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Conserved domains on  [gi|122937177|ref|NP_001038483|]
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general transcription factor 3C polypeptide 2 [Danio rerio]

Protein Classification

WD40 repeat domain-containing protein( domain architecture ID 10646020)

WD40 repeat domain-containing protein folds into a beta-propeller structure and functions as a scaffold, providing a platform for the interaction and assembly of several proteins into a signalosome; similar to 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

CATH:  2.130.10.10
Gene Ontology:  GO:0005515
PubMed:  10322433|8090199|30069656|29026209
SCOP:  4002744

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PLN03237 super family cl33668
DNA topoisomerase 2; Provisional
 37-194 1.21e-04

DNA topoisomerase 2; Provisional


The actual alignment was detected with superfamily member PLN03237:

Pssm-ID: 215641 [Multi-domain]  Cd Length: 1465  Bit Score: 46.01  E-value: 1.21e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122937177   37 EESEDSKPKKIKADTqlSEQAPCSQVSSGVDQENSFNVE-----QTKK--------NEELKAKTPAKRRKKEIIPQTTPQ 103
Cdd:PLN03237 1287 ETVKAVPARRAAARK--KPLASVSVISDSDDDDDDFAVEvslaeRLKKkggrkpaaANKKAAKPPAAAKKRGPATVQSGQ 1364

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122937177  104 QDVPALTDTSElASSGRPKRRAAKVALDYLH----SLAKDIGTP--SESSTPARPKSGEA---VVTSQKKKPARSR--GV 172
Cdd:PLN03237 1365 KLLTEMLKPAE-AIGISPEKKVRKMRASPFNkksgSVLGRAATNkeTESSENVSGSSSSEkdeIDVSAKPRPQRANrkQT 1443

                         170       180
                  ....*....|....*....|..
gi 122937177  173 KRKAPDSDSDCDGDEDFAPEKD 194
Cdd:PLN03237 1444 TYVLSDSESESADDSDFDDDED 1465
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 521-558 9.36e-04

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: 37.68  E-value: 9.36e-04
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 122937177   521 PYHCFHAHDENIRTLSWCKaSSHLLVTVGDDRMAKMWD 558
Cdd:smart00320   4 LLKTLKGHTGPVTSVAFSP-DGKYLASGSDDGTIKLWD 40
 
Name Accession Description Interval E-value
PLN03237 PLN03237
DNA topoisomerase 2; Provisional
 37-194 1.21e-04

DNA topoisomerase 2; Provisional


Pssm-ID: 215641 [Multi-domain]  Cd Length: 1465  Bit Score: 46.01  E-value: 1.21e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122937177   37 EESEDSKPKKIKADTqlSEQAPCSQVSSGVDQENSFNVE-----QTKK--------NEELKAKTPAKRRKKEIIPQTTPQ 103
Cdd:PLN03237 1287 ETVKAVPARRAAARK--KPLASVSVISDSDDDDDDFAVEvslaeRLKKkggrkpaaANKKAAKPPAAAKKRGPATVQSGQ 1364

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122937177  104 QDVPALTDTSElASSGRPKRRAAKVALDYLH----SLAKDIGTP--SESSTPARPKSGEA---VVTSQKKKPARSR--GV 172
Cdd:PLN03237 1365 KLLTEMLKPAE-AIGISPEKKVRKMRASPFNkksgSVLGRAATNkeTESSENVSGSSSSEkdeIDVSAKPRPQRANrkQT 1443

                         170       180
                  ....*....|....*....|..
gi 122937177  173 KRKAPDSDSDCDGDEDFAPEKD 194
Cdd:PLN03237 1444 TYVLSDSESESADDSDFDDDED 1465
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 521-558 9.36e-04

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: 37.68  E-value: 9.36e-04
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 122937177   521 PYHCFHAHDENIRTLSWCKaSSHLLVTVGDDRMAKMWD 558
Cdd:smart00320   4 LLKTLKGHTGPVTSVAFSP-DGKYLASGSDDGTIKLWD 40
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 429-561 1.56e-03

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: 41.55  E-value: 1.56e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122937177 429 PRLGVLAATFANGTIGVYSLPHPEALEK---HyqskdQHFMGCFMLFLQVKKLLSlkmGSNqaDHKAQslvgLWDLSSKS 505
Cdd:cd00200   19 PDGKLLATGSGDGTIKVWDLETGELLRTlkgH-----TGPVRDVAASADGTYLAS---GSS--DKTIR----LWDLETGE 84

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 122937177 506 TLlrvrcpdggvslypyHCFHAHDENIRTLSWcKASSHLLVTVGDDRMAKMWDVRK 561
Cdd:cd00200   85 CV---------------RTLTGHTSYVSSVAF-SPDGRILSSSSRDKTIKVWDVET 124
 
Name Accession Description Interval E-value
PLN03237 PLN03237
DNA topoisomerase 2; Provisional
 37-194 1.21e-04

DNA topoisomerase 2; Provisional


Pssm-ID: 215641 [Multi-domain]  Cd Length: 1465  Bit Score: 46.01  E-value: 1.21e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122937177   37 EESEDSKPKKIKADTqlSEQAPCSQVSSGVDQENSFNVE-----QTKK--------NEELKAKTPAKRRKKEIIPQTTPQ 103
Cdd:PLN03237 1287 ETVKAVPARRAAARK--KPLASVSVISDSDDDDDDFAVEvslaeRLKKkggrkpaaANKKAAKPPAAAKKRGPATVQSGQ 1364

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122937177  104 QDVPALTDTSElASSGRPKRRAAKVALDYLH----SLAKDIGTP--SESSTPARPKSGEA---VVTSQKKKPARSR--GV 172
Cdd:PLN03237 1365 KLLTEMLKPAE-AIGISPEKKVRKMRASPFNkksgSVLGRAATNkeTESSENVSGSSSSEkdeIDVSAKPRPQRANrkQT 1443

                         170       180
                  ....*....|....*....|..
gi 122937177  173 KRKAPDSDSDCDGDEDFAPEKD 194
Cdd:PLN03237 1444 TYVLSDSESESADDSDFDDDED 1465
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 521-558 9.36e-04

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: 37.68  E-value: 9.36e-04
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 122937177   521 PYHCFHAHDENIRTLSWCKaSSHLLVTVGDDRMAKMWD 558
Cdd:smart00320   4 LLKTLKGHTGPVTSVAFSP-DGKYLASGSDDGTIKLWD 40
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 429-561 1.56e-03

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: 41.55  E-value: 1.56e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122937177 429 PRLGVLAATFANGTIGVYSLPHPEALEK---HyqskdQHFMGCFMLFLQVKKLLSlkmGSNqaDHKAQslvgLWDLSSKS 505
Cdd:cd00200   19 PDGKLLATGSGDGTIKVWDLETGELLRTlkgH-----TGPVRDVAASADGTYLAS---GSS--DKTIR----LWDLETGE 84

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 122937177 506 TLlrvrcpdggvslypyHCFHAHDENIRTLSWcKASSHLLVTVGDDRMAKMWDVRK 561
Cdd:cd00200   85 CV---------------RTLTGHTSYVSSVAF-SPDGRILSSSSRDKTIKVWDVET 124
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 496-564 6.58e-03

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: 39.24  E-value: 6.58e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 122937177 496 VGLWDLSSkstllrvrcpdggvsLYPYHCFHAHDENIRTLSWCKASSHLLVTvGDDRMAKMWDVRKTHT 564
Cdd:cd00200  159 IKLWDLRT---------------GKCVATLTGHTGEVNSVAFSPDGEKLLSS-SSDGTIKLWDLSTGKC 211
PLN03237 PLN03237
DNA topoisomerase 2; Provisional
 84-192 7.96e-03

DNA topoisomerase 2; Provisional


Pssm-ID: 215641 [Multi-domain]  Cd Length: 1465  Bit Score: 39.85  E-value: 7.96e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 122937177   84 KAKTPAKRRKKEIIPQTTPQQDVPALTDTSELASSGRPKRRAA-----------KVALDYLHSLAKDIGTPSESSTPARP 152
Cdd:PLN03237 1203 KKPAPKKTTKKASESETTEETYGSSAMETENVAEVVKPKGRAGakkkapaaakeKEEEDEILDLKDRLAAYNLDSAPAQS 1282

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 122937177  153 KSGEAVVTSQKKKPARSRGVKRKAPDSDSDCDGDED-FAPE 192
Cdd:PLN03237 1283 AKMEETVKAVPARRAAARKKPLASVSVISDSDDDDDdFAVE 1323
 
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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