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Conserved domains on  [gi|115533709|ref|NP_492169|]
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Transcription initiation factor TFIID subunit 5 [Caenorhabditis elegans]

Protein Classification

TAF5 family protein( domain architecture ID 10169025)

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

Gene Ontology:  GO:0006357

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
WD40 COG2319
WD40 repeat [General function prediction only];
379-593 3.80e-44

WD40 repeat [General function prediction only];


:

Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 162.77  E-value: 3.80e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115533709 379 FDLQGSTTSVRYTGHGGPVFSVNFSPDRRLLISSAGDRTVRLWSMET-QRNAVIYRTPAVVWQAQFCSRGYYFATASADK 457
Cdd:COG2319  147 WDLATGKLLRTLTGHSGAVTSVAFSPDGKLLASGSDDGTVRLWDLATgKLLRTLTGHTGAVRSVAFSPDGKLLASGSADG 226

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115533709 458 TAAMWSTDRMHPLRIFADPYGDVGCIDYHPNCNYIAGGSDDRYVRVWDVCSGTRVRIFSGHKASIIAVKFSPCGRYIVSL 537
Cdd:COG2319  227 TVRLWDLATGKLLRTLTGHSGSVRSVAFSPDGRLLASGSADGTVRLWDLATGELLRTLTGHSGGVNSVAFSPDGKLLASG 306

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 115533709 538 DAIGNLMIWDLAYQRLVaAEITEQAGTKGSITFSRDGGVFAVSHGNSSIQLYSLDT 593
Cdd:COG2319  307 SDDGTVRLWDLATGKLL-RTLTGHTGAVRSVAFSPDGKTLASGSDDGTVRLWDLAT 361
TAF5_NTD2 cd08044
TAF5_NTD2 is the second conserved N-terminal region of TATA Binding Protein (TBP) Associated ...
 79-207 1.02e-29

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: 114.21  E-value: 1.02e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115533709  79 EAISVEFDTFVQHANDCTDVVQAEFSQLLFPIFAHSYIALIEK-HAATARIFFNRFKIFIPECFSEFVYQLSLIEDAMTL 157
Cdd:cd08044    2 NDYEQAYSKLRKWIESSLDIYKYELSQLLYPIFVHSYLDLVASgHLEEAKSFFERFSGDFEDSHSEDIKKLSSITTPEHL 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 115533709 158 RANEHVHILRENKFLVRLSRPTLKHLESIQTRV--IGVKNIIAKHICIENAD 207
Cdd:cd08044   82 KENELAKLFRSNKYVIRMSRDAYSLLLRFLESWggSLLLKILNEHIDIDVRD 133
 
Name Accession Description Interval E-value
WD40 COG2319
WD40 repeat [General function prediction only];
379-593 3.80e-44

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 162.77  E-value: 3.80e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115533709 379 FDLQGSTTSVRYTGHGGPVFSVNFSPDRRLLISSAGDRTVRLWSMET-QRNAVIYRTPAVVWQAQFCSRGYYFATASADK 457
Cdd:COG2319  147 WDLATGKLLRTLTGHSGAVTSVAFSPDGKLLASGSDDGTVRLWDLATgKLLRTLTGHTGAVRSVAFSPDGKLLASGSADG 226

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115533709 458 TAAMWSTDRMHPLRIFADPYGDVGCIDYHPNCNYIAGGSDDRYVRVWDVCSGTRVRIFSGHKASIIAVKFSPCGRYIVSL 537
Cdd:COG2319  227 TVRLWDLATGKLLRTLTGHSGSVRSVAFSPDGRLLASGSADGTVRLWDLATGELLRTLTGHSGGVNSVAFSPDGKLLASG 306

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 115533709 538 DAIGNLMIWDLAYQRLVaAEITEQAGTKGSITFSRDGGVFAVSHGNSSIQLYSLDT 593
Cdd:COG2319  307 SDDGTVRLWDLATGKLL-RTLTGHTGAVRSVAFSPDGKTLASGSDDGTVRLWDLAT 361
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 390-593 1.85e-39

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: 146.71  E-value: 1.85e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115533709 390 YTGHGGPVFSVNFSPDRRLLISSAGDRTVRLWSMETQRnavIYRTPAV----VWQAQFCSRGYYFATASADKTAAMWSTD 465
Cdd:cd00200    5 LKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGE---LLRTLKGhtgpVRDVAASADGTYLASGSSDKTIRLWDLE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115533709 466 RMHPLRIFADPYGDVGCIDYHPNCNYIAGGSDDRYVRVWDVCSGTRVRIFSGHKASIIAVKFSPCGRYIVSLDAIGNLMI 545
Cdd:cd00200   82 TGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKL 161

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 115533709 546 WDLAYQRLVA------AEITeqagtkgSITFSRDGGVFAVSHGNSSIQLYSLDT 593
Cdd:cd00200  162 WDLRTGKCVAtltghtGEVN-------SVAFSPDGEKLLSSSSDGTIKLWDLST 208
TAF5_NTD2 cd08044
TAF5_NTD2 is the second conserved N-terminal region of TATA Binding Protein (TBP) Associated ...
 79-207 1.02e-29

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: 114.21  E-value: 1.02e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115533709  79 EAISVEFDTFVQHANDCTDVVQAEFSQLLFPIFAHSYIALIEK-HAATARIFFNRFKIFIPECFSEFVYQLSLIEDAMTL 157
Cdd:cd08044    2 NDYEQAYSKLRKWIESSLDIYKYELSQLLYPIFVHSYLDLVASgHLEEAKSFFERFSGDFEDSHSEDIKKLSSITTPEHL 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 115533709 158 RANEHVHILRENKFLVRLSRPTLKHLESIQTRV--IGVKNIIAKHICIENAD 207
Cdd:cd08044   82 KENELAKLFRSNKYVIRMSRDAYSLLLRFLESWggSLLLKILNEHIDIDVRD 133
TFIID_NTD2 pfam04494
WD40 associated region in TFIID subunit, NTD2 domain; This region is an all-alpha domain ...
 97-201 5.06e-15

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


Pssm-ID: 461330  Cd Length: 130  Bit Score: 72.14  E-value: 5.06e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115533709   97 DVVQAEFSQLLFPIFAHSYIALIEK-HAATARIFFNRFK-IFIPEcFSEFVYQLSLIEDAMTLRANEHVHILRENKFLVR 174
Cdd:pfam04494  23 DIYKPELRRLLYPVFVHSYLDLVAKgHIEEAKEFFEKFRgDHEAL-HGDDLRKLAGITLPEHLEENELAKLFRSNKYRIR 101

                          90       100       110
                  ....*....|....*....|....*....|.
gi 115533709  175 LSRPT----LKHLESIQTRVIgvKNIIAKHI 201
Cdd:pfam04494 102 LSRYSfdllLRFLQENESSVI--LRIINEHL 130
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 390-422 2.30e-07

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


Pssm-ID: 197651 [Multi-domain]  Cd Length: 40  Bit Score: 47.31  E-value: 2.30e-07
                           10        20        30
                   ....*....|....*....|....*....|...
gi 115533709   390 YTGHGGPVFSVNFSPDRRLLISSAGDRTVRLWS 422
Cdd:smart00320   8 LKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 pfam00400
WD domain, G-beta repeat;
390-422 2.87e-07

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 46.95  E-value: 2.87e-07
                          10        20        30
                  ....*....|....*....|....*....|...
gi 115533709  390 YTGHGGPVFSVNFSPDRRLLISSAGDRTVRLWS 422
Cdd:pfam00400   7 LEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
 
Name Accession Description Interval E-value
WD40 COG2319
WD40 repeat [General function prediction only];
379-593 3.80e-44

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 162.77  E-value: 3.80e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115533709 379 FDLQGSTTSVRYTGHGGPVFSVNFSPDRRLLISSAGDRTVRLWSMET-QRNAVIYRTPAVVWQAQFCSRGYYFATASADK 457
Cdd:COG2319  147 WDLATGKLLRTLTGHSGAVTSVAFSPDGKLLASGSDDGTVRLWDLATgKLLRTLTGHTGAVRSVAFSPDGKLLASGSADG 226

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115533709 458 TAAMWSTDRMHPLRIFADPYGDVGCIDYHPNCNYIAGGSDDRYVRVWDVCSGTRVRIFSGHKASIIAVKFSPCGRYIVSL 537
Cdd:COG2319  227 TVRLWDLATGKLLRTLTGHSGSVRSVAFSPDGRLLASGSADGTVRLWDLATGELLRTLTGHSGGVNSVAFSPDGKLLASG 306

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 115533709 538 DAIGNLMIWDLAYQRLVaAEITEQAGTKGSITFSRDGGVFAVSHGNSSIQLYSLDT 593
Cdd:COG2319  307 SDDGTVRLWDLATGKLL-RTLTGHTGAVRSVAFSPDGKTLASGSDDGTVRLWDLAT 361
WD40 COG2319
WD40 repeat [General function prediction only];
377-593 8.03e-44

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 162.00  E-value: 8.03e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115533709 377 QMFDLQGSTTSVRYTGHGGPVFSVNFSPDRRLLISSAGDRTVRLWSMETQRN-AVIYRTPAVVWQAQFCSRGYYFATASA 455
Cdd:COG2319  103 RLWDLATGLLLRTLTGHTGAVRSVAFSPDGKTLASGSADGTVRLWDLATGKLlRTLTGHSGAVTSVAFSPDGKLLASGSD 182

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115533709 456 DKTAAMWSTDRMHPLRIFADPYGDVGCIDYHPNCNYIAGGSDDRYVRVWDVCSGTRVRIFSGHKASIIAVKFSPCGRYIV 535
Cdd:COG2319  183 DGTVRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKLLASGSADGTVRLWDLATGKLLRTLTGHSGSVRSVAFSPDGRLLA 262

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 115533709 536 SLDAIGNLMIWDLAYQRLVaAEITEQAGTKGSITFSRDGGVFAVSHGNSSIQLYSLDT 593
Cdd:COG2319  263 SGSADGTVRLWDLATGELL-RTLTGHSGGVNSVAFSPDGKLLASGSDDGTVRLWDLAT 319
WD40 COG2319
WD40 repeat [General function prediction only];
379-593 4.67e-43

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 160.08  E-value: 4.67e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115533709 379 FDLQGSTTSVRYTGHGGPVFSVNFSPDRRLLISSAGDRTVRLWSMETQRNAVIYRTP-AVVWQAQFCSRGYYFATASADK 457
Cdd:COG2319  189 WDLATGKLLRTLTGHTGAVRSVAFSPDGKLLASGSADGTVRLWDLATGKLLRTLTGHsGSVRSVAFSPDGRLLASGSADG 268

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115533709 458 TAAMWSTDRMHPLRIFADPYGDVGCIDYHPNCNYIAGGSDDRYVRVWDVCSGTRVRIFSGHKASIIAVKFSPCGRYIVSL 537
Cdd:COG2319  269 TVRLWDLATGELLRTLTGHSGGVNSVAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKTLASG 348

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 115533709 538 DAIGNLMIWDLAYQRLVaAEITEQAGTKGSITFSRDGGVFAVSHGNSSIQLYSLDT 593
Cdd:COG2319  349 SDDGTVRLWDLATGELL-RTLTGHTGAVTSVAFSPDGRTLASGSADGTVRLWDLAT 403
WD40 COG2319
WD40 repeat [General function prediction only];
380-593 1.08e-39

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 150.45  E-value: 1.08e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115533709 380 DLQGSTTSVRYTGHGGPVFSVNFSPDRRLLISSAGDRTVRLWSMET-QRNAVIYRTPAVVWQAQFCSRGYYFATASADKT 458
Cdd:COG2319   64 DAAAGALLATLLGHTAAVLSVAFSPDGRLLASASADGTVRLWDLATgLLLRTLTGHTGAVRSVAFSPDGKTLASGSADGT 143

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115533709 459 AAMWSTDRMHPLRIFADPYGDVGCIDYHPNCNYIAGGSDDRYVRVWDVCSGTRVRIFSGHKASIIAVKFSPCGRYIVSLD 538
Cdd:COG2319  144 VRLWDLATGKLLRTLTGHSGAVTSVAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKLLASGS 223

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 115533709 539 AIGNLMIWDLAYQRLVaAEITEQAGTKGSITFSRDGGVFAVSHGNSSIQLYSLDT 593
Cdd:COG2319  224 ADGTVRLWDLATGKLL-RTLTGHSGSVRSVAFSPDGRLLASGSADGTVRLWDLAT 277
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 390-593 1.85e-39

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: 146.71  E-value: 1.85e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115533709 390 YTGHGGPVFSVNFSPDRRLLISSAGDRTVRLWSMETQRnavIYRTPAV----VWQAQFCSRGYYFATASADKTAAMWSTD 465
Cdd:cd00200    5 LKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGE---LLRTLKGhtgpVRDVAASADGTYLASGSSDKTIRLWDLE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115533709 466 RMHPLRIFADPYGDVGCIDYHPNCNYIAGGSDDRYVRVWDVCSGTRVRIFSGHKASIIAVKFSPCGRYIVSLDAIGNLMI 545
Cdd:cd00200   82 TGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKL 161

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 115533709 546 WDLAYQRLVA------AEITeqagtkgSITFSRDGGVFAVSHGNSSIQLYSLDT 593
Cdd:cd00200  162 WDLRTGKCVAtltghtGEVN-------SVAFSPDGEKLLSSSSDGTIKLWDLST 208
WD40 COG2319
WD40 repeat [General function prediction only];
377-549 1.27e-37

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 144.67  E-value: 1.27e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115533709 377 QMFDLQGSTTSVRYTGHGGPVFSVNFSPDRRLLISSAGDRTVRLWSMETQRNAVIYRTP-AVVWQAQFCSRGYYFATASA 455
Cdd:COG2319  229 RLWDLATGKLLRTLTGHSGSVRSVAFSPDGRLLASGSADGTVRLWDLATGELLRTLTGHsGGVNSVAFSPDGKLLASGSD 308

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115533709 456 DKTAAMWSTDRMHPLRIFADPYGDVGCIDYHPNCNYIAGGSDDRYVRVWDVCSGTRVRIFSGHKASIIAVKFSPCGRYIV 535
Cdd:COG2319  309 DGTVRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKTLASGSDDGTVRLWDLATGELLRTLTGHTGAVTSVAFSPDGRTLA 388

                        170
                 ....*....|....
gi 115533709 536 SLDAIGNLMIWDLA 549
Cdd:COG2319  389 SGSADGTVRLWDLA 402
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 321-590 1.42e-36

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: 138.62  E-value: 1.42e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115533709 321 GVASCDFTDDSSLIAMGLSDSSIVMNAMDPMNKMKKLRDME-FLDKID--------IETADNVQSQMFDLQGSTTSVRYT 391
Cdd:cd00200   11 GVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTgPVRDVAasadgtylASGSSDKTIRLWDLETGECVRTLT 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115533709 392 GHGGPVFSVNFSPDRRLLISSAGDRTVRLWSMETQRNAVIYRT-PAVVWQAQFCSRGYYFATASADKTAAMWSTDRMHPL 470
Cdd:cd00200   91 GHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGhTDWVNSVAFSPDGTFVASSSQDGTIKLWDLRTGKCV 170

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115533709 471 RIFADPYGDVGCIDYHPNCNYIAGGSDDRYVRVWDVCSGTRVRIFSGHKASIIAVKFSPCGRYIVSLDAIGNLMIWDLAY 550
Cdd:cd00200  171 ATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGTLRGHENGVNSVAFSPDGYLLASGSEDGTIRVWDLRT 250

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|
gi 115533709 551 QRLVaAEITEQAGTKGSITFSRDGGVFAVSHGNSSIQLYS 590
Cdd:cd00200  251 GECV-QTLSGHTNSVTSLAWSPDGKRLASGSADGTIRIWD 289
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 311-547 4.85e-32

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: 125.91  E-value: 4.85e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115533709 311 CMYTTVNAPIGVASCDFTDDSSLIAMGLSDSSI-VMNAMDPmnkmKKLRDME----------FLDKIDIETADNVQSQ-- 377
Cdd:cd00200   43 LLRTLKGHTGPVRDVAASADGTYLASGSSDKTIrLWDLETG----ECVRTLTghtsyvssvaFSPDGRILSSSSRDKTik 118

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115533709 378 MFDLQGSTTSVRYTGHGGPVFSVNFSPDRRLLISSAGDRTVRLWSMETQR-NAVIYRTPAVVWQAQFCSRGYYFATASAD 456
Cdd:cd00200  119 VWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDLRTGKcVATLTGHTGEVNSVAFSPDGEKLLSSSSD 198

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115533709 457 KTAAMWSTDRMHPLRIFADPYGDVGCIDYHPNCNYIAGGSDDRYVRVWDVCSGTRVRIFSGHKASIIAVKFSPCGRYIVS 536
Cdd:cd00200  199 GTIKLWDLSTGKCLGTLRGHENGVNSVAFSPDGYLLASGSEDGTIRVWDLRTGECVQTLSGHTNSVTSLAWSPDGKRLAS 278

                        250
                 ....*....|.
gi 115533709 537 LDAIGNLMIWD 547
Cdd:cd00200  279 GSADGTIRIWD 289
WD40 COG2319
WD40 repeat [General function prediction only];
380-593 3.19e-31

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 126.18  E-value: 3.19e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115533709 380 DLQGSTTSVRYTGHGGPVFSVNFSPDRRLLISSAGDRTVRLWSMETQRNAVIYRTP-AVVWQAQFCSRGYYFATASADKT 458
Cdd:COG2319   22 AAALGALLLLLLGLAAAVASLAASPDGARLAAGAGDLTLLLLDAAAGALLATLLGHtAAVLSVAFSPDGRLLASASADGT 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115533709 459 AAMWSTDRMHPLRIFADPYGDVGCIDYHPNCNYIAGGSDDRYVRVWDVCSGTRVRIFSGHKASIIAVKFSPCGRYIVSLD 538
Cdd:COG2319  102 VRLWDLATGLLLRTLTGHTGAVRSVAFSPDGKTLASGSADGTVRLWDLATGKLLRTLTGHSGAVTSVAFSPDGKLLASGS 181

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 115533709 539 AIGNLMIWDLAYQRLVaAEITEQAGTKGSITFSRDGGVFAVSHGNSSIQLYSLDT 593
Cdd:COG2319  182 DDGTVRLWDLATGKLL-RTLTGHTGAVRSVAFSPDGKLLASGSADGTVRLWDLAT 235
TAF5_NTD2 cd08044
TAF5_NTD2 is the second conserved N-terminal region of TATA Binding Protein (TBP) Associated ...
 79-207 1.02e-29

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: 114.21  E-value: 1.02e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115533709  79 EAISVEFDTFVQHANDCTDVVQAEFSQLLFPIFAHSYIALIEK-HAATARIFFNRFKIFIPECFSEFVYQLSLIEDAMTL 157
Cdd:cd08044    2 NDYEQAYSKLRKWIESSLDIYKYELSQLLYPIFVHSYLDLVASgHLEEAKSFFERFSGDFEDSHSEDIKKLSSITTPEHL 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 115533709 158 RANEHVHILRENKFLVRLSRPTLKHLESIQTRV--IGVKNIIAKHICIENAD 207
Cdd:cd08044   82 KENELAKLFRSNKYVIRMSRDAYSLLLRFLESWggSLLLKILNEHIDIDVRD 133
WD40 COG2319
WD40 repeat [General function prediction only];
402-593 1.07e-20

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 94.98  E-value: 1.07e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115533709 402 FSPDRRLLISSAGDRTVRLWSMETQRN-AVIYRTPAVVWQAQFCSRGYYFATASADKTAAMWSTDRMHPLRIFADPYGDV 480
Cdd:COG2319    2 LSADGAALAAASADLALALLAAALGALlLLLLGLAAAVASLAASPDGARLAAGAGDLTLLLLDAAAGALLATLLGHTAAV 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115533709 481 GCIDYHPNCNYIAGGSDDRYVRVWDVCSGTRVRIFSGHKASIIAVKFSPCGRYIVSLDAIGNLMIWDLAYQRLVaAEITE 560
Cdd:COG2319   82 LSVAFSPDGRLLASASADGTVRLWDLATGLLLRTLTGHTGAVRSVAFSPDGKTLASGSADGTVRLWDLATGKLL-RTLTG 160

                        170       180       190
                 ....*....|....*....|....*....|...
gi 115533709 561 QAGTKGSITFSRDGGVFAVSHGNSSIQLYSLDT 593
Cdd:COG2319  161 HSGAVTSVAFSPDGKLLASGSDDGTVRLWDLAT 193
TFIID_NTD2 pfam04494
WD40 associated region in TFIID subunit, NTD2 domain; This region is an all-alpha domain ...
 97-201 5.06e-15

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


Pssm-ID: 461330  Cd Length: 130  Bit Score: 72.14  E-value: 5.06e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115533709   97 DVVQAEFSQLLFPIFAHSYIALIEK-HAATARIFFNRFK-IFIPEcFSEFVYQLSLIEDAMTLRANEHVHILRENKFLVR 174
Cdd:pfam04494  23 DIYKPELRRLLYPVFVHSYLDLVAKgHIEEAKEFFEKFRgDHEAL-HGDDLRKLAGITLPEHLEENELAKLFRSNKYRIR 101

                          90       100       110
                  ....*....|....*....|....*....|.
gi 115533709  175 LSRPT----LKHLESIQTRVIgvKNIIAKHI 201
Cdd:pfam04494 102 LSRYSfdllLRFLQENESSVI--LRIINEHL 130
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 390-422 2.30e-07

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


Pssm-ID: 197651 [Multi-domain]  Cd Length: 40  Bit Score: 47.31  E-value: 2.30e-07
                           10        20        30
                   ....*....|....*....|....*....|...
gi 115533709   390 YTGHGGPVFSVNFSPDRRLLISSAGDRTVRLWS 422
Cdd:smart00320   8 LKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 pfam00400
WD domain, G-beta repeat;
390-422 2.87e-07

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 46.95  E-value: 2.87e-07
                          10        20        30
                  ....*....|....*....|....*....|...
gi 115533709  390 YTGHGGPVFSVNFSPDRRLLISSAGDRTVRLWS 422
Cdd:pfam00400   7 LEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 512-593 5.59e-07

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: 51.57  E-value: 5.59e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115533709 512 VRIFSGHKASIIAVKFSPCGRYIVSLDAIGNLMIWDLAYQRLVaAEITEQAGTKGSITFSRDGGVFAVSHGNSSIQLYSL 591
Cdd:cd00200    2 RRTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELL-RTLKGHTGPVRDVAASADGTYLASGSSDKTIRLWDL 80


                 ..
gi 115533709 592 DT 593
Cdd:cd00200   81 ET 82
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 467-505 5.11e-06

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


Pssm-ID: 197651 [Multi-domain]  Cd Length: 40  Bit Score: 43.46  E-value: 5.11e-06
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 115533709   467 MHPLRIFADPYGDVGCIDYHPNCNYIAGGSDDRYVRVWD 505
Cdd:smart00320   2 GELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 508-547 7.71e-06

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


Pssm-ID: 197651 [Multi-domain]  Cd Length: 40  Bit Score: 43.07  E-value: 7.71e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 115533709   508 SGTRVRIFSGHKASIIAVKFSPCGRYIVSLDAIGNLMIWD 547
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 pfam00400
WD domain, G-beta repeat;
469-505 1.03e-05

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 42.72  E-value: 1.03e-05
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 115533709  469 PLRIFADPYGDVGCIDYHPNCNYIAGGSDDRYVRVWD 505
Cdd:pfam00400   3 LLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
WD40_like pfam17005
WD40-like domain; This is a family of proteins which have weak homology to the WD40 repeat ...
 483-599 2.47e-05

WD40-like domain; This is a family of proteins which have weak homology to the WD40 repeat family. Members are largely from microsporidia and related species.


Pssm-ID: 407205 [Multi-domain]  Cd Length: 301  Bit Score: 46.59  E-value: 2.47e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115533709  483 IDYHPNCNYIAGGSDDRYVRVWDVCSGTRVRIFSGHKASIIAVKFSPCGRYIV-SLDaiGNLMIWDLAYQrlvaaEITEQ 561
Cdd:pfam17005   6 IDISKKGSYILYGGKDDTCTVYDFENLDLVSIVEGFSDSVIFCKFLDDDLILVvTLD--GTIMESLLKND-----QEIEN 78

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 115533709  562 AGTKGSITFSR-DGGVFAVSHGNSSIQLYSLDTLIGTVL 599
Cdd:pfam17005  79 TKINEDISTVKvTDDKLLIGTNTGSIHVFSLDLQLQNVF 117
WD40 pfam00400
WD domain, G-beta repeat;
509-547 3.00e-04

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 38.48  E-value: 3.00e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 115533709  509 GTRVRIFSGHKASIIAVKFSPCGRYIV--SLDaiGNLMIWD 547
Cdd:pfam00400   1 GKLLKTLEGHTGSVTSLAFSPDGKLLAsgSDD--GTVKVWD 39
Nsa1 cd22858
Ribosome Biogenesis Protein Nsa1; Ribosome biogenesis protein Nsa1 (Nop7-associated 1) from ...
 474-525 1.84e-03

Ribosome Biogenesis Protein Nsa1; Ribosome biogenesis protein Nsa1 (Nop7-associated 1) from fungi is an essential factor for ribosome assembly. In cooperation with the assembly factor Rix7, Nsa1 participates in an early cleavage of the pre-rRNA processing pathway. Rix7 is a type II double ring, AAA-ATPase, that may mediate the release of Nsa1 from nucleolar pre-60S particles. The release of Nsa1 from a discrete preribosomal particle may trigger the progression of 60S ribosome biogenesis. Nsa1 is essential for cell viability in yeast. It contains an N-terminal seven-bladed beta-propeller WD40 domain that associates with the D1-AAA domain of the AAA-ATPase Rix7, and a flexible lysine-rich C-terminus that extends outward from the WD40 domain, and is required for nucleolar localization.


Pssm-ID: 439304  Cd Length: 399  Bit Score: 41.05  E-value: 1.84e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 115533709 474 ADPYGDVGCIDYHPNcNYIAGGSDDRYVRVWDVCSGTRV-RIFSGHKASIIAV 525
Cdd:cd22858  304 GDITGAVSAVDVFED-KYLATGGLDRYLRVFDLETRELLaKVYVGSKISSVLL 355
WD40 COG2319
WD40 repeat [General function prediction only];
492-606 2.43e-03

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 40.66  E-value: 2.43e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115533709 492 IAGGSDDRYVRVWDVCSGTRVRIFSGHKASIIAVKFSPCGRYIVSLDAIGNLMIWDLAYQRLVAAeITEQAGTKGSITFS 571
Cdd:COG2319    9 LAAASADLALALLAAALGALLLLLLGLAAAVASLAASPDGARLAAGAGDLTLLLLDAAAGALLAT-LLGHTAAVLSVAFS 87

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 115533709 572 RDGGVFAVSHGNSSIQLYSLDTLIGTVLAAGQNDS 606
Cdd:COG2319   88 PDGRLLASASADGTVRLWDLATGLLLRTLTGHTGA 122
TolB COG0823
Periplasmic component TolB of the Tol biopolymer transport system [Intracellular trafficking, ...
 494-604 8.17e-03

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


Pssm-ID: 440585 [Multi-domain]  Cd Length: 158  Bit Score: 37.34  E-value: 8.17e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115533709 494 GGSDDRYVrvWDVCSGTRVRIfSGHKASIIAVKFSPCGRYIV-SLDAIGNLMIWDLAYQRLVAAEITEQAGTKGSITFSR 572
Cdd:COG0823    8 DGNSDIYV--VDLDGGEPRRL-TNSPGIDTSPAWSPDGRRIAfTSDRGGGPQIYVVDADGGEPRRLTFGGGYNASPSWSP 84

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 115533709 573 DGGVFAVSH---GNSSIQLYSLDTLIGTVLAAGQN 604
Cdd:COG0823   85 DGKRLAFVSrsdGRFDIYVLDLDGGAPRRLTDGPG 119
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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