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Conserved domains on  [gi|19075402|ref|NP_587902|]
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transcription initiation factor TFIID subunit 5 [Schizosaccharomyces pombe]

Protein Classification

TAF5_NTD2 and WD40 domain-containing protein( domain architecture ID 11274420)

protein containing domains LisH, TAF5_NTD2, and WD40

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
WD40 COG2319
WD40 repeat [General function prediction only];
316-576 3.04e-77

WD40 repeat [General function prediction only];


:

Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 251.75  E-value: 3.04e-77
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402 316 CMYTFHHTNNNMNCAEFSPDSTMIACGFQESYIRLWSIKADKKSLpkstsvedsdgsvRLLSHSGPVYGTTFSPDNKYLL 395
Cdd:COG2319 154 LLRTLTGHSGAVTSVAFSPDGKLLASGSDDGTVRLWDLATGKLLR-------------TLTGHTGAVRSVAFSPDGKLLA 220

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402 396 SCSEDASARLWSVDTKTALVAYKGHTGPVWDVAFGPFGHYFATASHDQTAQLWSCDHIYPLRVFAGHLSDVDCVTFHPNS 475
Cdd:COG2319 221 SGSADGTVRLWDLATGKLLRTLTGHSGSVRSVAFSPDGRLLASGSADGTVRLWDLATGELLRTLTGHSGGVNSVAFSPDG 300

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402 476 AYVLTGSSDKTCRLWDVHRGHSVRVFNGHTQPVTAVAIAPDGHTMASADSEGLIHLWDIGTGRRIKTMRGHRGNIYSLSF 555
Cdd:COG2319 301 KLLASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKTLASGSDDGTVRLWDLATGELLRTLTGHTGAVTSVAF 380

                       250       260
                ....*....|....*....|.
gi 19075402 556 SRESTVLVSGGSDCTVRAWDV 576
Cdd:COG2319 381 SPDGRTLASGSADGTVRLWDL 401
TFIID_NTD2 pfam04494
WD40 associated region in TFIID subunit, NTD2 domain; This region is an all-alpha domain ...
 51-183 1.27e-59

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: 195.40  E-value: 1.27e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402    51 EETPDAYTHTYTILRDWVDSSLELYKAELHRILFPIFVHSYLNLLSQDHYEAAKQFYELFKDDHTDLHDFDVKNLKSLSL 130
Cdd:pfam04494   1 EGDPQKYERAYSLLRNWIESSLDIYKPELRRLLYPVFVHSYLDLVAKGHIEEAKEFFEKFRGDHEALHGDDLRKLAGITL 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 19075402   131 PSHVAEDRTAQQYRQNKYQLHFSRITFDLLLHFLFENVSNggsIIIKLINQHI 183
Cdd:pfam04494  81 PEHLEENELAKLFRSNKYRIRLSRYSFDLLLRFLQENESS---VILRIINEHL 130
LisH smart00667
Lissencephaly type-1-like homology motif; Alpha-helical motif present in Lis1, treacle, ...
 7-37 6.14e-05

Lissencephaly type-1-like homology motif; Alpha-helical motif present in Lis1, treacle, Nopp140, some katanin p60 subunits, muskelin, tonneau, LEUNIG and numerous WD40 repeat-containing proteins. It is suggested that LisH motifs contribute to the regulation of microtubule dynamics, either by mediating dimerisation, or else by binding cytoplasmic dynein heavy chain or microtubules directly.


:

Pssm-ID: 128913  Cd Length: 34  Bit Score: 40.50  E-value: 6.14e-05
                           10        20        30
                   ....*....|....*....|....*....|.
gi 19075402      7 PQPQDLNRIVLDYLAKKGYSRTEAMLRLEAS 37
Cdd:smart00667   1 ISRSELNRLILEYLLRNGYEETAETLQKESG 31
 
Name Accession Description Interval E-value
WD40 COG2319
WD40 repeat [General function prediction only];
316-576 3.04e-77

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 251.75  E-value: 3.04e-77
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402 316 CMYTFHHTNNNMNCAEFSPDSTMIACGFQESYIRLWSIKADKKSLpkstsvedsdgsvRLLSHSGPVYGTTFSPDNKYLL 395
Cdd:COG2319 154 LLRTLTGHSGAVTSVAFSPDGKLLASGSDDGTVRLWDLATGKLLR-------------TLTGHTGAVRSVAFSPDGKLLA 220

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402 396 SCSEDASARLWSVDTKTALVAYKGHTGPVWDVAFGPFGHYFATASHDQTAQLWSCDHIYPLRVFAGHLSDVDCVTFHPNS 475
Cdd:COG2319 221 SGSADGTVRLWDLATGKLLRTLTGHSGSVRSVAFSPDGRLLASGSADGTVRLWDLATGELLRTLTGHSGGVNSVAFSPDG 300

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402 476 AYVLTGSSDKTCRLWDVHRGHSVRVFNGHTQPVTAVAIAPDGHTMASADSEGLIHLWDIGTGRRIKTMRGHRGNIYSLSF 555
Cdd:COG2319 301 KLLASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKTLASGSDDGTVRLWDLATGELLRTLTGHTGAVTSVAF 380

                       250       260
                ....*....|....*....|.
gi 19075402 556 SRESTVLVSGGSDCTVRAWDV 576
Cdd:COG2319 381 SPDGRTLASGSADGTVRLWDL 401
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 332-575 1.53e-65

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: 217.20  E-value: 1.53e-65
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402 332 FSPDSTMIACGFQESYIRLWSIKADKKSlpkstsvedsdgsVRLLSHSGPVYGTTFSPDNKYLLSCSEDASARLWSVDTK 411
Cdd:cd00200  59 ASADGTYLASGSSDKTIRLWDLETGECV-------------RTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETG 125

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402 412 TALVAYKGHTGPVWDVAFGPFGHYFATASHDQTAQLWSCDHIYPLRVFAGHLSDVDCVTFHPNSAYVLTGSSDKTCRLWD 491
Cdd:cd00200 126 KCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDLRTGKCVATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWD 205

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402 492 VHRGHSVRVFNGHTQPVTAVAIAPDGHTMASADSEGLIHLWDIGTGRRIKTMRGHRGNIYSLSFSRESTVLVSGGSDCTV 571
Cdd:cd00200 206 LSTGKCLGTLRGHENGVNSVAFSPDGYLLASGSEDGTIRVWDLRTGECVQTLSGHTNSVTSLAWSPDGKRLASGSADGTI 285


                ....
gi 19075402 572 RAWD 575
Cdd:cd00200 286 RIWD 289
TFIID_NTD2 pfam04494
WD40 associated region in TFIID subunit, NTD2 domain; This region is an all-alpha domain ...
 51-183 1.27e-59

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: 195.40  E-value: 1.27e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402    51 EETPDAYTHTYTILRDWVDSSLELYKAELHRILFPIFVHSYLNLLSQDHYEAAKQFYELFKDDHTDLHDFDVKNLKSLSL 130
Cdd:pfam04494   1 EGDPQKYERAYSLLRNWIESSLDIYKPELRRLLYPVFVHSYLDLVAKGHIEEAKEFFEKFRGDHEALHGDDLRKLAGITL 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 19075402   131 PSHVAEDRTAQQYRQNKYQLHFSRITFDLLLHFLFENVSNggsIIIKLINQHI 183
Cdd:pfam04494  81 PEHLEENELAKLFRSNKYRIRLSRYSFDLLLRFLQENESS---VILRIINEHL 130
TAF5_NTD2 cd08044
TAF5_NTD2 is the second conserved N-terminal region of TATA Binding Protein (TBP) Associated ...
 54-189 5.88e-52

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: 175.07  E-value: 5.88e-52
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402  54 PDAYTHTYTILRDWVDSSLELYKAELHRILFPIFVHSYLNLLSQDHYEAAKQFYELFKDDHTDLHDFDVKNLKSLSLPSH 133
Cdd:cd08044   1 PNDYEQAYSKLRKWIESSLDIYKYELSQLLYPIFVHSYLDLVASGHLEEAKSFFERFSGDFEDSHSEDIKKLSSITTPEH 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 19075402 134 VAEDRTAQQYRQNKYQLHFSRITFDLLLHFLFEnvsNGGSIIIKLINQHIDIHIVP 189
Cdd:cd08044  81 LKENELAKLFRSNKYVIRMSRDAYSLLLRFLES---WGGSLLLKILNEHIDIDVRD 133
WD40 pfam00400
WD domain, G-beta repeat;
455-491 1.01e-08

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 51.19  E-value: 1.01e-08
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 19075402   455 PLRVFAGHLSDVDCVTFHPNSAYVLTGSSDKTCRLWD 491
Cdd:pfam00400   3 LLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
PTZ00421 PTZ00421
coronin; Provisional
 419-560 1.90e-08

coronin; Provisional


Pssm-ID: 173611 [Multi-domain]  Cd Length: 493  Bit Score: 57.21  E-value: 1.90e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402  419 GHTGPVWDVAFGPF-GHYFATASHDQTAQLWS----------CDHIYPLRvfaGHLSDVDCVTFHPNSAYVL-TGSSDKT 486
Cdd:PTZ00421  73 GQEGPIIDVAFNPFdPQKLFTASEDGTIMGWGipeegltqniSDPIVHLQ---GHTKKVGIVSFHPSAMNVLaSAGADMV 149

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19075402  487 CRLWDVHRGHSVRVFNGHTQPVTAVAIAPDGHTMASADSEglihlwdigtgRRIKTMRGHRGNIYSLSFSREST 560
Cdd:PTZ00421 150 VNVWDVERGKAVEVIKCHSDQITSLEWNLDGSLLCTTSKD-----------KKLNIIDPRDGTIVSSVEAHASA 212
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 455-491 3.13e-08

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: 50.00  E-value: 3.13e-08
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 19075402    455 PLRVFAGHLSDVDCVTFHPNSAYVLTGSSDKTCRLWD 491
Cdd:smart00320   4 LLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
LisH smart00667
Lissencephaly type-1-like homology motif; Alpha-helical motif present in Lis1, treacle, ...
 7-37 6.14e-05

Lissencephaly type-1-like homology motif; Alpha-helical motif present in Lis1, treacle, Nopp140, some katanin p60 subunits, muskelin, tonneau, LEUNIG and numerous WD40 repeat-containing proteins. It is suggested that LisH motifs contribute to the regulation of microtubule dynamics, either by mediating dimerisation, or else by binding cytoplasmic dynein heavy chain or microtubules directly.


Pssm-ID: 128913  Cd Length: 34  Bit Score: 40.50  E-value: 6.14e-05
                           10        20        30
                   ....*....|....*....|....*....|.
gi 19075402      7 PQPQDLNRIVLDYLAKKGYSRTEAMLRLEAS 37
Cdd:smart00667   1 ISRSELNRLILEYLLRNGYEETAETLQKESG 31
LisH pfam08513
LisH; The LisH (lis homology) domain mediates protein dimerization and tetramerization. The ...
 11-35 1.23e-04

LisH; The LisH (lis homology) domain mediates protein dimerization and tetramerization. The LisH domain is found in Sif2, a component of the Set3 complex which is responsible for repressing meiotic genes. It has been shown that the LisH domain helps mediate interaction with components of the Set3 complex.


Pssm-ID: 462501  Cd Length: 25  Bit Score: 39.22  E-value: 1.23e-04
                          10        20
                  ....*....|....*....|....*
gi 19075402    11 DLNRIVLDYLAKKGYSRTEAMLRLE 35
Cdd:pfam08513   1 ELNRLIYDYLVKEGYEETAEAFEKE 25
 
Name Accession Description Interval E-value
WD40 COG2319
WD40 repeat [General function prediction only];
316-576 3.04e-77

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 251.75  E-value: 3.04e-77
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402 316 CMYTFHHTNNNMNCAEFSPDSTMIACGFQESYIRLWSIKADKKSLpkstsvedsdgsvRLLSHSGPVYGTTFSPDNKYLL 395
Cdd:COG2319 154 LLRTLTGHSGAVTSVAFSPDGKLLASGSDDGTVRLWDLATGKLLR-------------TLTGHTGAVRSVAFSPDGKLLA 220

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402 396 SCSEDASARLWSVDTKTALVAYKGHTGPVWDVAFGPFGHYFATASHDQTAQLWSCDHIYPLRVFAGHLSDVDCVTFHPNS 475
Cdd:COG2319 221 SGSADGTVRLWDLATGKLLRTLTGHSGSVRSVAFSPDGRLLASGSADGTVRLWDLATGELLRTLTGHSGGVNSVAFSPDG 300

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402 476 AYVLTGSSDKTCRLWDVHRGHSVRVFNGHTQPVTAVAIAPDGHTMASADSEGLIHLWDIGTGRRIKTMRGHRGNIYSLSF 555
Cdd:COG2319 301 KLLASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKTLASGSDDGTVRLWDLATGELLRTLTGHTGAVTSVAF 380

                       250       260
                ....*....|....*....|.
gi 19075402 556 SRESTVLVSGGSDCTVRAWDV 576
Cdd:COG2319 381 SPDGRTLASGSADGTVRLWDL 401
WD40 COG2319
WD40 repeat [General function prediction only];
332-618 2.86e-74

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 244.05  E-value: 2.86e-74
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402 332 FSPDSTMIACGFQESYIRLWSikadkkslpkstsVEDSDGSVRLLSHSGPVYGTTFSPDNKYLLSCSEDASARLWSVDTK 411
Cdd:COG2319  86 FSPDGRLLASASADGTVRLWD-------------LATGLLLRTLTGHTGAVRSVAFSPDGKTLASGSADGTVRLWDLATG 152

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402 412 TALVAYKGHTGPVWDVAFGPFGHYFATASHDQTAQLWSCDHIYPLRVFAGHLSDVDCVTFHPNSAYVLTGSSDKTCRLWD 491
Cdd:COG2319 153 KLLRTLTGHSGAVTSVAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKLLASGSADGTVRLWD 232

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402 492 VHRGHSVRVFNGHTQPVTAVAIAPDGHTMASADSEGLIHLWDIGTGRRIKTMRGHRGNIYSLSFSRESTVLVSGGSDCTV 571
Cdd:COG2319 233 LATGKLLRTLTGHSGSVRSVAFSPDGRLLASGSADGTVRLWDLATGELLRTLTGHSGGVNSVAFSPDGKLLASGSDDGTV 312

                       250       260       270       280
                ....*....|....*....|....*....|....*....|....*...
gi 19075402 572 RAWDVfktnynnpvsssLTGSVVTPFSAKTSTFNEVNWstSPD-QMVA 618
Cdd:COG2319 313 RLWDL------------ATGKLLRTLTGHTGAVRSVAF--SPDgKTLA 346
WD40 COG2319
WD40 repeat [General function prediction only];
319-576 6.22e-74

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 243.28  E-value: 6.22e-74
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402 319 TFHHTNNNMNCAEFSPDSTMIACGFQESYIRLWSIkADKKSLPkstsvedsdgsvRLLSHSGPVYGTTFSPDNKYLLSCS 398
Cdd:COG2319 115 TLTGHTGAVRSVAFSPDGKTLASGSADGTVRLWDL-ATGKLLR------------TLTGHSGAVTSVAFSPDGKLLASGS 181

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402 399 EDASARLWSVDTKTALVAYKGHTGPVWDVAFGPFGHYFATASHDQTAQLWSCDHIYPLRVFAGHLSDVDCVTFHPNSAYV 478
Cdd:COG2319 182 DDGTVRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKLLASGSADGTVRLWDLATGKLLRTLTGHSGSVRSVAFSPDGRLL 261

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402 479 LTGSSDKTCRLWDVHRGHSVRVFNGHTQPVTAVAIAPDGHTMASADSEGLIHLWDIGTGRRIKTMRGHRGNIYSLSFSRE 558
Cdd:COG2319 262 ASGSADGTVRLWDLATGELLRTLTGHSGGVNSVAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAFSPD 341

                       250
                ....*....|....*...
gi 19075402 559 STVLVSGGSDCTVRAWDV 576
Cdd:COG2319 342 GKTLASGSDDGTVRLWDL 359
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 332-575 1.53e-65

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: 217.20  E-value: 1.53e-65
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402 332 FSPDSTMIACGFQESYIRLWSIKADKKSlpkstsvedsdgsVRLLSHSGPVYGTTFSPDNKYLLSCSEDASARLWSVDTK 411
Cdd:cd00200  59 ASADGTYLASGSSDKTIRLWDLETGECV-------------RTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETG 125

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402 412 TALVAYKGHTGPVWDVAFGPFGHYFATASHDQTAQLWSCDHIYPLRVFAGHLSDVDCVTFHPNSAYVLTGSSDKTCRLWD 491
Cdd:cd00200 126 KCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDLRTGKCVATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWD 205

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402 492 VHRGHSVRVFNGHTQPVTAVAIAPDGHTMASADSEGLIHLWDIGTGRRIKTMRGHRGNIYSLSFSRESTVLVSGGSDCTV 571
Cdd:cd00200 206 LSTGKCLGTLRGHENGVNSVAFSPDGYLLASGSEDGTIRVWDLRTGECVQTLSGHTNSVTSLAWSPDGKRLASGSADGTI 285


                ....
gi 19075402 572 RAWD 575
Cdd:cd00200 286 RIWD 289
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 375-618 2.07e-62

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: 208.73  E-value: 2.07e-62
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402 375 LLSHSGPVYGTTFSPDNKYLLSCSEDASARLWSVDTKTALVAYKGHTGPVWDVAFGPFGHYFATASHDQTAQLWSCDHIY 454
Cdd:cd00200   5 LKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASADGTYLASGSSDKTIRLWDLETGE 84

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402 455 PLRVFAGHLSDVDCVTFHPNSAYVLTGSSDKTCRLWDVHRGHSVRVFNGHTQPVTAVAIAPDGHTMASADSEGLIHLWDI 534
Cdd:cd00200  85 CVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDL 164

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402 535 GTGRRIKTMRGHRGNIYSLSFSRESTVLVSGGSDCTVRAWDVfktnynnpvsssLTGSVVTPFSAKTSTFNEVNWSTSPD 614
Cdd:cd00200 165 RTGKCVATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDL------------STGKCLGTLRGHENGVNSVAFSPDGY 232


                ....
gi 19075402 615 QMVA 618
Cdd:cd00200 233 LLAS 236
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 328-576 1.66e-61

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: 206.42  E-value: 1.66e-61
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402 328 NCAEFSPDSTMIACGFQESYIRLWSikadkkslpkstsVEDSDGSVRLLSHSGPVYGTTFSPDNKYLLSCSEDASARLWS 407
Cdd:cd00200  13 TCVAFSPDGKLLATGSGDGTIKVWD-------------LETGELLRTLKGHTGPVRDVAASADGTYLASGSSDKTIRLWD 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402 408 VDTKTALVAYKGHTGPVWDVAFGPFGHYFATASHDQTAQLWSCDHIYPLRVFAGHLSDVDCVTFHPNSAYVLTGSSDKTC 487
Cdd:cd00200  80 LETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTI 159

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402 488 RLWDVHRGHSVRVFNGHTQPVTAVAIAPDGHTMASADSEGLIHLWDIGTGRRIKTMRGHRGNIYSLSFSRESTVLVSGGS 567
Cdd:cd00200 160 KLWDLRTGKCVATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGTLRGHENGVNSVAFSPDGYLLASGSE 239


                ....*....
gi 19075402 568 DCTVRAWDV 576
Cdd:cd00200 240 DGTIRVWDL 248
TFIID_NTD2 pfam04494
WD40 associated region in TFIID subunit, NTD2 domain; This region is an all-alpha domain ...
 51-183 1.27e-59

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: 195.40  E-value: 1.27e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402    51 EETPDAYTHTYTILRDWVDSSLELYKAELHRILFPIFVHSYLNLLSQDHYEAAKQFYELFKDDHTDLHDFDVKNLKSLSL 130
Cdd:pfam04494   1 EGDPQKYERAYSLLRNWIESSLDIYKPELRRLLYPVFVHSYLDLVAKGHIEEAKEFFEKFRGDHEALHGDDLRKLAGITL 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 19075402   131 PSHVAEDRTAQQYRQNKYQLHFSRITFDLLLHFLFENVSNggsIIIKLINQHI 183
Cdd:pfam04494  81 PEHLEENELAKLFRSNKYRIRLSRYSFDLLLRFLQENESS---VILRIINEHL 130
WD40 COG2319
WD40 repeat [General function prediction only];
374-618 2.28e-58

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 201.68  E-value: 2.28e-58
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402 374 RLLSHSGPVYGTTFSPDNKYLLSCSEDASARLWSVDTKTALVAYKGHTGPVWDVAFGPFGHYFATASHDQTAQLWSCDHI 453
Cdd:COG2319  31 LLLGLAAAVASLAASPDGARLAAGAGDLTLLLLDAAAGALLATLLGHTAAVLSVAFSPDGRLLASASADGTVRLWDLATG 110

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402 454 YPLRVFAGHLSDVDCVTFHPNSAYVLTGSSDKTCRLWDVHRGHSVRVFNGHTQPVTAVAIAPDGHTMASADSEGLIHLWD 533
Cdd:COG2319 111 LLLRTLTGHTGAVRSVAFSPDGKTLASGSADGTVRLWDLATGKLLRTLTGHSGAVTSVAFSPDGKLLASGSDDGTVRLWD 190

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402 534 IGTGRRIKTMRGHRGNIYSLSFSRESTVLVSGGSDCTVRAWDVfktnynnpvsssLTGSVVTPFSAKTSTFNEVNWstSP 613
Cdd:COG2319 191 LATGKLLRTLTGHTGAVRSVAFSPDGKLLASGSADGTVRLWDL------------ATGKLLRTLTGHSGSVRSVAF--SP 256


                ....*.
gi 19075402 614 D-QMVA 618
Cdd:COG2319 257 DgRLLA 262
TAF5_NTD2 cd08044
TAF5_NTD2 is the second conserved N-terminal region of TATA Binding Protein (TBP) Associated ...
 54-189 5.88e-52

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: 175.07  E-value: 5.88e-52
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402  54 PDAYTHTYTILRDWVDSSLELYKAELHRILFPIFVHSYLNLLSQDHYEAAKQFYELFKDDHTDLHDFDVKNLKSLSLPSH 133
Cdd:cd08044   1 PNDYEQAYSKLRKWIESSLDIYKYELSQLLYPIFVHSYLDLVASGHLEEAKSFFERFSGDFEDSHSEDIKKLSSITTPEH 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 19075402 134 VAEDRTAQQYRQNKYQLHFSRITFDLLLHFLFEnvsNGGSIIIKLINQHIDIHIVP 189
Cdd:cd08044  81 LKENELAKLFRSNKYVIRMSRDAYSLLLRFLES---WGGSLLLKILNEHIDIDVRD 133
WD40 COG2319
WD40 repeat [General function prediction only];
387-618 1.43e-42

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 158.54  E-value: 1.43e-42
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402 387 FSPDNKYLLSCSEDASARLWSVDTKTALVAYKGHTGPVWDVAFGPFGHYFATASHDQTAQLWSCDHIYPLRVFAGHLSDV 466
Cdd:COG2319   2 LSADGAALAAASADLALALLAAALGALLLLLLGLAAAVASLAASPDGARLAAGAGDLTLLLLDAAAGALLATLLGHTAAV 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402 467 DCVTFHPNSAYVLTGSSDKTCRLWDVHRGHSVRVFNGHTQPVTAVAIAPDGHTMASADSEGLIHLWDIGTGRRIKTMRGH 546
Cdd:COG2319  82 LSVAFSPDGRLLASASADGTVRLWDLATGLLLRTLTGHTGAVRSVAFSPDGKTLASGSADGTVRLWDLATGKLLRTLTGH 161

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19075402 547 RGNIYSLSFSRESTVLVSGGSDCTVRAWDVfktnynnpvsssLTGSVVTPFSAKTSTFNEVNWstSPD-QMVA 618
Cdd:COG2319 162 SGAVTSVAFSPDGKLLASGSDDGTVRLWDL------------ATGKLLRTLTGHTGAVRSVAF--SPDgKLLA 220
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 316-491 1.55e-34

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: 132.84  E-value: 1.55e-34
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402 316 CMYTFHHTNNNMNCAEFSPDSTMIACGFQESYIRLWSIKADKkslpkstsvedsdgSVRLLS-HSGPVYGTTFSPDNKYL 394
Cdd:cd00200 127 CLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDLRTGK--------------CVATLTgHTGEVNSVAFSPDGEKL 192

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402 395 LSCSEDASARLWSVDTKTALVAYKGHTGPVWDVAFGPFGHYFATASHDQTAQLWSCDHIYPLRVFAGHLSDVDCVTFHPN 474
Cdd:cd00200 193 LSSSSDGTIKLWDLSTGKCLGTLRGHENGVNSVAFSPDGYLLASGSEDGTIRVWDLRTGECVQTLSGHTNSVTSLAWSPD 272

                       170
                ....*....|....*..
gi 19075402 475 SAYVLTGSSDKTCRLWD 491
Cdd:cd00200 273 GKRLASGSADGTIRIWD 289
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 455-618 4.86e-32

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


Pssm-ID: 238121 [Multi-domain]  Cd Length: 289  Bit Score: 125.53  E-value: 4.86e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402 455 PLRVFAGHLSDVDCVTFHPNSAYVLTGSSDKTCRLWDVHRGHSVRVFNGHTQPVTAVAIAPDGHTMASADSEGLIHLWDI 534
Cdd:cd00200   1 LRRTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASADGTYLASGSSDKTIRLWDL 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402 535 GTGRRIKTMRGHRGNIYSLSFSRESTVLVSGGSDCTVRAWDVfktnynnpvsssLTGSVVTPFSAKTSTFNEVNWSTSpD 614
Cdd:cd00200  81 ETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDV------------ETGKCLTTLRGHTDWVNSVAFSPD-G 147


                ....
gi 19075402 615 QMVA 618
Cdd:cd00200 148 TFVA 151
WD40 COG2319
WD40 repeat [General function prediction only];
428-618 1.97e-24

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 106.15  E-value: 1.97e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402 428 AFGPFGHYFATASHDQTAQLWSCDHIYPLRVFAGHLSDVDCVTFHPNSAYVLTGSSDKTCRLWDVHRGHSVRVFNGHTQP 507
Cdd:COG2319   1 ALSADGAALAAASADLALALLAAALGALLLLLLGLAAAVASLAASPDGARLAAGAGDLTLLLLDAAAGALLATLLGHTAA 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402 508 VTAVAIAPDGHTMASADSEGLIHLWDIGTGRRIKTMRGHRGNIYSLSFSRESTVLVSGGSDCTVRAWDVFktnynnpvss 587
Cdd:COG2319  81 VLSVAFSPDGRLLASASADGTVRLWDLATGLLLRTLTGHTGAVRSVAFSPDGKTLASGSADGTVRLWDLA---------- 150

                       170       180       190
                ....*....|....*....|....*....|..
gi 19075402 588 slTGSVVTPFSAKTSTFNEVNWstSPD-QMVA 618
Cdd:COG2319 151 --TGKLLRTLTGHSGAVTSVAF--SPDgKLLA 178
WD40 pfam00400
WD domain, G-beta repeat;
455-491 1.01e-08

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 51.19  E-value: 1.01e-08
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 19075402   455 PLRVFAGHLSDVDCVTFHPNSAYVLTGSSDKTCRLWD 491
Cdd:pfam00400   3 LLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
PTZ00421 PTZ00421
coronin; Provisional
 419-560 1.90e-08

coronin; Provisional


Pssm-ID: 173611 [Multi-domain]  Cd Length: 493  Bit Score: 57.21  E-value: 1.90e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402  419 GHTGPVWDVAFGPF-GHYFATASHDQTAQLWS----------CDHIYPLRvfaGHLSDVDCVTFHPNSAYVL-TGSSDKT 486
Cdd:PTZ00421  73 GQEGPIIDVAFNPFdPQKLFTASEDGTIMGWGipeegltqniSDPIVHLQ---GHTKKVGIVSFHPSAMNVLaSAGADMV 149

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19075402  487 CRLWDVHRGHSVRVFNGHTQPVTAVAIAPDGHTMASADSEglihlwdigtgRRIKTMRGHRGNIYSLSFSREST 560
Cdd:PTZ00421 150 VNVWDVERGKAVEVIKCHSDQITSLEWNLDGSLLCTTSKD-----------KKLNIIDPRDGTIVSSVEAHASA 212
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 455-491 3.13e-08

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: 50.00  E-value: 3.13e-08
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 19075402    455 PLRVFAGHLSDVDCVTFHPNSAYVLTGSSDKTCRLWD 491
Cdd:smart00320   4 LLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 536-575 3.73e-08

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: 49.62  E-value: 3.73e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 19075402    536 TGRRIKTMRGHRGNIYSLSFSRESTVLVSGGSDCTVRAWD 575
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 pfam00400
WD domain, G-beta repeat;
537-575 2.21e-07

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 47.34  E-value: 2.21e-07
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 19075402   537 GRRIKTMRGHRGNIYSLSFSRESTVLVSGGSDCTVRAWD 575
Cdd:pfam00400   1 GKLLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 495-533 2.60e-07

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


Pssm-ID: 197651 [Multi-domain]  Cd Length: 40  Bit Score: 47.31  E-value: 2.60e-07
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 19075402    495 GHSVRVFNGHTQPVTAVAIAPDGHTMASADSEGLIHLWD 533
Cdd:smart00320   2 GELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 417-449 7.13e-07

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


Pssm-ID: 197651 [Multi-domain]  Cd Length: 40  Bit Score: 46.15  E-value: 7.13e-07
                           10        20        30
                   ....*....|....*....|....*....|...
gi 19075402    417 YKGHTGPVWDVAFGPFGHYFATASHDQTAQLWS 449
Cdd:smart00320   8 LKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
PLN00181 PLN00181
protein SPA1-RELATED; Provisional
 427-576 2.73e-06

protein SPA1-RELATED; Provisional


Pssm-ID: 177776 [Multi-domain]  Cd Length: 793  Bit Score: 50.47  E-value: 2.73e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402  427 VAFGPFGHYFATASHDQTAQLWSCDHI--------YPLRVFAGH--LSDVdCVTFHPNSAyVLTGSSDKTCRLWDVHRGH 496
Cdd:PLN00181 489 IGFDRDGEFFATAGVNKKIKIFECESIikdgrdihYPVVELASRskLSGI-CWNSYIKSQ-VASSNFEGVVQVWDVARSQ 566

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402  497 SVRVFNGHTQPVTAVAI-APDGHTMASADSEGLIHLWDIGTGRRIKTMRGhRGNIYSLSFSRES-TVLVSGGSDCTVRAW 574
Cdd:PLN00181 567 LVTEMKEHEKRVWSIDYsSADPTLLASGSDDGSVKLWSINQGVSIGTIKT-KANICCVQFPSESgRSLAFGSADHKVYYY 645


                 ..
gi 19075402  575 DV 576
Cdd:PLN00181 646 DL 647
WD40 pfam00400
WD domain, G-beta repeat;
417-449 3.27e-06

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 44.26  E-value: 3.27e-06
                          10        20        30
                  ....*....|....*....|....*....|...
gi 19075402   417 YKGHTGPVWDVAFGPFGHYFATASHDQTAQLWS 449
Cdd:pfam00400   7 LEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
WD40 pfam00400
WD domain, G-beta repeat;
495-533 3.51e-06

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 43.87  E-value: 3.51e-06
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 19075402   495 GHSVRVFNGHTQPVTAVAIAPDGHTMASADSEGLIHLWD 533
Cdd:pfam00400   1 GKLLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
PTZ00420 PTZ00420
coronin; Provisional
 395-492 5.65e-06

coronin; Provisional


Pssm-ID: 240412 [Multi-domain]  Cd Length: 568  Bit Score: 49.56  E-value: 5.65e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402  395 LSCSEDASARLWSVD--------------TKTALVAYKGHTGPVWDVAFGP-FGHYFATASHDQTAQLWSCDH------- 452
Cdd:PTZ00420  34 IACSSGFVAVPWEVEgggligairlenqmRKPPVIKLKGHTSSILDLQFNPcFSEILASGSEDLTIRVWEIPHndesvke 113

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 19075402  453 -IYPLRVFAGHLSDVDCVTFHPNSAYVLTGSS-DKTCRLWDV 492
Cdd:PTZ00420 114 iKDPQCILKGHKKKISIIDWNPMNYYIMCSSGfDSFVNIWDI 155
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 378-407 2.00e-05

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: 41.91  E-value: 2.00e-05
                           10        20        30
                   ....*....|....*....|....*....|
gi 19075402    378 HSGPVYGTTFSPDNKYLLSCSEDASARLWS 407
Cdd:smart00320  11 HTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 pfam00400
WD domain, G-beta repeat;
375-407 4.33e-05

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 40.79  E-value: 4.33e-05
                          10        20        30
                  ....*....|....*....|....*....|...
gi 19075402   375 LLSHSGPVYGTTFSPDNKYLLSCSEDASARLWS 407
Cdd:pfam00400   7 LEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
LisH smart00667
Lissencephaly type-1-like homology motif; Alpha-helical motif present in Lis1, treacle, ...
 7-37 6.14e-05

Lissencephaly type-1-like homology motif; Alpha-helical motif present in Lis1, treacle, Nopp140, some katanin p60 subunits, muskelin, tonneau, LEUNIG and numerous WD40 repeat-containing proteins. It is suggested that LisH motifs contribute to the regulation of microtubule dynamics, either by mediating dimerisation, or else by binding cytoplasmic dynein heavy chain or microtubules directly.


Pssm-ID: 128913  Cd Length: 34  Bit Score: 40.50  E-value: 6.14e-05
                           10        20        30
                   ....*....|....*....|....*....|.
gi 19075402      7 PQPQDLNRIVLDYLAKKGYSRTEAMLRLEAS 37
Cdd:smart00667   1 ISRSELNRLILEYLLRNGYEETAETLQKESG 31
LisH pfam08513
LisH; The LisH (lis homology) domain mediates protein dimerization and tetramerization. The ...
 11-35 1.23e-04

LisH; The LisH (lis homology) domain mediates protein dimerization and tetramerization. The LisH domain is found in Sif2, a component of the Set3 complex which is responsible for repressing meiotic genes. It has been shown that the LisH domain helps mediate interaction with components of the Set3 complex.


Pssm-ID: 462501  Cd Length: 25  Bit Score: 39.22  E-value: 1.23e-04
                          10        20
                  ....*....|....*....|....*
gi 19075402    11 DLNRIVLDYLAKKGYSRTEAMLRLE 35
Cdd:pfam08513   1 ELNRLIYDYLVKEGYEETAEAFEKE 25
WDR74 cd22857
WD repeat-containing protein 74; WDR74 (WD repeat-containing protein 74) from mammals and ...
 468-576 1.27e-03

WD repeat-containing protein 74; WDR74 (WD repeat-containing protein 74) from mammals and plants is an essential factor for ribosome assembly. In cooperation with the assembly factor NVL2, WDR74 participates in an early cleavage of the pre-rRNA processing pathway. NVL2 is a type II double ring, AAA-ATPase, that may mediate the release of WDR74 from nucleolar pre-60S particles. WDR74 has been implicated in tumorigenesis. In lung cancer, it regulates cell proliferation, cell cycle progression, chemoresistance and cell aggressiveness, by inducing nuclear beta-catenin accumulation and driving downstream Wnt-responsive genes expression. In melanoma, it promotes apoptosis resistance and aggressive behavior by regulating the RPL5-MDM2-p53 pathway. WDR74 contains an N-terminal seven-bladed beta-propeller WD40 domain that associates with the D1-AAA domain of the AAA-ATPase NVL2, and a flexible lysine-rich C-terminus that extends outward from the WD40 domain, and is required for nucleolar localization.


Pssm-ID: 439303 [Multi-domain]  Cd Length: 325  Bit Score: 41.44  E-value: 1.27e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402 468 CVTFHPNSA--YVLTGSSDKTCRLWDVHRG-HSVRVFNGHTQPVTAVAIAPDGHTMASADSEGLIHLWDIGTGRRIKTMR 544
Cdd:cd22857 183 DLTFLSKDDhrKIVTGTGYHQVRLYDTRAQrRPVVSVDFGETPIKAVAEDPDGHTVYVGDTSGDLASIDLRTGKLLGCFK 262

                        90       100       110
                ....*....|....*....|....*....|...
gi 19075402 545 GHRG-NIYSLSFSRESTVLVSGGSDCTVRAWDV 576
Cdd:cd22857 263 GKCGgSIRSIARHPELPLIASCGLDRYLRIWDT 295
TolB COG0823
Periplasmic component TolB of the Tol biopolymer transport system [Intracellular trafficking, ...
 332-451 2.38e-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: 39.27  E-value: 2.38e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402 332 FSPDSTMIA-CGFQESYIRLWSIKADkkslpkstsvedsDGSVRLLSHSGPVYGT-TFSPDNKYLLSCS-EDASARLW-- 406
Cdd:COG0823  38 WSPDGRRIAfTSDRGGGPQIYVVDAD-------------GGEPRRLTFGGGYNASpSWSPDGKRLAFVSrSDGRFDIYvl 104

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*.
gi 19075402 407 SVDTKTALVAYKGHTGPVWDvafgPFGHYFA-TASHDQTAQLWSCD 451
Cdd:COG0823 105 DLDGGAPRRLTDGPGSPSWS----PDGRRIVfSSDRGGRPDLYVVD 146
PTZ00420 PTZ00420
coronin; Provisional
 373-448 4.02e-03

coronin; Provisional


Pssm-ID: 240412 [Multi-domain]  Cd Length: 568  Bit Score: 40.32  E-value: 4.02e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19075402  373 VRLLSHSGPVYGTTFSP-DNKYLLSCSEDASARLWSV--------DTKTALVAYKGHTGPVWDVAFGPFGHY-FATASHD 442
Cdd:PTZ00420  68 IKLKGHTSSILDLQFNPcFSEILASGSEDLTIRVWEIphndesvkEIKDPQCILKGHKKKISIIDWNPMNYYiMCSSGFD 147


                 ....*.
gi 19075402  443 QTAQLW 448
Cdd:PTZ00420 148 SFVNIW 153
ANAPC4_WD40 pfam12894
Anaphase-promoting complex subunit 4 WD40 domain; Apc4 contains an N-terminal propeller-shaped ...
 492-556 5.82e-03

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


Pssm-ID: 403945 [Multi-domain]  Cd Length: 91  Bit Score: 36.49  E-value: 5.82e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19075402   492 VHRGHSVRVF----NGHTQPVTAVAIAPDGHTMASADSEGLIHLWDIGTGRRIKTMRGHRGNIYSLSFS 556
Cdd:pfam12894  21 LHRLNWQRVWtlspDKEDLEVTSLAWRPDGKLLAVGYSDGTVRLLDAENGKIVHHFSAGSDLITCLGWG 89
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 313-352 7.27e-03

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: 34.60  E-value: 7.27e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 19075402    313 PSVCMYTFHHTNNNMNCAEFSPDSTMIACGFQESYIRLWS 352
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
 
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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