRLWD 740
Cdd:pfam00400   4 LRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
WD40 COG2319
WD40 repeat [General function prediction only];
460-741 3.75e-52

WD40 repeat [General function prediction only];


Pssm-ID: 225201 [Multi-domain]  Cd Length: 466  Bit Score: 188.76  E-value: 3.75e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 460 PSICFYTFLNAYQGLTAVDVT-DDSSLIAGGFADSTVRVWSV-TPKKLRSVKQASD-----------LSLIDKESDDVLE 526
Cdd:COG2319  144 PGKLIRTLEGHSESVTSLAFSpDGKLLASGSSLDGTIKLWDLrTGKPLSTLAGHTDpvsslafspdgGLLIASGSSDGTI 223
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 527 RIMDEKTASELKI-LYGHSGPVYGaSFSPDRNYLLSSSEDGTVRLWSLQTF-TCLVGYKGHNYPVWDTQFSPYGYYFVSG 604
Cdd:COG2319  224 RLWDLSTGKLLRStLSGHSDSVVS-SFSPDGSLLASGSSDGTIRLWDLRSSsSLLRTLSGHSSSVLSVAFSPDGKLLASG 302
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 605 GHDRVARLWATDHYQPLRIFA--GHLADVNCTRFHPNSNYVATG-SADRTVRLWDVLNGNCVRIFTGHkGPIHSLTFSPN 681
Cdd:COG2319  303 SSDGTVRLWDLETGKLLSSLTlkGHEGPVSSLSFSPDGSLLVSGgSDDGTIRLWDLRTGKPLKTLEGH-SNVLSVSFSPD 381
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 682 GRFLATGATDGRVLLWDIGHGLMVGELKGHTDTVCSLRFSRDGEILASGSMDNTVRLWDA 741
Cdd:COG2319  382 GRVVSSGSTDGTVRLWDLSTGSLLRNLDGHTSRVTSLDFSPDGKSLASGSSDNTIRLWDL 441
PLN00181 PLN00181
protein SPA1-RELATED; Provisional
643-762 2.32e-10

protein SPA1-RELATED; Provisional


Pssm-ID: 177776 [Multi-domain]  Cd Length: 793  Bit Score: 62.80  E-value: 2.32e-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
PTZ00421 PTZ00421
coronin; Provisional
532-743 3.27e-08

coronin; Provisional


Pssm-ID: 173611 [Multi-domain]  Cd Length: 493  Bit Score: 55.28  E-value: 3.27e-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
eIF2A pfam08662
Eukaryotic translation initiation factor eIF2A; This is a family of eukaryotic translation ...
638-739 1.14e-03

Eukaryotic translation initiation factor eIF2A; This is a family of eukaryotic translation initiation factors.


Pssm-ID: 149648 [Multi-domain]  Cd Length: 194  Bit Score: 39.55  E-value: 1.14e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722  638 PNSN--YVATGSADRTVRLWDVlngNCVRIFTGHKGPIHSLTFSPNGRFLAT---GATDGRVLLWDIGHGLMVGELKGHT 712
Cdd:pfam08662  69 PNGKefAVIYGYMPAKITFFDL---KGNVIHSLGEQPRNTIFWSPFGRLVLLagfGNLAGQIEFWDVKNKKKIATAEASN 145
                          90       100       110
                  ....*....|....*....|....*....|...
gi 110665722  713 DTVCSlrFSRDGEILASGS------MDNTVRLW 739
Cdd:pfam08662 146 ATDCE--WSPDGRYFLTATtsprlrVDNGFKIW 176
PRK13875 PRK13875
conjugal transfer protein TrbL; Provisional
127-223 7.99e-03

conjugal transfer protein TrbL; Provisional


Pssm-ID: 237537 [Multi-domain]  Cd Length: 440  Bit Score: 37.97  E-value: 7.99e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 127 AVAGSGAPGELDGAGAEAASALLS--RVTASVPGSAAPEPpGTGASVTSVFSGSASGPAAPGKVASVAVedqpdVSAVLS 204
Cdd:PRK13875 285 AVAAAAGAGLAAGGGAAAAGGAAAaaRGGAAAAGGASSAY-SAGAAGGSGAAGVAAGLGGVARAGASAA-----ASPLRR 358
                         90
                 ....*....|....*....
gi 110665722 205 AYNQQGDpTMYEEYYSGLK 223
Cdd:PRK13875 359 AASRAAE-SMKSSFRAGAR 376
 
Name Accession Description Interval E-value
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
473-743 1.05e-76

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


Pssm-ID: 238121 [Multi-domain]  Cd Length: 289  Bit Score: 251.87  E-value: 1.05e-76
                         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
TAF5_NTD2 cd08044
TAF5_NTD2 is the second conserved N-terminal region of TATA Binding Protein (TBP) Associated ...
212-344 2.53e-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: 2.53e-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 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
463-740 4.34e-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: 4.34e-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 2.99e-68

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


Pssm-ID: 238121 [Multi-domain]  Cd Length: 289  Bit Score: 228.76  E-value: 2.99e-68
                         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_90kDa pfam04494
WD40 associated region in TFIID subunit; This region, possibly a domain is found in subunits ...
212-339 2.94e-49

WD40 associated region in TFIID subunit; This region, possibly a domain is found in subunits of transcription factor TFIID. The function of this region is unknown.


Pssm-ID: 252629  Cd Length: 131  Bit Score: 170.08  E-value: 2.94e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722  212 PTMYEEYYSGLKHFIECSLDCHRAELSQLFYPLFVHMYLELVYNQHENEAKSFFEKFHGDQECYYQDDLRVLSSLTKKEH 291
Cdd:pfam04494   1 PQQYERAYALLRNWIESSLDIYKPELSRLLYPLFVHSYLDLVAKGHPSEARAFFDKFHGDFEQLHGEDIEKLRGISLPEH 80
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 110665722  292 MKGNETMLDFRTSKFVLRISRDSYQLLKRHLQEKQNNQ---IWNIVQEHLY 339
Cdd:pfam04494  81 IKENELAKAFRDNKYRIRLSRYSFSLLLRFLEENENVGgslLLRILNQHLQ 131
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
659-698 2.00e-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: 60.40  E-value: 2.00e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 110665722   659 NGNCVRIFTGHKGPIHSLTFSPNGRFLATGATDGRVLLWD 698
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 pfam00400
WD domain, G-beta repeat;
705-740 2.07e-11

WD domain, G-beta repeat;


Pssm-ID: 249832  Cd Length: 39  Bit Score: 60.45  E-value: 2.07e-11
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 110665722  705 VGELKGHTDTVCSLRFSRDGEILASGSMDNTVRLWD 740
Cdd:pfam00400   4 LRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
WD40 pfam00400
WD domain, G-beta repeat;
619-656 2.63e-11

WD domain, G-beta repeat;


Pssm-ID: 249832  Cd Length: 39  Bit Score: 60.06  E-value: 2.63e-11
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 110665722  619 QPLRIFAGHLADVNCTRFHPNSNYVATGSADRTVRLWD 656
Cdd:pfam00400   2 KLLRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
WD40 pfam00400
WD domain, G-beta repeat;
660-698 6.43e-11

WD domain, G-beta repeat;


Pssm-ID: 249832  Cd Length: 39  Bit Score: 58.91  E-value: 6.43e-11
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 110665722  660 GNCVRIFTGHKGPIHSLTFSPNGRFLATGATDGRVLLWD 698
Cdd:pfam00400   1 GKLLRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
705-740 1.41e-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: 58.09  E-value: 1.41e-10
                           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 1.54e-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: 57.71  E-value: 1.54e-10
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 110665722   619 QPLRIFAGHLADVNCTRFHPNSNYVATGSADRTVRLWD 656
Cdd:smart00320   3 ELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 pfam00400
WD domain, G-beta repeat;
535-572 2.06e-10

WD domain, G-beta repeat;


Pssm-ID: 249832  Cd Length: 39  Bit Score: 57.37  E-value: 2.06e-10
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 110665722  535 SELKILYGHSGPVYGASFSPDRNYLLSSSEDGTVRLWS 572
Cdd:pfam00400   2 KLLRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
533-572 3.69e-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: 56.55  E-value: 3.69e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 110665722   533 TASELKILYGHSGPVYGASFSPDRNYLLSSSEDGTVRLWS 572
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 pfam00400
WD domain, G-beta repeat;
576-613 8.38e-07

WD domain, G-beta repeat;


Pssm-ID: 249832  Cd Length: 39  Bit Score: 46.97  E-value: 8.38e-07
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 110665722  576 FTCLVGYKGHNYPVWDTQFSPYGYYFVSGGHDRVARLW 613
Cdd:pfam00400   1 GKLLRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVW 38
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
575-613 1.50e-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: 46.15  E-value: 1.50e-06
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 110665722   575 TFTCLVGYKGHNYPVWDTQFSPYGYYFVSGGHDRVARLW 613
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLW 39
WD40 COG2319
WD40 repeat [General function prediction only];
460-741 3.75e-52

WD40 repeat [General function prediction only];


Pssm-ID: 225201 [Multi-domain]  Cd Length: 466  Bit Score: 188.76  E-value: 3.75e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 460 PSICFYTFLNAYQGLTAVDVT-DDSSLIAGGFADSTVRVWSV-TPKKLRSVKQASD-----------LSLIDKESDDVLE 526
Cdd:COG2319  144 PGKLIRTLEGHSESVTSLAFSpDGKLLASGSSLDGTIKLWDLrTGKPLSTLAGHTDpvsslafspdgGLLIASGSSDGTI 223
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 527 RIMDEKTASELKI-LYGHSGPVYGaSFSPDRNYLLSSSEDGTVRLWSLQTF-TCLVGYKGHNYPVWDTQFSPYGYYFVSG 604
Cdd:COG2319  224 RLWDLSTGKLLRStLSGHSDSVVS-SFSPDGSLLASGSSDGTIRLWDLRSSsSLLRTLSGHSSSVLSVAFSPDGKLLASG 302
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 605 GHDRVARLWATDHYQPLRIFA--GHLADVNCTRFHPNSNYVATG-SADRTVRLWDVLNGNCVRIFTGHkGPIHSLTFSPN 681
Cdd:COG2319  303 SSDGTVRLWDLETGKLLSSLTlkGHEGPVSSLSFSPDGSLLVSGgSDDGTIRLWDLRTGKPLKTLEGH-SNVLSVSFSPD 381
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 682 GRFLATGATDGRVLLWDIGHGLMVGELKGHTDTVCSLRFSRDGEILASGSMDNTVRLWDA 741
Cdd:COG2319  382 GRVVSSGSTDGTVRLWDLSTGSLLRNLDGHTSRVTSLDFSPDGKSLASGSSDNTIRLWDL 441
WD40 COG2319
WD40 repeat [General function prediction only];
473-799 1.50e-48

WD40 repeat [General function prediction only];


Pssm-ID: 225201 [Multi-domain]  Cd Length: 466  Bit Score: 178.36  E-value: 1.50e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 473 GLTAVDVTDDSSLIAGGFADSTVRVWSVTPKKL-------RSVKQASDLSLIDKESDDVLE---------RIMDEKTASE 536
Cdd:COG2319   67 SITSIAFSPDGELLLSGSSDGTIKLWDLDNGEKlikslegLHDSSVSKLALSSPDGNSILLasssldgtvKLWDLSTPGK 146
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 537 -LKILYGHSGPVYGASFSPDRNYLLSSSE-DGTVRLWSLQTFTCLVGYKGHNYPVWDTQFSPYG-YYFVSGGHDRVARLW 613
Cdd:COG2319  147 lIRTLEGHSESVTSLAFSPDGKLLASGSSlDGTIKLWDLRTGKPLSTLAGHTDPVSSLAFSPDGgLLIASGSSDGTIRLW 226
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 614 ATDHYQPLRI-FAGHLaDVNCTRFHPNSNYVATGSADRTVRLWDVLNG-NCVRIFTGHKGPIHSLTFSPNGRFLATGATD 691
Cdd:COG2319  227 DLSTGKLLRStLSGHS-DSVVSSFSPDGSLLASGSSDGTIRLWDLRSSsSLLRTLSGHSSSVLSVAFSPDGKLLASGSSD 305
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 692 GRVLLWDIGHG--LMVGELKGHTDTVCSLRFSRDGEILASG-SMDNTVRLWDAVKAFEDLETDDFTTAT----------- 757
Cdd:COG2319  306 GTVRLWDLETGklLSSLTLKGHEGPVSSLSFSPDGSLLVSGgSDDGTIRLWDLRTGKPLKTLEGHSNVLsvsfspdgrvv 385
                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....*...
gi 110665722 758 ------GHINLPENSQELLLGTYMTKSTPVVHLHFTRRNLVLAAGAYS 799
Cdd:COG2319  386 ssgstdGTVRLWDLSTGSLLRNLDGHTSRVTSLDFSPDGKSLASGSSD 433
WD40 COG2319
WD40 repeat [General function prediction only];
499-752 3.40e-41

WD40 repeat [General function prediction only];


Pssm-ID: 225201 [Multi-domain]  Cd Length: 466  Bit Score: 157.17  E-value: 3.40e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 499 SVTPKKLRSVKQASDLSLIDKESDDVLERIMDEKTASELKILYGHSGPVYGASFSPDRNYLLSSSEDGTVRLWSLQTFTC 578
Cdd:COG2319   20 ELGPSLNSLSLLSLGSSESGILLLALLSDSLVSLPDLSSLLLRGHEDSITSIAFSPDGELLLSGSSDGTIKLWDLDNGEK 99
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 579 LVG--YKGHNYPVWDTQF-SPYGYYFVS--GGHDRVARLWA-TDHYQPLRIFAGHLADVNCTRFHPNSNYVATGS-ADRT 651
Cdd:COG2319  100 LIKslEGLHDSSVSKLALsSPDGNSILLasSSLDGTVKLWDlSTPGKLIRTLEGHSESVTSLAFSPDGKLLASGSsLDGT 179
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 652 VRLWDVLNGNCVRIFTGHKGPIHSLTFSPNGRF-LATGATDGRVLLWDIGHG-LMVGELKGHTDTVCSLrFSRDGEILAS 729
Cdd:COG2319  180 IKLWDLRTGKPLSTLAGHTDPVSSLAFSPDGGLlIASGSSDGTIRLWDLSTGkLLRSTLSGHSDSVVSS-FSPDGSLLAS 258
                        250       260
                 ....*....|....*....|...
gi 110665722 730 GSMDNTVRLWDAVKAFEDLETDD 752
Cdd:COG2319  259 GSSDGTIRLWDLRSSSSLLRTLS 281
WD40 COG2319
WD40 repeat [General function prediction only];
457-694 8.45e-28

WD40 repeat [General function prediction only];


Pssm-ID: 225201 [Multi-domain]  Cd Length: 466  Bit Score: 116.34  E-value: 8.45e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 457 DCLPSICFYTFLNAYQGLTAVDVTDDSSLIAGGFADSTVRVWSVTPKK------------LRSVKQASDLSLIDKESDDV 524
Cdd:COG2319  227 DLSTGKLLRSTLSGHSDSVVSSFSPDGSLLASGSSDGTIRLWDLRSSSsllrtlsghsssVLSVAFSPDGKLLASGSSDG 306
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 525 LERIMDEKTASELKIL--YGHSGPVYGASFSPDRNYLLSS-SEDGTVRLWSLQTFTCLVGYKGHNyPVWDTQFSPYGYYF 601
Cdd:COG2319  307 TVRLWDLETGKLLSSLtlKGHEGPVSSLSFSPDGSLLVSGgSDDGTIRLWDLRTGKPLKTLEGHS-NVLSVSFSPDGRVV 385
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 602 VSGGHDRVARLWATDHYQPLRIFAGHLADVNCTRFHPNSNYVATGSADRTVRLWDVlngncvriftghKGPIHSLTFSPN 681
Cdd:COG2319  386 SSGSTDGTVRLWDLSTGSLLRNLDGHTSRVTSLDFSPDGKSLASGSSDNTIRLWDL------------KTSLKSVSFSPD 453
                        250
                 ....*....|...
gi 110665722 682 GRFLATGATDGRV 694
Cdd:COG2319  454 GKVLASKSSDLSV 466
PLN00181 PLN00181
protein SPA1-RELATED; Provisional
643-762 2.32e-10

protein SPA1-RELATED; Provisional


Pssm-ID: 177776 [Multi-domain]  Cd Length: 793  Bit Score: 62.80  E-value: 2.32e-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
PTZ00421 PTZ00421
coronin; Provisional
532-743 3.27e-08

coronin; Provisional


Pssm-ID: 173611 [Multi-domain]  Cd Length: 493  Bit Score: 55.28  E-value: 3.27e-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
PTZ00420 PTZ00420
coronin; Provisional
566-659 4.25e-06

coronin; Provisional


Pssm-ID: 240412 [Multi-domain]  Cd Length: 568  Bit Score: 48.79  E-value: 4.25e-06
                         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
PLN00181 PLN00181
protein SPA1-RELATED; Provisional
553-697 7.54e-06

protein SPA1-RELATED; Provisional


Pssm-ID: 177776 [Multi-domain]  Cd Length: 793  Bit Score: 48.16  E-value: 7.54e-06
                         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
TolB COG0823
Periplasmic component of the Tol biopolymer transport system [Intracellular trafficking, ...
466-685 6.00e-04

Periplasmic component of the Tol biopolymer transport system [Intracellular trafficking, secretion, and vesicular transport]; linked to 3D-structure


Pssm-ID: 223893 [Multi-domain]  Cd Length: 425  Bit Score: 41.67  E-value: 6.00e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 466 TFLNAYQGLTAVDVTDDSSLIaggfadSTVRVWSVTPKKLRSVKQASDLSLIdkesddvleRIMDEKTASELKILyGHSG 545
Cdd:COG0823  175 LALGDYDGYNQQKLTDSGSLI------LTPAWSPDGKKLAYVSFELGGCPRI---------YYLDLNTGKRPVIL-NFNG 238
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 546 PVYGASFSPDRNYL-LSSSEDGTVRLW----SLQTFTCLVGYKGHNypvWDTQFSPYG--YYFVS--GGHDRVARLwATD 616
Cdd:COG0823  239 NNGAPAFSPDGSKLaFSSSRDGSPDIYlmdlDGKNLPRLTNGFGIN---TSPSWSPDGskIVFTSdrGGRPQIYLY-DLE 314
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 110665722 617 HYQPLRIFAGHLADVNcTRFHPNSNYVATGSADRTVR---LWDVLNGNCVRIFTgHKGPIHSLTFSPNGRFL 685
Cdd:COG0823  315 GSQVTRLTFSGGGNSN-PVWSPDGDKIVFESSSGGQWdidKNDLASGGKIRILT-STYLNESPSWAPNGRMI 384
eIF2A pfam08662
Eukaryotic translation initiation factor eIF2A; This is a family of eukaryotic translation ...
638-739 1.14e-03

Eukaryotic translation initiation factor eIF2A; This is a family of eukaryotic translation initiation factors.


Pssm-ID: 149648 [Multi-domain]  Cd Length: 194  Bit Score: 39.55  E-value: 1.14e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722  638 PNSN--YVATGSADRTVRLWDVlngNCVRIFTGHKGPIHSLTFSPNGRFLAT---GATDGRVLLWDIGHGLMVGELKGHT 712
Cdd:pfam08662  69 PNGKefAVIYGYMPAKITFFDL---KGNVIHSLGEQPRNTIFWSPFGRLVLLagfGNLAGQIEFWDVKNKKKIATAEASN 145
                          90       100       110
                  ....*....|....*....|....*....|...
gi 110665722  713 DTVCSlrFSRDGEILASGS------MDNTVRLW 739
Cdd:pfam08662 146 ATDCE--WSPDGRYFLTATtsprlrVDNGFKIW 176
PTZ00420 PTZ00420
coronin; Provisional
697-740 3.20e-03

coronin; Provisional


Pssm-ID: 240412 [Multi-domain]  Cd Length: 568  Bit Score: 39.55  E-value: 3.20e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 110665722 697 WDIGHGLMVG--------------ELKGHTDTVCSLRFSR-DGEILASGSMDNTVRLWD 740
Cdd:PTZ00420  45 WEVEGGGLIGairlenqmrkppviKLKGHTSSILDLQFNPcFSEILASGSEDLTIRVWE 103
PTZ00420 PTZ00420
coronin; Provisional
668-746 3.57e-03

coronin; Provisional


Pssm-ID: 240412 [Multi-domain]  Cd Length: 568  Bit Score: 39.16  E-value: 3.57e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 668 GHKGPIHSLTFSP-NGRFLATGATDGRVLLWDIGHG-LMVGE-------LKGHTDTVCSLRFS-RDGEILASGSMDNTVR 737
Cdd:PTZ00420  72 GHTSSILDLQFNPcFSEILASGSEDLTIRVWEIPHNdESVKEikdpqciLKGHKKKISIIDWNpMNYYIMCSSGFDSFVN 151
                         90
                 ....*....|..
gi 110665722 738 LWD---AVKAFE 746
Cdd:PTZ00420 152 IWDienEKRAFQ 163
PTZ00420 PTZ00420
coronin; Provisional
604-699 3.92e-03

coronin; Provisional


Pssm-ID: 240412 [Multi-domain]  Cd Length: 568  Bit Score: 39.16  E-value: 3.92e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 604 GGHDRVARLWATDHYQPLRIFAGHLADVNCTRFHP-NSNYVATGSADRTVRLWDVL-NGNCVR-------IFTGHKGPIH 674
Cdd:PTZ00420  50 GGLIGAIRLENQMRKPPVIKLKGHTSSILDLQFNPcFSEILASGSEDLTIRVWEIPhNDESVKeikdpqcILKGHKKKIS 129
                         90       100
                 ....*....|....*....|....*.
gi 110665722 675 SLTFSP-NGRFLATGATDGRVLLWDI 699
Cdd:PTZ00420 130 IIDWNPmNYYIMCSSGFDSFVNIWDI 155
PRK13875 PRK13875
conjugal transfer protein TrbL; Provisional
127-223 7.99e-03

conjugal transfer protein TrbL; Provisional


Pssm-ID: 237537 [Multi-domain]  Cd Length: 440  Bit Score: 37.97  E-value: 7.99e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110665722 127 AVAGSGAPGELDGAGAEAASALLS--RVTASVPGSAAPEPpGTGASVTSVFSGSASGPAAPGKVASVAVedqpdVSAVLS 204
Cdd:PRK13875 285 AVAAAAGAGLAAGGGAAAAGGAAAaaRGGAAAAGGASSAY-SAGAAGGSGAAGVAAGLGGVARAGASAA-----ASPLRR 358
                         90
                 ....*....|....*....
gi 110665722 205 AYNQQGDpTMYEEYYSGLK 223
Cdd:PRK13875 359 AASRAAE-SMKSSFRAGAR 376
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.14
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • 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 et al. (2009), "CDD: specific functional annotation with the Conserved Domain Database.", Nucleic Acids Res.37(D)205-10.
  • 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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