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Conserved domains on  [gi|383873101|ref|NP_001244427|]
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TAF5-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 5L [Macaca mulatta]

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];
272-541 2.91e-78

WD40 repeat [General function prediction only];


:

Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 252.91  E-value: 2.91e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101 272 NTAEISPDSKLLAAGFDNSCIKLWSLRSkklksephqvdvsrihlacdileeeddeddnaGTEMKILRGHCGPVYSTRFL 351
Cdd:COG2319  166 TSVAFSPDGKLLASGSDDGTVRLWDLAT--------------------------------GKLLRTLTGHTGAVRSVAFS 213

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101 352 ADSSGLLSCSEDMSIRYWDLGSFTNTVLYQGHAYPVWDLDISPYSLYFASGSHDRTARLWSFDRTYPLRIYAGHLADVDC 431
Cdd:COG2319  214 PDGKLLASGSADGTVRLWDLATGKLLRTLTGHSGSVRSVAFSPDGRLLASGSADGTVRLWDLATGELLRTLTGHSGGVNS 293

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101 432 VKFHPNSNYLATGSTDKTVRLWSAQQGNSVRLFTGHRGPVLSLAFSPNGKYLASAGEDQRLKLWDLASGTLYKELRGHTD 511
Cdd:COG2319  294 VAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKTLASGSDDGTVRLWDLATGELLRTLTGHTG 373

                        250       260       270
                 ....*....|....*....|....*....|
gi 383873101 512 NITSLTFSPDSGLIASASMDNSVRVWDIRN 541
Cdd:COG2319  374 AVTSVAFSPDGRTLASGSADGTVRLWDLAT 403
TAF5_NTD2 cd08044
TAF5_NTD2 is the second conserved N-terminal region of TATA Binding Protein (TBP) Associated ...
 67-201 1.16e-44

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: 154.66  E-value: 1.16e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101  67 PQQYEVQFGRLRNFLTDSDSQHSHEVMPLLYPLFVYLHLNLVQNSPKSTVESFYSRFHGMFlqNASQKDVIEQLQTTQTI 146
Cdd:cd08044    1 PNDYEQAYSKLRKWIESSLDIYKYELSQLLYPIFVHSYLDLVASGHLEEAKSFFERFSGDF--EDSHSEDIKKLSSITTP 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 383873101 147 QDILSNFKLRAFLDNKYVVRLQEDSYNYLIRYLQSDNNTALCKVLTLHIHLDVQP 201
Cdd:cd08044   79 EHLKENELAKLFRSNKYVIRMSRDAYSLLLRFLESWGGSLLLKILNEHIDIDVRD 133
 
Name Accession Description Interval E-value
WD40 COG2319
WD40 repeat [General function prediction only];
272-541 2.91e-78

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 252.91  E-value: 2.91e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101 272 NTAEISPDSKLLAAGFDNSCIKLWSLRSkklksephqvdvsrihlacdileeeddeddnaGTEMKILRGHCGPVYSTRFL 351
Cdd:COG2319  166 TSVAFSPDGKLLASGSDDGTVRLWDLAT--------------------------------GKLLRTLTGHTGAVRSVAFS 213

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101 352 ADSSGLLSCSEDMSIRYWDLGSFTNTVLYQGHAYPVWDLDISPYSLYFASGSHDRTARLWSFDRTYPLRIYAGHLADVDC 431
Cdd:COG2319  214 PDGKLLASGSADGTVRLWDLATGKLLRTLTGHSGSVRSVAFSPDGRLLASGSADGTVRLWDLATGELLRTLTGHSGGVNS 293

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101 432 VKFHPNSNYLATGSTDKTVRLWSAQQGNSVRLFTGHRGPVLSLAFSPNGKYLASAGEDQRLKLWDLASGTLYKELRGHTD 511
Cdd:COG2319  294 VAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKTLASGSDDGTVRLWDLATGELLRTLTGHTG 373

                        250       260       270
                 ....*....|....*....|....*....|
gi 383873101 512 NITSLTFSPDSGLIASASMDNSVRVWDIRN 541
Cdd:COG2319  374 AVTSVAFSPDGRTLASGSADGTVRLWDLAT 403
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 276-581 4.43e-72

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: 233.00  E-value: 4.43e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101 276 ISPDSKLLAAGFDNSCIKLWSLRSkklksephqvdvsrihlacdileeeddeddnaGTEMKILRGHCGPVYSTRFLADSS 355
Cdd:cd00200   17 FSPDGKLLATGSGDGTIKVWDLET--------------------------------GELLRTLKGHTGPVRDVAASADGT 64

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101 356 GLLSCSEDMSIRYWDLGSFTNTVLYQGHAYPVWDLDISPYSLYFASGSHDRTARLWSFDRTYPLRIYAGHLADVDCVKFH 435
Cdd:cd00200   65 YLASGSSDKTIRLWDLETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFS 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101 436 PNSNYLATGSTDKTVRLWSAQQGNSVRLFTGHRGPVLSLAFSPNGKYLASAGEDQRLKLWDLASGTLYKELRGHTDNITS 515
Cdd:cd00200  145 PDGTFVASSSQDGTIKLWDLRTGKCVATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGTLRGHENGVNS 224

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 383873101 516 LTFSPDSGLIASASMDNSVRVWDIRNTygsapadgsssELVGVYTGQMSNVLSVQFMACNLLLVTG 581
Cdd:cd00200  225 VAFSPDGYLLASGSEDGTIRVWDLRTG-----------ECVQTLSGHTNSVTSLAWSPDGKRLASG 279
TAF5_NTD2 cd08044
TAF5_NTD2 is the second conserved N-terminal region of TATA Binding Protein (TBP) Associated ...
 67-201 1.16e-44

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: 154.66  E-value: 1.16e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101  67 PQQYEVQFGRLRNFLTDSDSQHSHEVMPLLYPLFVYLHLNLVQNSPKSTVESFYSRFHGMFlqNASQKDVIEQLQTTQTI 146
Cdd:cd08044    1 PNDYEQAYSKLRKWIESSLDIYKYELSQLLYPIFVHSYLDLVASGHLEEAKSFFERFSGDF--EDSHSEDIKKLSSITTP 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 383873101 147 QDILSNFKLRAFLDNKYVVRLQEDSYNYLIRYLQSDNNTALCKVLTLHIHLDVQP 201
Cdd:cd08044   79 EHLKENELAKLFRSNKYVIRMSRDAYSLLLRFLESWGGSLLLKILNEHIDIDVRD 133
TFIID_NTD2 pfam04494
WD40 associated region in TFIID subunit, NTD2 domain; This region is an all-alpha domain ...
 64-195 3.60e-42

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: 148.03  E-value: 3.60e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101   64 QAEPQQYEVQFGRLRNFLTDSDSQHSHEVMPLLYPLFVYLHLNLVQNSPKSTVESFYSRFHGMFLqnASQKDVIEQLQTT 143
Cdd:pfam04494   1 EGDPQKYERAYSLLRNWIESSLDIYKPELRRLLYPVFVHSYLDLVAKGHIEEAKEFFEKFRGDHE--ALHGDDLRKLAGI 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 383873101  144 QTIQDILSNFKLRAFLDNKYVVRLQEDSYNYLIRYLQSDNNTALCKVLTLHI 195
Cdd:pfam04494  79 TLPEHLEENELAKLFRSNKYRIRLSRYSFDLLLRFLQENESSVILRIINEHL 130
PTZ00421 PTZ00421
coronin; Provisional
 421-554 2.40e-11

coronin; Provisional


Pssm-ID: 173611 [Multi-domain]  Cd Length: 493  Bit Score: 66.07  E-value: 2.40e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101 421 IYAGHLADVDCVKFHP-NSNYLATGSTDKTVRLWSA-----QQGNSVRL--FTGHRGPVLSLAFSPNGK-YLASAGEDQR 491
Cdd:PTZ00421  70 ILLGQEGPIIDVAFNPfDPQKLFTASEDGTIMGWGIpeeglTQNISDPIvhLQGHTKKVGIVSFHPSAMnVLASAGADMV 149

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 383873101 492 LKLWDLASGTLYKELRGHTDNITSLTFSPDSGLIASASMDNSVRVWDIRNtyGSAPADGSSSE 554
Cdd:PTZ00421 150 VNVWDVERGKAVEVIKCHSDQITSLEWNLDGSLLCTTSKDKKLNIIDPRD--GTIVSSVEAHA 210
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 499-538 3.78e-11

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


Pssm-ID: 197651 [Multi-domain]  Cd Length: 40  Bit Score: 58.09  E-value: 3.78e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 383873101   499 SGTLYKELRGHTDNITSLTFSPDSGLIASASMDNSVRVWD 538
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 pfam00400
WD domain, G-beta repeat;
500-538 2.48e-10

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 55.81  E-value: 2.48e-10
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 383873101  500 GTLYKELRGHTDNITSLTFSPDSGLIASASMDNSVRVWD 538
Cdd:pfam00400   1 GKLLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
 
Name Accession Description Interval E-value
WD40 COG2319
WD40 repeat [General function prediction only];
272-541 2.91e-78

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 252.91  E-value: 2.91e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101 272 NTAEISPDSKLLAAGFDNSCIKLWSLRSkklksephqvdvsrihlacdileeeddeddnaGTEMKILRGHCGPVYSTRFL 351
Cdd:COG2319  166 TSVAFSPDGKLLASGSDDGTVRLWDLAT--------------------------------GKLLRTLTGHTGAVRSVAFS 213

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101 352 ADSSGLLSCSEDMSIRYWDLGSFTNTVLYQGHAYPVWDLDISPYSLYFASGSHDRTARLWSFDRTYPLRIYAGHLADVDC 431
Cdd:COG2319  214 PDGKLLASGSADGTVRLWDLATGKLLRTLTGHSGSVRSVAFSPDGRLLASGSADGTVRLWDLATGELLRTLTGHSGGVNS 293

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101 432 VKFHPNSNYLATGSTDKTVRLWSAQQGNSVRLFTGHRGPVLSLAFSPNGKYLASAGEDQRLKLWDLASGTLYKELRGHTD 511
Cdd:COG2319  294 VAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKTLASGSDDGTVRLWDLATGELLRTLTGHTG 373

                        250       260       270
                 ....*....|....*....|....*....|
gi 383873101 512 NITSLTFSPDSGLIASASMDNSVRVWDIRN 541
Cdd:COG2319  374 AVTSVAFSPDGRTLASGSADGTVRLWDLAT 403
WD40 COG2319
WD40 repeat [General function prediction only];
271-581 3.99e-73

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 239.43  E-value: 3.99e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101 271 LNTAEISPDSKLLAAGFDNSCIKLWSLRSkklksephqvdvsrihlacdileeeddeddnaGTEMKILRGHCGPVYSTRF 350
Cdd:COG2319   81 VLSVAFSPDGRLLASASADGTVRLWDLAT--------------------------------GLLLRTLTGHTGAVRSVAF 128

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101 351 LADSSGLLSCSEDMSIRYWDLGSFTNTVLYQGHAYPVWDLDISPYSLYFASGSHDRTARLWSFDRTYPLRIYAGHLADVD 430
Cdd:COG2319  129 SPDGKTLASGSADGTVRLWDLATGKLLRTLTGHSGAVTSVAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHTGAVR 208

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101 431 CVKFHPNSNYLATGSTDKTVRLWSAQQGNSVRLFTGHRGPVLSLAFSPNGKYLASAGEDQRLKLWDLASGTLYKELRGHT 510
Cdd:COG2319  209 SVAFSPDGKLLASGSADGTVRLWDLATGKLLRTLTGHSGSVRSVAFSPDGRLLASGSADGTVRLWDLATGELLRTLTGHS 288

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 383873101 511 DNITSLTFSPDSGLIASASMDNSVRVWDIrntygsapadgSSSELVGVYTGQMSNVLSVQFMACNLLLVTG 581
Cdd:COG2319  289 GGVNSVAFSPDGKLLASGSDDGTVRLWDL-----------ATGKLLRTLTGHTGAVRSVAFSPDGKTLASG 348
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 276-581 4.43e-72

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: 233.00  E-value: 4.43e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101 276 ISPDSKLLAAGFDNSCIKLWSLRSkklksephqvdvsrihlacdileeeddeddnaGTEMKILRGHCGPVYSTRFLADSS 355
Cdd:cd00200   17 FSPDGKLLATGSGDGTIKVWDLET--------------------------------GELLRTLKGHTGPVRDVAASADGT 64

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101 356 GLLSCSEDMSIRYWDLGSFTNTVLYQGHAYPVWDLDISPYSLYFASGSHDRTARLWSFDRTYPLRIYAGHLADVDCVKFH 435
Cdd:cd00200   65 YLASGSSDKTIRLWDLETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFS 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101 436 PNSNYLATGSTDKTVRLWSAQQGNSVRLFTGHRGPVLSLAFSPNGKYLASAGEDQRLKLWDLASGTLYKELRGHTDNITS 515
Cdd:cd00200  145 PDGTFVASSSQDGTIKLWDLRTGKCVATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGTLRGHENGVNS 224

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 383873101 516 LTFSPDSGLIASASMDNSVRVWDIRNTygsapadgsssELVGVYTGQMSNVLSVQFMACNLLLVTG 581
Cdd:cd00200  225 VAFSPDGYLLASGSEDGTIRVWDLRTG-----------ECVQTLSGHTNSVTSLAWSPDGKRLASG 279
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 334-581 4.22e-67

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


Pssm-ID: 238121 [Multi-domain]  Cd Length: 289  Bit Score: 219.90  E-value: 4.22e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101 334 EMKILRGHCGPVYSTRFLADSSGLLSCSEDMSIRYWDLGSFTNTVLYQGHAYPVWDLDISPYSLYFASGSHDRTARLWSF 413
Cdd:cd00200    1 LRRTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASADGTYLASGSSDKTIRLWDL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101 414 DRTYPLRIYAGHLADVDCVKFHPNSNYLATGSTDKTVRLWSAQQGNSVRLFTGHRGPVLSLAFSPNGKYLASAGEDQRLK 493
Cdd:cd00200   81 ETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIK 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101 494 LWDLASGTLYKELRGHTDNITSLTFSPDSGLIASASMDNSVRVWDIRntygsapadgsSSELVGVYTGQMSNVLSVQFMA 573
Cdd:cd00200  161 LWDLRTGKCVATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLS-----------TGKCLGTLRGHENGVNSVAFSP 229


                 ....*...
gi 383873101 574 CNLLLVTG 581
Cdd:cd00200  230 DGYLLASG 237
WD40 COG2319
WD40 repeat [General function prediction only];
338-581 6.98e-66

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 220.55  E-value: 6.98e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101 338 LRGHCGPVYSTRFLADSSGLLSCSEDMSIRYWDLGSFTNTVLYQGHAYPVWDLDISPYSLYFASGSHDRTARLWSFDRTY 417
Cdd:COG2319   32 LLGLAAAVASLAASPDGARLAAGAGDLTLLLLDAAAGALLATLLGHTAAVLSVAFSPDGRLLASASADGTVRLWDLATGL 111

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101 418 PLRIYAGHLADVDCVKFHPNSNYLATGSTDKTVRLWSAQQGNSVRLFTGHRGPVLSLAFSPNGKYLASAGEDQRLKLWDL 497
Cdd:COG2319  112 LLRTLTGHTGAVRSVAFSPDGKTLASGSADGTVRLWDLATGKLLRTLTGHSGAVTSVAFSPDGKLLASGSDDGTVRLWDL 191

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101 498 ASGTLYKELRGHTDNITSLTFSPDSGLIASASMDNSVRVWDIRntygsapadgsSSELVGVYTGQMSNVLSVQFMACNLL 577
Cdd:COG2319  192 ATGKLLRTLTGHTGAVRSVAFSPDGKLLASGSADGTVRLWDLA-----------TGKLLRTLTGHSGSVRSVAFSPDGRL 260


                 ....
gi 383873101 578 LVTG 581
Cdd:COG2319  261 LASG 264
WD40 COG2319
WD40 repeat [General function prediction only];
349-581 6.15e-51

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 180.49  E-value: 6.15e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101 349 RFLADSSGLLSCSEDMSIRYWDLGSFTNTVLYQGHAYPVWDLDISPYSLYFASGSHDRTARLWSFDRTYPLRIYAGHLAD 428
Cdd:COG2319    1 ALSADGAALAAASADLALALLAAALGALLLLLLGLAAAVASLAASPDGARLAAGAGDLTLLLLDAAAGALLATLLGHTAA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101 429 VDCVKFHPNSNYLATGSTDKTVRLWSAQQGNSVRLFTGHRGPVLSLAFSPNGKYLASAGEDQRLKLWDLASGTLYKELRG 508
Cdd:COG2319   81 VLSVAFSPDGRLLASASADGTVRLWDLATGLLLRTLTGHTGAVRSVAFSPDGKTLASGSADGTVRLWDLATGKLLRTLTG 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 383873101 509 HTDNITSLTFSPDSGLIASASMDNSVRVWDIRntygsapadgsSSELVGVYTGQMSNVLSVQFMACNLLLVTG 581
Cdd:COG2319  161 HSGAVTSVAFSPDGKLLASGSDDGTVRLWDLA-----------TGKLLRTLTGHTGAVRSVAFSPDGKLLASG 222
TAF5_NTD2 cd08044
TAF5_NTD2 is the second conserved N-terminal region of TATA Binding Protein (TBP) Associated ...
 67-201 1.16e-44

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: 154.66  E-value: 1.16e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101  67 PQQYEVQFGRLRNFLTDSDSQHSHEVMPLLYPLFVYLHLNLVQNSPKSTVESFYSRFHGMFlqNASQKDVIEQLQTTQTI 146
Cdd:cd08044    1 PNDYEQAYSKLRKWIESSLDIYKYELSQLLYPIFVHSYLDLVASGHLEEAKSFFERFSGDF--EDSHSEDIKKLSSITTP 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 383873101 147 QDILSNFKLRAFLDNKYVVRLQEDSYNYLIRYLQSDNNTALCKVLTLHIHLDVQP 201
Cdd:cd08044   79 EHLKENELAKLFRSNKYVIRMSRDAYSLLLRFLESWGGSLLLKILNEHIDIDVRD 133
TFIID_NTD2 pfam04494
WD40 associated region in TFIID subunit, NTD2 domain; This region is an all-alpha domain ...
 64-195 3.60e-42

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: 148.03  E-value: 3.60e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101   64 QAEPQQYEVQFGRLRNFLTDSDSQHSHEVMPLLYPLFVYLHLNLVQNSPKSTVESFYSRFHGMFLqnASQKDVIEQLQTT 143
Cdd:pfam04494   1 EGDPQKYERAYSLLRNWIESSLDIYKPELRRLLYPVFVHSYLDLVAKGHIEEAKEFFEKFRGDHE--ALHGDDLRKLAGI 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 383873101  144 QTIQDILSNFKLRAFLDNKYVVRLQEDSYNYLIRYLQSDNNTALCKVLTLHI 195
Cdd:pfam04494  79 TLPEHLEENELAKLFRSNKYRIRLSRYSFDLLLRFLQENESSVILRIINEHL 130
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 276-454 3.23e-35

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: 134.38  E-value: 3.23e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101 276 ISPDSKLLAAGFDNSCIKLWSLRSKKLksephqvdvsrihlacdileeeddeddnagteMKILRGHCGPVYSTRFLADSS 355
Cdd:cd00200  143 FSPDGTFVASSSQDGTIKLWDLRTGKC--------------------------------VATLTGHTGEVNSVAFSPDGE 190

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101 356 GLLSCSEDMSIRYWDLGSFTNTVLYQGHAYPVWDLDISPYSLYFASGSHDRTARLWSFDRTYPLRIYAGHLADVDCVKFH 435
Cdd:cd00200  191 KLLSSSSDGTIKLWDLSTGKCLGTLRGHENGVNSVAFSPDGYLLASGSEDGTIRVWDLRTGECVQTLSGHTNSVTSLAWS 270

                        170
                 ....*....|....*....
gi 383873101 436 PNSNYLATGSTDKTVRLWS 454
Cdd:cd00200  271 PDGKRLASGSADGTIRIWD 289
PTZ00421 PTZ00421
coronin; Provisional
 421-554 2.40e-11

coronin; Provisional


Pssm-ID: 173611 [Multi-domain]  Cd Length: 493  Bit Score: 66.07  E-value: 2.40e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101 421 IYAGHLADVDCVKFHP-NSNYLATGSTDKTVRLWSA-----QQGNSVRL--FTGHRGPVLSLAFSPNGK-YLASAGEDQR 491
Cdd:PTZ00421  70 ILLGQEGPIIDVAFNPfDPQKLFTASEDGTIMGWGIpeeglTQNISDPIvhLQGHTKKVGIVSFHPSAMnVLASAGADMV 149

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 383873101 492 LKLWDLASGTLYKELRGHTDNITSLTFSPDSGLIASASMDNSVRVWDIRNtyGSAPADGSSSE 554
Cdd:PTZ00421 150 VNVWDVERGKAVEVIKCHSDQITSLEWNLDGSLLCTTSKDKKLNIIDPRD--GTIVSSVEAHA 210
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 499-538 3.78e-11

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


Pssm-ID: 197651 [Multi-domain]  Cd Length: 40  Bit Score: 58.09  E-value: 3.78e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 383873101   499 SGTLYKELRGHTDNITSLTFSPDSGLIASASMDNSVRVWD 538
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 457-496 1.33e-10

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


Pssm-ID: 197651 [Multi-domain]  Cd Length: 40  Bit Score: 56.55  E-value: 1.33e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 383873101   457 QGNSVRLFTGHRGPVLSLAFSPNGKYLASAGEDQRLKLWD 496
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 pfam00400
WD domain, G-beta repeat;
500-538 2.48e-10

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 55.81  E-value: 2.48e-10
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 383873101  500 GTLYKELRGHTDNITSLTFSPDSGLIASASMDNSVRVWD 538
Cdd:pfam00400   1 GKLLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
WD40 pfam00400
WD domain, G-beta repeat;
458-496 5.58e-10

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 54.66  E-value: 5.58e-10
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 383873101  458 GNSVRLFTGHRGPVLSLAFSPNGKYLASAGEDQRLKLWD 496
Cdd:pfam00400   1 GKLLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
PLN00181 PLN00181
protein SPA1-RELATED; Provisional
 355-537 1.11e-09

protein SPA1-RELATED; Provisional


Pssm-ID: 177776 [Multi-domain]  Cd Length: 793  Bit Score: 61.26  E-value: 1.11e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101 355 SGLLSCSEDMSIRYWDLGSFTNTVLYQGHAYPVWDLDISPYS-LYFASGSHDRTARLWSFDRTYPLRIYAGHlADVDCVK 433
Cdd:PLN00181 546 SQVASSNFEGVVQVWDVARSQLVTEMKEHEKRVWSIDYSSADpTLLASGSDDGSVKLWSINQGVSIGTIKTK-ANICCVQ 624

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101 434 FHPNSNY-LATGSTDKTVRLWSAQQgNSVRLFT--GHRGPVLSLAFSpNGKYLASAGEDQRLKLWDL---ASG---TLYK 504
Cdd:PLN00181 625 FPSESGRsLAFGSADHKVYYYDLRN-PKLPLCTmiGHSKTVSYVRFV-DSSTLVSSSTDNTLKLWDLsmsISGineTPLH 702

                        170       180       190
                 ....*....|....*....|....*....|...
gi 383873101 505 ELRGHTDNITSLTFSPDSGLIASASMDNSVRVW 537
Cdd:PLN00181 703 SFMGHTNVKNFVGLSVSDGYIATGSETNEVFVY 735
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 418-454 1.98e-09

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: 53.09  E-value: 1.98e-09
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 383873101   418 PLRIYAGHLADVDCVKFHPNSNYLATGSTDKTVRLWS 454
Cdd:smart00320   4 LLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 pfam00400
WD domain, G-beta repeat;
418-454 3.19e-09

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 52.35  E-value: 3.19e-09
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 383873101  418 PLRIYAGHLADVDCVKFHPNSNYLATGSTDKTVRLWS 454
Cdd:pfam00400   3 LLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
COG4946 COG4946
Uncharacterized N-terminal domain of tricorn protease, contains WD40 repeats [Function unknown] ...
 471-541 5.54e-09

Uncharacterized N-terminal domain of tricorn protease, contains WD40 repeats [Function unknown];


Pssm-ID: 443973 [Multi-domain]  Cd Length: 1072  Bit Score: 59.28  E-value: 5.54e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 383873101  471 VLSLAFSPNGKYLASAGEDQRLKLWDLASGTLYKELRG-HTDNITSLTFSPDSGLIA-SASMDN---SVRVWDIRN 541
Cdd:COG4946   391 VFNPVWSPDGKKIAFTDNRGRLWVVDLASGKVRKVDTDgYGDGISDLAWSPDSKWLAySKPGPNqlsQIFLYDVET 466
PLN00181 PLN00181
protein SPA1-RELATED; Provisional
 400-539 3.27e-07

protein SPA1-RELATED; Provisional


Pssm-ID: 177776 [Multi-domain]  Cd Length: 793  Bit Score: 53.55  E-value: 3.27e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101 400 ASGSHDRTARLWSFDRTYPLRIYAGHLADVDCVKFHP-NSNYLATGSTDKTVRLWSAQQGNSVRLFTGhRGPVLSLAF-S 477
Cdd:PLN00181 549 ASSNFEGVVQVWDVARSQLVTEMKEHEKRVWSIDYSSaDPTLLASGSDDGSVKLWSINQGVSIGTIKT-KANICCVQFpS 627

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 383873101 478 PNGKYLASAGEDQRLKLWDLASGTL-YKELRGHTDNITSLTFSpDSGLIASASMDNSVRVWDI 539
Cdd:PLN00181 628 ESGRSLAFGSADHKVYYYDLRNPKLpLCTMIGHSKTVSYVRFV-DSSTLVSSSTDNTLKLWDL 689
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 380-412 1.64e-06

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


Pssm-ID: 197651 [Multi-domain]  Cd Length: 40  Bit Score: 45.00  E-value: 1.64e-06
                           10        20        30
                   ....*....|....*....|....*....|...
gi 383873101   380 YQGHAYPVWDLDISPYSLYFASGSHDRTARLWS 412
Cdd:smart00320   8 LKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 332-370 4.13e-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: 43.84  E-value: 4.13e-06
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 383873101   332 GTEMKILRGHCGPVYSTRFLADSSGLLSCSEDMSIRYWD 370
Cdd:smart00320   2 GELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 pfam00400
WD domain, G-beta repeat;
380-412 4.49e-06

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 43.49  E-value: 4.49e-06
                          10        20        30
                  ....*....|....*....|....*....|...
gi 383873101  380 YQGHAYPVWDLDISPYSLYFASGSHDRTARLWS 412
Cdd:pfam00400   7 LEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
ANAPC4_WD40 pfam12894
Anaphase-promoting complex subunit 4 WD40 domain; Apc4 contains an N-terminal propeller-shaped ...
 432-519 6.70e-06

Anaphase-promoting complex subunit 4 WD40 domain; Apc4 contains an N-terminal propeller-shaped WD40 domain.The N-terminus of Afi1 serves to stabilize the union between Apc4 and Apc5, both of which lie towards the bottom-front of the APC,


Pssm-ID: 403945 [Multi-domain]  Cd Length: 91  Bit Score: 44.58  E-value: 6.70e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101  432 VKFHPNSNYLATGSTDKTVRLwsaQQGNSVRLFTG----HRGPVLSLAFSPNGKYLASAGEDQRLKLWDLASGTLYKELR 507
Cdd:pfam12894   1 MSWCPTMDLIALATEDGELLL---HRLNWQRVWTLspdkEDLEVTSLAWRPDGKLLAVGYSDGTVRLLDAENGKIVHHFS 77

                          90
                  ....*....|..
gi 383873101  508 GHTDNITSLTFS 519
Cdd:pfam12894  78 AGSDLITCLGWG 89
PTZ00420 PTZ00420
coronin; Provisional
 450-541 9.20e-06

coronin; Provisional


Pssm-ID: 240412 [Multi-domain]  Cd Length: 568  Bit Score: 48.41  E-value: 9.20e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101 450 VRLWSAQQGNSVRLFTGHRGPVLSLAFSP-NGKYLASAGEDQRLKLWDLA-SGTLYKE-------LRGHTDNITSLTFSP 520
Cdd:PTZ00420  56 IRLENQMRKPPVIKLKGHTSSILDLQFNPcFSEILASGSEDLTIRVWEIPhNDESVKEikdpqciLKGHKKKISIIDWNP 135

                         90       100
                 ....*....|....*....|..
gi 383873101 521 DSGLI-ASASMDNSVRVWDIRN 541
Cdd:PTZ00420 136 MNYYImCSSGFDSFVNIWDIEN 157
WD40 pfam00400
WD domain, G-beta repeat;
332-370 1.12e-05

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 42.33  E-value: 1.12e-05
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 383873101  332 GTEMKILRGHCGPVYSTRFLADSSGLLSCSEDMSIRYWD 370
Cdd:pfam00400   1 GKLLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
YncE COG3391
DNA-binding beta-propeller fold protein YncE [General function prediction only];
397-541 3.44e-04

DNA-binding beta-propeller fold protein YncE [General function prediction only];


Pssm-ID: 442618 [Multi-domain]  Cd Length: 237  Bit Score: 42.37  E-value: 3.44e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101 397 LYFASGSHDRTARLWSFDRTYPLRIYAGhlADVDCVKFHPNSNYL-ATGSTDKTVRLWSAQQGNSVRLFTGHRGPVlSLA 475
Cdd:COG3391   82 LYVANSGSGRVSVIDLATGKVVATIPVG--GGPRGLAVDPDGGRLyVADSGNGRVSVIDTATGKVVATIPVGAGPH-GIA 158

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 383873101 476 FSPNGKYL--ASAGEDQRLKL---WDLASGTLYKELRGHtDNITSLTFSPDSGLI--------ASASMDNSVRVWDIRN 541
Cdd:COG3391  159 VDPDGKRLyvANSGSNTVSVIvsvIDTATGKVVATIPVG-GGPVGVAVSPDGRRLyvanrgsnTSNGGSNTVSVIDLAT 236
TolB COG0823
Periplasmic component TolB of the Tol biopolymer transport system [Intracellular trafficking, ...
 444-556 4.31e-04

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: 41.20  E-value: 4.31e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101 444 GSTDktVRLWSAQQGNSVRLfTGHRGPVLSLAFSPNGKYLA-SAGEDQRLKLW--DLASGTLYKELRGHTDNiTSLTFSP 520
Cdd:COG0823    9 GNSD--IYVVDLDGGEPRRL-TNSPGIDTSPAWSPDGRRIAfTSDRGGGPQIYvvDADGGEPRRLTFGGGYN-ASPSWSP 84

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 383873101 521 DSGLIASASMDNSvrVWDIRntygSAPADGSSSELV 556
Cdd:COG0823   85 DGKRLAFVSRSDG--RFDIY----VLDLDGGAPRRL 114
PTZ00420 PTZ00420
coronin; Provisional
 338-501 8.97e-04

coronin; Provisional


Pssm-ID: 240412 [Multi-domain]  Cd Length: 568  Bit Score: 42.24  E-value: 8.97e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101 338 LRGHCGPVYSTRFLADSSGLL-SCSEDMSIRYWDLGSFTNTV--------LYQGHAYPVWDLDISPYSLY-FASGSHDRT 407
Cdd:PTZ00420  70 LKGHTSSILDLQFNPCFSEILaSGSEDLTIRVWEIPHNDESVkeikdpqcILKGHKKKISIIDWNPMNYYiMCSSGFDSF 149

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101 408 ARLW-------SFDRTYPLRIYA------GHLADVDCVKFHPN----------SNYLATGSTDKTVRLWsaqqgnsVRLF 464
Cdd:PTZ00420 150 VNIWdienekrAFQINMPKKLSSlkwnikGNLLSGTCVGKHMHiidprkqeiaSSFHIHDGGKNTKNIW-------IDGL 222

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 383873101 465 TGHRGPVLSLAFSPNGKylasagedQRLKLWDLASGT 501
Cdd:PTZ00420 223 GGDDNYILSTGFSKNNM--------REMKLWDLKNTT 251
COG4946 COG4946
Uncharacterized N-terminal domain of tricorn protease, contains WD40 repeats [Function unknown] ...
 436-521 9.03e-04

Uncharacterized N-terminal domain of tricorn protease, contains WD40 repeats [Function unknown];


Pssm-ID: 443973 [Multi-domain]  Cd Length: 1072  Bit Score: 42.33  E-value: 9.03e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101  436 PNSNYLATgsTDKTVRLW-----SaqqGNSVRLFTG-HRGPVLSLAFSPNGKYLA----SAGEDQRLKLWDLASGTLYKE 505
Cdd:COG4946   398 PDGKKIAF--TDNRGRLWvvdlaS---GKVRKVDTDgYGDGISDLAWSPDSKWLAyskpGPNQLSQIFLYDVETGKTVQL 472

                          90
                  ....*....|....*.
gi 383873101  506 LRGHTDNiTSLTFSPD 521
Cdd:COG4946   473 TDGRYDD-GSPAFSPD 487
PLN00181 PLN00181
protein SPA1-RELATED; Provisional
 483-571 1.43e-03

protein SPA1-RELATED; Provisional


Pssm-ID: 177776 [Multi-domain]  Cd Length: 793  Bit Score: 41.61  E-value: 1.43e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101 483 LASAGEDQRLKLWDLASGTLYKELRGHTDNITSLTF-SPDSGLIASASMDNSVRVWDIRNtygsapadgssselvGVYTG 561
Cdd:PLN00181 548 VASSNFEGVVQVWDVARSQLVTEMKEHEKRVWSIDYsSADPTLLASGSDDGSVKLWSINQ---------------GVSIG 612

                         90
                 ....*....|...
gi 383873101 562 QM---SNVLSVQF 571
Cdd:PLN00181 613 TIktkANICCVQF 625
TolB COG0823
Periplasmic component TolB of the Tol biopolymer transport system [Intracellular trafficking, ...
 434-529 2.21e-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: 38.88  E-value: 2.21e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101 434 FHPNSNYLA-TGSTDKTVRLW--SAQQGNSVRLfTGHRGPVLSLAFSPNGKYLA-SAGEDQRLKLW--DLASGtlykELR 507
Cdd:COG0823   38 WSPDGRRIAfTSDRGGGPQIYvvDADGGEPRRL-TFGGGYNASPSWSPDGKRLAfVSRSDGRFDIYvlDLDGG----APR 112

                         90       100
                 ....*....|....*....|..
gi 383873101 508 GHTDNITSLTFSPDSGLIASAS 529
Cdd:COG0823  113 RLTDGPGSPSWSPDGRRIVFSS 134
TolB COG0823
Periplasmic component TolB of the Tol biopolymer transport system [Intracellular trafficking, ...
 386-495 2.25e-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: 38.88  E-value: 2.25e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383873101 386 PVWdldiSPY--SLYFASgSHDRTARLWSFDR--TYPLRIYAGHLADVDCVkFHPNSNYLA-TGSTDKTVRLW--SAQQG 458
Cdd:COG0823   36 PAW----SPDgrRIAFTS-DRGGGPQIYVVDAdgGEPRRLTFGGGYNASPS-WSPDGKRLAfVSRSDGRFDIYvlDLDGG 109

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 383873101 459 NSVRLFTGHRGPvlslAFSPNGKYLA-SAGEDQRLKLW 495
Cdd:COG0823  110 APRRLTDGPGSP----SWSPDGRRIVfSSDRGGRPDLY 143
NBCH_WD40 pfam20426
Neurobeachin beta propeller domain; This entry represents the beta propeller domain found at ...
 477-539 7.07e-03

Neurobeachin beta propeller domain; This entry represents the beta propeller domain found at the C-terminus of neurobeachin-like proteins.


Pssm-ID: 466575 [Multi-domain]  Cd Length: 350  Bit Score: 38.90  E-value: 7.07e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 383873101  477 SPNGKYLASAGE-DQRLKLWDLASGTLYKELRGHTDNITSLTFSPDSGLIASASMDNSVRVWDI 539
Cdd:pfam20426  90 TPSENFLISCGNwENSFQVISLNDGRMVQSIRQHKDVVSCVAVTSDGSILATGSYDTTVMVWEV 153
 
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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