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Conserved domains on  [gi|2462507947|ref|XP_054191983|]
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TAF5-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 5L isoform X3 [Homo sapiens]

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];
180-449 2.75e-78

WD40 repeat [General function prediction only];


:

Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 250.21  E-value: 2.75e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 180 NTAEISPDSKLLAAGFDNSCIKLWSLRSkklksephqvdvsrihlacdileeeddeddnaGTEMKILRGHCGPVYSTRFL 259
Cdd:COG2319   166 TSVAFSPDGKLLASGSDDGTVRLWDLAT--------------------------------GKLLRTLTGHTGAVRSVAFS 213

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 260 ADSSGLLSCSEDMSIRYWDLGSFTNTVLYQGHAYPVWDLDISPYSLYFASGSHDRTARLWSFDRTYPLRIYAGHLADVDC 339
Cdd:COG2319   214 PDGKLLASGSADGTVRLWDLATGKLLRTLTGHSGSVRSVAFSPDGRLLASGSADGTVRLWDLATGELLRTLTGHSGGVNS 293

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 340 VKFHPNSNYLATGSTDKTVRLWSAQQGNSVRLFTGHRGPVLSLAFSPNGKYLASAGEDQRLKLWDLASGTLYKELRGHTD 419
Cdd:COG2319   294 VAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKTLASGSDDGTVRLWDLATGELLRTLTGHTG 373

                         250       260       270
                  ....*....|....*....|....*....|
gi 2462507947 420 NITSLTFSPDSGLIASASMDNSVRVWDIRN 449
Cdd:COG2319   374 AVTSVAFSPDGRTLASGSADGTVRLWDLAT 403
TAF5_NTD2 cd08044
TAF5_NTD2 is the second conserved N-terminal region of TATA Binding Protein (TBP) Associated ...
 2-109 7.84e-34

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: 124.23  E-value: 7.84e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947   2 PLLYPLFVYLHLNLVQNSPKSTVESFYSRFHGMFlqNASQKDVIEQLQTTQTIQDILSNFKLRAFLDNKYVVRLQEDSYN 81
Cdd:cd08044    28 QLLYPIFVHSYLDLVASGHLEEAKSFFERFSGDF--EDSHSEDIKKLSSITTPEHLKENELAKLFRSNKYVIRMSRDAYS 105

                          90       100
                  ....*....|....*....|....*...
gi 2462507947  82 YLIRYLQSDNNTALCKVLTLHIHLDVQP 109
Cdd:cd08044   106 LLLRFLESWGGSLLLKILNEHIDIDVRD 133
 
Name Accession Description Interval E-value
WD40 COG2319
WD40 repeat [General function prediction only];
180-449 2.75e-78

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 250.21  E-value: 2.75e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 180 NTAEISPDSKLLAAGFDNSCIKLWSLRSkklksephqvdvsrihlacdileeeddeddnaGTEMKILRGHCGPVYSTRFL 259
Cdd:COG2319   166 TSVAFSPDGKLLASGSDDGTVRLWDLAT--------------------------------GKLLRTLTGHTGAVRSVAFS 213

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 260 ADSSGLLSCSEDMSIRYWDLGSFTNTVLYQGHAYPVWDLDISPYSLYFASGSHDRTARLWSFDRTYPLRIYAGHLADVDC 339
Cdd:COG2319   214 PDGKLLASGSADGTVRLWDLATGKLLRTLTGHSGSVRSVAFSPDGRLLASGSADGTVRLWDLATGELLRTLTGHSGGVNS 293

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 340 VKFHPNSNYLATGSTDKTVRLWSAQQGNSVRLFTGHRGPVLSLAFSPNGKYLASAGEDQRLKLWDLASGTLYKELRGHTD 419
Cdd:COG2319   294 VAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKTLASGSDDGTVRLWDLATGELLRTLTGHTG 373

                         250       260       270
                  ....*....|....*....|....*....|
gi 2462507947 420 NITSLTFSPDSGLIASASMDNSVRVWDIRN 449
Cdd:COG2319   374 AVTSVAFSPDGRTLASGSADGTVRLWDLAT 403
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 184-489 5.90e-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: 229.91  E-value: 5.90e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 184 ISPDSKLLAAGFDNSCIKLWSLRSkklksephqvdvsrihlacdileeeddeddnaGTEMKILRGHCGPVYSTRFLADSS 263
Cdd:cd00200    17 FSPDGKLLATGSGDGTIKVWDLET--------------------------------GELLRTLKGHTGPVRDVAASADGT 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 264 GLLSCSEDMSIRYWDLGSFTNTVLYQGHAYPVWDLDISPYSLYFASGSHDRTARLWSFDRTYPLRIYAGHLADVDCVKFH 343
Cdd:cd00200    65 YLASGSSDKTIRLWDLETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFS 144

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 344 PNSNYLATGSTDKTVRLWSAQQGNSVRLFTGHRGPVLSLAFSPNGKYLASAGEDQRLKLWDLASGTLYKELRGHTDNITS 423
Cdd:cd00200   145 PDGTFVASSSQDGTIKLWDLRTGKCVATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGTLRGHENGVNS 224

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462507947 424 LTFSPDSGLIASASMDNSVRVWDIRNTYCSAPADGSSSElvgvytgqmsnVLSVQFMACNLLLVTG 489
Cdd:cd00200   225 VAFSPDGYLLASGSEDGTIRVWDLRTGECVQTLSGHTNS-----------VTSLAWSPDGKRLASG 279
TAF5_NTD2 cd08044
TAF5_NTD2 is the second conserved N-terminal region of TATA Binding Protein (TBP) Associated ...
 2-109 7.84e-34

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: 124.23  E-value: 7.84e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947   2 PLLYPLFVYLHLNLVQNSPKSTVESFYSRFHGMFlqNASQKDVIEQLQTTQTIQDILSNFKLRAFLDNKYVVRLQEDSYN 81
Cdd:cd08044    28 QLLYPIFVHSYLDLVASGHLEEAKSFFERFSGDF--EDSHSEDIKKLSSITTPEHLKENELAKLFRSNKYVIRMSRDAYS 105

                          90       100
                  ....*....|....*....|....*...
gi 2462507947  82 YLIRYLQSDNNTALCKVLTLHIHLDVQP 109
Cdd:cd08044   106 LLLRFLESWGGSLLLKILNEHIDIDVRD 133
TFIID_NTD2 pfam04494
WD40 associated region in TFIID subunit, NTD2 domain; This region is an all-alpha domain ...
 1-103 9.38e-31

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: 115.67  E-value: 9.38e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947   1 MPLLYPLFVYLHLNLVQNSPKSTVESFYSRFHGMFLqnASQKDVIEQLQTTQTIQDILSNFKLRAFLDNKYVVRLQEDSY 80
Cdd:pfam04494  30 RRLLYPVFVHSYLDLVAKGHIEEAKEFFEKFRGDHE--ALHGDDLRKLAGITLPEHLEENELAKLFRSNKYRIRLSRYSF 107

                          90       100
                  ....*....|....*....|...
gi 2462507947  81 NYLIRYLQSDNNTALCKVLTLHI 103
Cdd:pfam04494 108 DLLLRFLQENESSVILRIINEHL 130
PTZ00421 PTZ00421
coronin; Provisional
 329-462 6.63e-12

coronin; Provisional


Pssm-ID: 173611 [Multi-domain]  Cd Length: 493  Bit Score: 67.61  E-value: 6.63e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 329 IYAGHLADVDCVKFHP-NSNYLATGSTDKTVRLWSA-----QQGNSVRL--FTGHRGPVLSLAFSPNGK-YLASAGEDQR 399
Cdd:PTZ00421   70 ILLGQEGPIIDVAFNPfDPQKLFTASEDGTIMGWGIpeeglTQNISDPIvhLQGHTKKVGIVSFHPSAMnVLASAGADMV 149

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462507947 400 LKLWDLASGTLYKELRGHTDNITSLTFSPDSGLIASASMDNSVRVWDIRNtyCSAPADGSSSE 462
Cdd:PTZ00421  150 VNVWDVERGKAVEVIKCHSDQITSLEWNLDGSLLCTTSKDKKLNIIDPRD--GTIVSSVEAHA 210
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 407-446 6.84e-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: 56.94  E-value: 6.84e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 2462507947  407 SGTLYKELRGHTDNITSLTFSPDSGLIASASMDNSVRVWD 446
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 pfam00400
WD domain, G-beta repeat;
408-446 4.32e-10

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 54.66  E-value: 4.32e-10
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 2462507947 408 GTLYKELRGHTDNITSLTFSPDSGLIASASMDNSVRVWD 446
Cdd:pfam00400   1 GKLLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
 
Name Accession Description Interval E-value
WD40 COG2319
WD40 repeat [General function prediction only];
180-449 2.75e-78

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 250.21  E-value: 2.75e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 180 NTAEISPDSKLLAAGFDNSCIKLWSLRSkklksephqvdvsrihlacdileeeddeddnaGTEMKILRGHCGPVYSTRFL 259
Cdd:COG2319   166 TSVAFSPDGKLLASGSDDGTVRLWDLAT--------------------------------GKLLRTLTGHTGAVRSVAFS 213

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 260 ADSSGLLSCSEDMSIRYWDLGSFTNTVLYQGHAYPVWDLDISPYSLYFASGSHDRTARLWSFDRTYPLRIYAGHLADVDC 339
Cdd:COG2319   214 PDGKLLASGSADGTVRLWDLATGKLLRTLTGHSGSVRSVAFSPDGRLLASGSADGTVRLWDLATGELLRTLTGHSGGVNS 293

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 340 VKFHPNSNYLATGSTDKTVRLWSAQQGNSVRLFTGHRGPVLSLAFSPNGKYLASAGEDQRLKLWDLASGTLYKELRGHTD 419
Cdd:COG2319   294 VAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKTLASGSDDGTVRLWDLATGELLRTLTGHTG 373

                         250       260       270
                  ....*....|....*....|....*....|
gi 2462507947 420 NITSLTFSPDSGLIASASMDNSVRVWDIRN 449
Cdd:COG2319   374 AVTSVAFSPDGRTLASGSADGTVRLWDLAT 403
WD40 COG2319
WD40 repeat [General function prediction only];
180-489 2.43e-77

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 247.90  E-value: 2.43e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 180 NTAEISPDSKLLAAGFDNSCIKLWSLRSkklksephqvdvsrihlacdileeeddeddnaGTEMKILRGHCGPVYSTRFL 259
Cdd:COG2319   124 RSVAFSPDGKTLASGSADGTVRLWDLAT--------------------------------GKLLRTLTGHSGAVTSVAFS 171

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 260 ADSSGLLSCSEDMSIRYWDLGSFTNTVLYQGHAYPVWDLDISPYSLYFASGSHDRTARLWSFDRTYPLRIYAGHLADVDC 339
Cdd:COG2319   172 PDGKLLASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKLLASGSADGTVRLWDLATGKLLRTLTGHSGSVRS 251

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 340 VKFHPNSNYLATGSTDKTVRLWSAQQGNSVRLFTGHRGPVLSLAFSPNGKYLASAGEDQRLKLWDLASGTLYKELRGHTD 419
Cdd:COG2319   252 VAFSPDGRLLASGSADGTVRLWDLATGELLRTLTGHSGGVNSVAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHTG 331

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 420 NITSLTFSPDSGLIASASMDNSVRVWDIrntycsapadgSSSELVGVYTGQMSNVLSVQFMACNLLLVTG 489
Cdd:COG2319   332 AVRSVAFSPDGKTLASGSDDGTVRLWDL-----------ATGELLRTLTGHTGAVTSVAFSPDGRTLASG 390
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 184-489 5.90e-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: 229.91  E-value: 5.90e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 184 ISPDSKLLAAGFDNSCIKLWSLRSkklksephqvdvsrihlacdileeeddeddnaGTEMKILRGHCGPVYSTRFLADSS 263
Cdd:cd00200    17 FSPDGKLLATGSGDGTIKVWDLET--------------------------------GELLRTLKGHTGPVRDVAASADGT 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 264 GLLSCSEDMSIRYWDLGSFTNTVLYQGHAYPVWDLDISPYSLYFASGSHDRTARLWSFDRTYPLRIYAGHLADVDCVKFH 343
Cdd:cd00200    65 YLASGSSDKTIRLWDLETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFS 144

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 344 PNSNYLATGSTDKTVRLWSAQQGNSVRLFTGHRGPVLSLAFSPNGKYLASAGEDQRLKLWDLASGTLYKELRGHTDNITS 423
Cdd:cd00200   145 PDGTFVASSSQDGTIKLWDLRTGKCVATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGTLRGHENGVNS 224

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462507947 424 LTFSPDSGLIASASMDNSVRVWDIRNTYCSAPADGSSSElvgvytgqmsnVLSVQFMACNLLLVTG 489
Cdd:cd00200   225 VAFSPDGYLLASGSEDGTIRVWDLRTGECVQTLSGHTNS-----------VTSLAWSPDGKRLASG 279
WD40 COG2319
WD40 repeat [General function prediction only];
239-479 4.21e-69

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 226.33  E-value: 4.21e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 239 AGTEMKILRGHCGPVYSTRFLADSSGLLSCSEDMSIRYWDLGSFTNTVLYQGHAYPVWDLDISPYSLYFASGSHDRTARL 318
Cdd:COG2319    67 AGALLATLLGHTAAVLSVAFSPDGRLLASASADGTVRLWDLATGLLLRTLTGHTGAVRSVAFSPDGKTLASGSADGTVRL 146

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 319 WSFDRTYPLRIYAGHLADVDCVKFHPNSNYLATGSTDKTVRLWSAQQGNSVRLFTGHRGPVLSLAFSPNGKYLASAGEDQ 398
Cdd:COG2319   147 WDLATGKLLRTLTGHSGAVTSVAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKLLASGSADG 226

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 399 RLKLWDLASGTLYKELRGHTDNITSLTFSPDSGLIASASMDNSVRVWDIrntycsapadgSSSELVGVYTGQMSNVLSVQ 478
Cdd:COG2319   227 TVRLWDLATGKLLRTLTGHSGSVRSVAFSPDGRLLASGSADGTVRLWDL-----------ATGELLRTLTGHSGGVNSVA 295


                  .
gi 2462507947 479 F 479
Cdd:COG2319   296 F 296
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 242-489 6.97e-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: 216.82  E-value: 6.97e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 242 EMKILRGHCGPVYSTRFLADSSGLLSCSEDMSIRYWDLGSFTNTVLYQGHAYPVWDLDISPYSLYFASGSHDRTARLWSF 321
Cdd:cd00200     1 LRRTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASADGTYLASGSSDKTIRLWDL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 322 DRTYPLRIYAGHLADVDCVKFHPNSNYLATGSTDKTVRLWSAQQGNSVRLFTGHRGPVLSLAFSPNGKYLASAGEDQRLK 401
Cdd:cd00200    81 ETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIK 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 402 LWDLASGTLYKELRGHTDNITSLTFSPDSGLIASASMDNSVRVWDIRntycsapadgsSSELVGVYTGQMSNVLSVQFMA 481
Cdd:cd00200   161 LWDLRTGKCVATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLS-----------TGKCLGTLRGHENGVNSVAFSP 229


                  ....*...
gi 2462507947 482 CNLLLVTG 489
Cdd:cd00200   230 DGYLLASG 237
WD40 COG2319
WD40 repeat [General function prediction only];
246-489 6.16e-66

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 218.24  E-value: 6.16e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 246 LRGHCGPVYSTRFLADSSGLLSCSEDMSIRYWDLGSFTNTVLYQGHAYPVWDLDISPYSLYFASGSHDRTARLWSFDRTY 325
Cdd:COG2319    32 LLGLAAAVASLAASPDGARLAAGAGDLTLLLLDAAAGALLATLLGHTAAVLSVAFSPDGRLLASASADGTVRLWDLATGL 111

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 326 PLRIYAGHLADVDCVKFHPNSNYLATGSTDKTVRLWSAQQGNSVRLFTGHRGPVLSLAFSPNGKYLASAGEDQRLKLWDL 405
Cdd:COG2319   112 LLRTLTGHTGAVRSVAFSPDGKTLASGSADGTVRLWDLATGKLLRTLTGHSGAVTSVAFSPDGKLLASGSDDGTVRLWDL 191

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 406 ASGTLYKELRGHTDNITSLTFSPDSGLIASASMDNSVRVWDIRntycsapadgsSSELVGVYTGQMSNVLSVQFMACNLL 485
Cdd:COG2319   192 ATGKLLRTLTGHTGAVRSVAFSPDGKLLASGSADGTVRLWDLA-----------TGKLLRTLTGHSGSVRSVAFSPDGRL 260


                  ....
gi 2462507947 486 LVTG 489
Cdd:COG2319   261 LASG 264
WD40 COG2319
WD40 repeat [General function prediction only];
257-489 4.71e-51

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 178.95  E-value: 4.71e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 257 RFLADSSGLLSCSEDMSIRYWDLGSFTNTVLYQGHAYPVWDLDISPYSLYFASGSHDRTARLWSFDRTYPLRIYAGHLAD 336
Cdd:COG2319     1 ALSADGAALAAASADLALALLAAALGALLLLLLGLAAAVASLAASPDGARLAAGAGDLTLLLLDAAAGALLATLLGHTAA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 337 VDCVKFHPNSNYLATGSTDKTVRLWSAQQGNSVRLFTGHRGPVLSLAFSPNGKYLASAGEDQRLKLWDLASGTLYKELRG 416
Cdd:COG2319    81 VLSVAFSPDGRLLASASADGTVRLWDLATGLLLRTLTGHTGAVRSVAFSPDGKTLASGSADGTVRLWDLATGKLLRTLTG 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462507947 417 HTDNITSLTFSPDSGLIASASMDNSVRVWDIRntycsapadgsSSELVGVYTGQMSNVLSVQFMACNLLLVTG 489
Cdd:COG2319   161 HSGAVTSVAFSPDGKLLASGSDDGTVRLWDLA-----------TGKLLRTLTGHTGAVRSVAFSPDGKLLASG 222
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 184-362 6.78e-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: 132.07  E-value: 6.78e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 184 ISPDSKLLAAGFDNSCIKLWSLRSKKLksephqvdvsrihlacdileeeddeddnagteMKILRGHCGPVYSTRFLADSS 263
Cdd:cd00200   143 FSPDGTFVASSSQDGTIKLWDLRTGKC--------------------------------VATLTGHTGEVNSVAFSPDGE 190

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 264 GLLSCSEDMSIRYWDLGSFTNTVLYQGHAYPVWDLDISPYSLYFASGSHDRTARLWSFDRTYPLRIYAGHLADVDCVKFH 343
Cdd:cd00200   191 KLLSSSSDGTIKLWDLSTGKCLGTLRGHENGVNSVAFSPDGYLLASGSEDGTIRVWDLRTGECVQTLSGHTNSVTSLAWS 270

                         170
                  ....*....|....*....
gi 2462507947 344 PNSNYLATGSTDKTVRLWS 362
Cdd:cd00200   271 PDGKRLASGSADGTIRIWD 289
TAF5_NTD2 cd08044
TAF5_NTD2 is the second conserved N-terminal region of TATA Binding Protein (TBP) Associated ...
 2-109 7.84e-34

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: 124.23  E-value: 7.84e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947   2 PLLYPLFVYLHLNLVQNSPKSTVESFYSRFHGMFlqNASQKDVIEQLQTTQTIQDILSNFKLRAFLDNKYVVRLQEDSYN 81
Cdd:cd08044    28 QLLYPIFVHSYLDLVASGHLEEAKSFFERFSGDF--EDSHSEDIKKLSSITTPEHLKENELAKLFRSNKYVIRMSRDAYS 105

                          90       100
                  ....*....|....*....|....*...
gi 2462507947  82 YLIRYLQSDNNTALCKVLTLHIHLDVQP 109
Cdd:cd08044   106 LLLRFLESWGGSLLLKILNEHIDIDVRD 133
TFIID_NTD2 pfam04494
WD40 associated region in TFIID subunit, NTD2 domain; This region is an all-alpha domain ...
 1-103 9.38e-31

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: 115.67  E-value: 9.38e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947   1 MPLLYPLFVYLHLNLVQNSPKSTVESFYSRFHGMFLqnASQKDVIEQLQTTQTIQDILSNFKLRAFLDNKYVVRLQEDSY 80
Cdd:pfam04494  30 RRLLYPVFVHSYLDLVAKGHIEEAKEFFEKFRGDHE--ALHGDDLRKLAGITLPEHLEENELAKLFRSNKYRIRLSRYSF 107

                          90       100
                  ....*....|....*....|...
gi 2462507947  81 NYLIRYLQSDNNTALCKVLTLHI 103
Cdd:pfam04494 108 DLLLRFLQENESSVILRIINEHL 130
PTZ00421 PTZ00421
coronin; Provisional
 329-462 6.63e-12

coronin; Provisional


Pssm-ID: 173611 [Multi-domain]  Cd Length: 493  Bit Score: 67.61  E-value: 6.63e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 329 IYAGHLADVDCVKFHP-NSNYLATGSTDKTVRLWSA-----QQGNSVRL--FTGHRGPVLSLAFSPNGK-YLASAGEDQR 399
Cdd:PTZ00421   70 ILLGQEGPIIDVAFNPfDPQKLFTASEDGTIMGWGIpeeglTQNISDPIvhLQGHTKKVGIVSFHPSAMnVLASAGADMV 149

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462507947 400 LKLWDLASGTLYKELRGHTDNITSLTFSPDSGLIASASMDNSVRVWDIRNtyCSAPADGSSSE 462
Cdd:PTZ00421  150 VNVWDVERGKAVEVIKCHSDQITSLEWNLDGSLLCTTSKDKKLNIIDPRD--GTIVSSVEAHA 210
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 407-446 6.84e-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: 56.94  E-value: 6.84e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 2462507947  407 SGTLYKELRGHTDNITSLTFSPDSGLIASASMDNSVRVWD 446
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 365-404 2.30e-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: 55.40  E-value: 2.30e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 2462507947  365 QGNSVRLFTGHRGPVLSLAFSPNGKYLASAGEDQRLKLWD 404
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 pfam00400
WD domain, G-beta repeat;
408-446 4.32e-10

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 54.66  E-value: 4.32e-10
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 2462507947 408 GTLYKELRGHTDNITSLTFSPDSGLIASASMDNSVRVWD 446
Cdd:pfam00400   1 GKLLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
PLN00181 PLN00181
protein SPA1-RELATED; Provisional
 263-445 8.13e-10

protein SPA1-RELATED; Provisional


Pssm-ID: 177776 [Multi-domain]  Cd Length: 793  Bit Score: 61.26  E-value: 8.13e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 263 SGLLSCSEDMSIRYWDLGSFTNTVLYQGHAYPVWDLDISPYS-LYFASGSHDRTARLWSFDRTYPLRIYAGHlADVDCVK 341
Cdd:PLN00181  546 SQVASSNFEGVVQVWDVARSQLVTEMKEHEKRVWSIDYSSADpTLLASGSDDGSVKLWSINQGVSIGTIKTK-ANICCVQ 624

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 342 FHPNSNY-LATGSTDKTVRLWSAQQgNSVRLFT--GHRGPVLSLAFSpNGKYLASAGEDQRLKLWDL---ASG---TLYK 412
Cdd:PLN00181  625 FPSESGRsLAFGSADHKVYYYDLRN-PKLPLCTmiGHSKTVSYVRFV-DSSTLVSSSTDNTLKLWDLsmsISGineTPLH 702

                         170       180       190
                  ....*....|....*....|....*....|...
gi 2462507947 413 ELRGHTDNITSLTFSPDSGLIASASMDNSVRVW 445
Cdd:PLN00181  703 SFMGHTNVKNFVGLSVSDGYIATGSETNEVFVY 735
WD40 pfam00400
WD domain, G-beta repeat;
366-404 9.45e-10

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 53.89  E-value: 9.45e-10
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 2462507947 366 GNSVRLFTGHRGPVLSLAFSPNGKYLASAGEDQRLKLWD 404
Cdd:pfam00400   1 GKLLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 326-362 3.26e-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: 52.31  E-value: 3.26e-09
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 2462507947  326 PLRIYAGHLADVDCVKFHPNSNYLATGSTDKTVRLWS 362
Cdd:smart00320   4 LLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
COG4946 COG4946
Uncharacterized N-terminal domain of tricorn protease, contains WD40 repeats [Function unknown] ...
 379-449 4.08e-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: 4.08e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462507947  379 VLSLAFSPNGKYLASAGEDQRLKLWDLASGTLYKELRG-HTDNITSLTFSPDSGLIA-SASMDN---SVRVWDIRN 449
Cdd:COG4946    391 VFNPVWSPDGKKIAFTDNRGRLWVVDLASGKVRKVDTDgYGDGISDLAWSPDSKWLAySKPGPNqlsQIFLYDVET 466
WD40 pfam00400
WD domain, G-beta repeat;
326-362 5.19e-09

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 51.58  E-value: 5.19e-09
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 2462507947 326 PLRIYAGHLADVDCVKFHPNSNYLATGSTDKTVRLWS 362
Cdd:pfam00400   3 LLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
PLN00181 PLN00181
protein SPA1-RELATED; Provisional
 308-447 2.48e-07

protein SPA1-RELATED; Provisional


Pssm-ID: 177776 [Multi-domain]  Cd Length: 793  Bit Score: 53.55  E-value: 2.48e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 308 ASGSHDRTARLWSFDRTYPLRIYAGHLADVDCVKFHP-NSNYLATGSTDKTVRLWSAQQGNSVRLFTGhRGPVLSLAF-S 385
Cdd:PLN00181  549 ASSNFEGVVQVWDVARSQLVTEMKEHEKRVWSIDYSSaDPTLLASGSDDGSVKLWSINQGVSIGTIKT-KANICCVQFpS 627

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462507947 386 PNGKYLASAGEDQRLKLWDLASGTL-YKELRGHTDNITSLTFSpDSGLIASASMDNSVRVWDI 447
Cdd:PLN00181  628 ESGRSLAFGSADHKVYYYDLRNPKLpLCTMIGHSKTVSYVRFV-DSSTLVSSSTDNTLKLWDL 689
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 288-320 2.40e-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: 44.23  E-value: 2.40e-06
                           10        20        30
                   ....*....|....*....|....*....|...
gi 2462507947  288 YQGHAYPVWDLDISPYSLYFASGSHDRTARLWS 320
Cdd:smart00320   8 LKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 240-278 5.92e-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: 5.92e-06
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 2462507947  240 GTEMKILRGHCGPVYSTRFLADSSGLLSCSEDMSIRYWD 278
Cdd:smart00320   2 GELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 pfam00400
WD domain, G-beta repeat;
288-320 6.50e-06

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 43.10  E-value: 6.50e-06
                          10        20        30
                  ....*....|....*....|....*....|...
gi 2462507947 288 YQGHAYPVWDLDISPYSLYFASGSHDRTARLWS 320
Cdd:pfam00400   7 LEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
PTZ00420 PTZ00420
coronin; Provisional
 358-449 7.12e-06

coronin; Provisional


Pssm-ID: 240412 [Multi-domain]  Cd Length: 568  Bit Score: 48.41  E-value: 7.12e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 358 VRLWSAQQGNSVRLFTGHRGPVLSLAFSP-NGKYLASAGEDQRLKLWDLA-SGTLYKE-------LRGHTDNITSLTFSP 428
Cdd:PTZ00420   56 IRLENQMRKPPVIKLKGHTSSILDLQFNPcFSEILASGSEDLTIRVWEIPhNDESVKEikdpqciLKGHKKKISIIDWNP 135

                          90       100
                  ....*....|....*....|..
gi 2462507947 429 DSGLI-ASASMDNSVRVWDIRN 449
Cdd:PTZ00420  136 MNYYImCSSGFDSFVNIWDIEN 157
ANAPC4_WD40 pfam12894
Anaphase-promoting complex subunit 4 WD40 domain; Apc4 contains an N-terminal propeller-shaped ...
 340-427 7.41e-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: 44.19  E-value: 7.41e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 340 VKFHPNSNYLATGSTDKTVRLwsaQQGNSVRLFTG----HRGPVLSLAFSPNGKYLASAGEDQRLKLWDLASGTLYKELR 415
Cdd:pfam12894   1 MSWCPTMDLIALATEDGELLL---HRLNWQRVWTLspdkEDLEVTSLAWRPDGKLLAVGYSDGTVRLLDAENGKIVHHFS 77

                          90
                  ....*....|..
gi 2462507947 416 GHTDNITSLTFS 427
Cdd:pfam12894  78 AGSDLITCLGWG 89
WD40 pfam00400
WD domain, G-beta repeat;
240-278 1.59e-05

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 41.95  E-value: 1.59e-05
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 2462507947 240 GTEMKILRGHCGPVYSTRFLADSSGLLSCSEDMSIRYWD 278
Cdd:pfam00400   1 GKLLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
YncE COG3391
DNA-binding beta-propeller fold protein YncE [General function prediction only];
305-449 2.76e-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: 2.76e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 305 LYFASGSHDRTARLWSFDRTYPLRIYAGhlADVDCVKFHPNSNYL-ATGSTDKTVRLWSAQQGNSVRLFTGHRGPVlSLA 383
Cdd:COG3391    82 LYVANSGSGRVSVIDLATGKVVATIPVG--GGPRGLAVDPDGGRLyVADSGNGRVSVIDTATGKVVATIPVGAGPH-GIA 158

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462507947 384 FSPNGKYL--ASAGEDQRLKL---WDLASGTLYKELRGHtDNITSLTFSPDSGLI--------ASASMDNSVRVWDIRN 449
Cdd:COG3391   159 VDPDGKRLyvANSGSNTVSVIvsvIDTATGKVVATIPVG-GGPVGVAVSPDGRRLyvanrgsnTSNGGSNTVSVIDLAT 236
TolB COG0823
Periplasmic component TolB of the Tol biopolymer transport system [Intracellular trafficking, ...
 352-464 5.93e-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: 40.43  E-value: 5.93e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 352 GSTDktVRLWSAQQGNSVRLfTGHRGPVLSLAFSPNGKYLA-SAGEDQRLKLW--DLASGTLYKELRGHTDNiTSLTFSP 428
Cdd:COG0823     9 GNSD--IYVVDLDGGEPRRL-TNSPGIDTSPAWSPDGRRIAfTSDRGGGPQIYvvDADGGEPRRLTFGGGYN-ASPSWSP 84

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2462507947 429 DSGLIASASMDNSvrVWDIRntycSAPADGSSSELV 464
Cdd:COG0823    85 DGKRLAFVSRSDG--RFDIY----VLDLDGGAPRRL 114
PTZ00420 PTZ00420
coronin; Provisional
 246-409 7.08e-04

coronin; Provisional


Pssm-ID: 240412 [Multi-domain]  Cd Length: 568  Bit Score: 42.24  E-value: 7.08e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 246 LRGHCGPVYSTRFLADSSGLL-SCSEDMSIRYWDLGSFTNTV--------LYQGHAYPVWDLDISPYSLY-FASGSHDRT 315
Cdd:PTZ00420   70 LKGHTSSILDLQFNPCFSEILaSGSEDLTIRVWEIPHNDESVkeikdpqcILKGHKKKISIIDWNPMNYYiMCSSGFDSF 149

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 316 ARLW-------SFDRTYPLRIYA------GHLADVDCVKFHPN----------SNYLATGSTDKTVRLWsaqqgnsVRLF 372
Cdd:PTZ00420  150 VNIWdienekrAFQINMPKKLSSlkwnikGNLLSGTCVGKHMHiidprkqeiaSSFHIHDGGKNTKNIW-------IDGL 222

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 2462507947 373 TGHRGPVLSLAFSPNGKylasagedQRLKLWDLASGT 409
Cdd:PTZ00420  223 GGDDNYILSTGFSKNNM--------REMKLWDLKNTT 251
COG4946 COG4946
Uncharacterized N-terminal domain of tricorn protease, contains WD40 repeats [Function unknown] ...
 344-429 7.09e-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: 7.09e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947  344 PNSNYLATgsTDKTVRLW-----SaqqGNSVRLFTG-HRGPVLSLAFSPNGKYLA----SAGEDQRLKLWDLASGTLYKE 413
Cdd:COG4946    398 PDGKKIAF--TDNRGRLWvvdlaS---GKVRKVDTDgYGDGISDLAWSPDSKWLAyskpGPNQLSQIFLYDVETGKTVQL 472

                           90
                   ....*....|....*.
gi 2462507947  414 LRGHTDNiTSLTFSPD 429
Cdd:COG4946    473 TDGRYDD-GSPAFSPD 487
PLN00181 PLN00181
protein SPA1-RELATED; Provisional
 391-479 1.13e-03

protein SPA1-RELATED; Provisional


Pssm-ID: 177776 [Multi-domain]  Cd Length: 793  Bit Score: 41.61  E-value: 1.13e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 391 LASAGEDQRLKLWDLASGTLYKELRGHTDNITSLTF-SPDSGLIASASMDNSVRVWDIRNtycsapadgssselvGVYTG 469
Cdd:PLN00181  548 VASSNFEGVVQVWDVARSQLVTEMKEHEKRVWSIDYsSADPTLLASGSDDGSVKLWSINQ---------------GVSIG 612

                          90
                  ....*....|...
gi 2462507947 470 QM---SNVLSVQF 479
Cdd:PLN00181  613 TIktkANICCVQF 625
TolB COG0823
Periplasmic component TolB of the Tol biopolymer transport system [Intracellular trafficking, ...
 342-437 2.93e-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: 38.50  E-value: 2.93e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 342 FHPNSNYLA-TGSTDKTVRLW--SAQQGNSVRLfTGHRGPVLSLAFSPNGKYLA-SAGEDQRLKLW--DLASGtlykELR 415
Cdd:COG0823    38 WSPDGRRIAfTSDRGGGPQIYvvDADGGEPRRL-TFGGGYNASPSWSPDGKRLAfVSRSDGRFDIYvlDLDGG----APR 112

                          90       100
                  ....*....|....*....|..
gi 2462507947 416 GHTDNITSLTFSPDSGLIASAS 437
Cdd:COG0823   113 RLTDGPGSPSWSPDGRRIVFSS 134
TolB COG0823
Periplasmic component TolB of the Tol biopolymer transport system [Intracellular trafficking, ...
 294-403 3.28e-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: 38.11  E-value: 3.28e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462507947 294 PVWdldiSPY--SLYFASgSHDRTARLWSFDR--TYPLRIYAGHLADVDCVkFHPNSNYLA-TGSTDKTVRLW--SAQQG 366
Cdd:COG0823    36 PAW----SPDgrRIAFTS-DRGGGPQIYVVDAdgGEPRRLTFGGGYNASPS-WSPDGKRLAfVSRSDGRFDIYvlDLDGG 109

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 2462507947 367 NSVRLFTGHRGPvlslAFSPNGKYLA-SAGEDQRLKLW 403
Cdd:COG0823   110 APRRLTDGPGSP----SWSPDGRRIVfSSDRGGRPDLY 143
NBCH_WD40 pfam20426
Neurobeachin beta propeller domain; This entry represents the beta propeller domain found at ...
 385-447 6.11e-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: 6.11e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462507947 385 SPNGKYLASAGE-DQRLKLWDLASGTLYKELRGHTDNITSLTFSPDSGLIASASMDNSVRVWDI 447
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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