NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1809665845|ref|NP_001365384|]
View 

cytoplasmic dynein 1 intermediate chain 2 isoform 6 [Homo sapiens]

Protein Classification

cytoplasmic dynein 1 intermediate chain( domain architecture ID 12110212)

cytoplasmic dynein 1 intermediate chain is a non-catalytic accessory component of the cytoplasmic dynein 1 complex and may be involved in linking dynein to cargos and to adapter proteins that regulate dynein function

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

Name Accession Description Interval E-value
WD40 COG2319
WD40 repeat [General function prediction only];
303-593 3.00e-16

WD40 repeat [General function prediction only];


:

Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 81.11  E-value: 3.00e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1809665845 303 PDGVALVWNMKYKKTTPEYVFHcQSAVMSATFakfHPN--LVVGGTYSGQIVLWDNRSNKrtpvQRTPLSAaaHTHPVYC 380
Cdd:COG2319    98 ADGTVRLWDLATGLLLRTLTGH-TGAVRSVAF---SPDgkTLASGSADGTVRLWDLATGK----LLRTLTG--HSGAVTS 167
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1809665845 381 VNVvgTQNAHNLISISTDGKICSWSLDmlshpqdSMELVHK-QSKAVAVTSMSF-PVGDVnnFVVGSEEGSVytacR--H 456
Cdd:COG2319   168 VAF--SPDGKLLASGSDDGTVRLWDLA-------TGKLLRTlTGHTGAVRSVAFsPDGKL--LASGSADGTV----RlwD 232
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1809665845 457 GSKAGISEMFEGHQGPITgihchaavgAVDFS---HLFVTSSFDWTVKLWTTKNNKPLYSFEDNADYVYDVMWSPThPAL 533
Cdd:COG2319   233 LATGKLLRTLTGHSGSVR---------SVAFSpdgRLLASGSADGTVRLWDLATGELLRTLTGHSGGVNSVAFSPD-GKL 302
                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1809665845 534 FACVDGMGRLDLWNLNNDTEVPTASISVEgnpALNRVRWTHSGREIAVGDSEGQIVIYDV 593
Cdd:COG2319   303 LASGSDDGTVRLWDLATGKLLRTLTGHTG---AVRSVAFSPDGKTLASGSDDGTVRLWDL 359
Dynein_IC2 pfam11540
Cytoplasmic dynein 1 intermediate chain 2; Intermediate chain IC 2 forms part of the complex ...
127-157 1.01e-13

Cytoplasmic dynein 1 intermediate chain 2; Intermediate chain IC 2 forms part of the complex cytoplasmic dynein 1 along with a heavy chain (HC), two light intermediate chains (LICs) and three light chains (LCs). The complex is responsible for hydrolysing ATP to generate force toward the minus end of microtubules. IC binds to the HC via the N terminal binding domain on the HC and ICs contain binding sites for the LCs. The ICs are responsible for binding to kinetochores and the Golgi apparatus through an interaction with the p150Glued subunit of dynactin which is another complex.


:

Pssm-ID: 463291  Cd Length: 31  Bit Score: 65.26  E-value: 1.01e-13
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1809665845 127 RGPIKLGMAKITQVDFPPREIVTYTKETQTP 157
Cdd:pfam11540   1 RKPPRLSVSKVQETDIPPKETVTYSKETQTP 31
 
Name Accession Description Interval E-value
WD40 COG2319
WD40 repeat [General function prediction only];
303-593 3.00e-16

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 81.11  E-value: 3.00e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1809665845 303 PDGVALVWNMKYKKTTPEYVFHcQSAVMSATFakfHPN--LVVGGTYSGQIVLWDNRSNKrtpvQRTPLSAaaHTHPVYC 380
Cdd:COG2319    98 ADGTVRLWDLATGLLLRTLTGH-TGAVRSVAF---SPDgkTLASGSADGTVRLWDLATGK----LLRTLTG--HSGAVTS 167
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1809665845 381 VNVvgTQNAHNLISISTDGKICSWSLDmlshpqdSMELVHK-QSKAVAVTSMSF-PVGDVnnFVVGSEEGSVytacR--H 456
Cdd:COG2319   168 VAF--SPDGKLLASGSDDGTVRLWDLA-------TGKLLRTlTGHTGAVRSVAFsPDGKL--LASGSADGTV----RlwD 232
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1809665845 457 GSKAGISEMFEGHQGPITgihchaavgAVDFS---HLFVTSSFDWTVKLWTTKNNKPLYSFEDNADYVYDVMWSPThPAL 533
Cdd:COG2319   233 LATGKLLRTLTGHSGSVR---------SVAFSpdgRLLASGSADGTVRLWDLATGELLRTLTGHSGGVNSVAFSPD-GKL 302
                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1809665845 534 FACVDGMGRLDLWNLNNDTEVPTASISVEgnpALNRVRWTHSGREIAVGDSEGQIVIYDV 593
Cdd:COG2319   303 LASGSDDGTVRLWDLATGKLLRTLTGHTG---AVRSVAFSPDGKTLASGSDDGTVRLWDL 359
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
270-592 4.27e-16

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: 79.30  E-value: 4.27e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1809665845 270 WSKHR-VVSCLDWSSQYPELLVASYnnnedaphepDGVALVWNMKYKKTTPEYVFHcQSAVMSATFAKFHPNLVVGGtYS 348
Cdd:cd00200     5 LKGHTgGVTCVAFSPDGKLLATGSG----------DGTIKVWDLETGELLRTLKGH-TGPVRDVAASADGTYLASGS-SD 72
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1809665845 349 GQIVLWDNRSNKRTpvqRTplsAAAHTHPVYCVNVvgTQNAHNLISISTDGKICSWSLDmlshpqdsmelvhkqsKAVAV 428
Cdd:cd00200    73 KTIRLWDLETGECV---RT---LTGHTSYVSSVAF--SPDGRILSSSSRDKTIKVWDVE----------------TGKCL 128
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1809665845 429 TSMSFPVGDVNNFVVGSEEGSVYTACRHG-------SKAGISEMFEGHQGPITGIHCHAAvgavdfSHLFVTSSFDWTVK 501
Cdd:cd00200   129 TTLRGHTDWVNSVAFSPDGTFVASSSQDGtiklwdlRTGKCVATLTGHTGEVNSVAFSPD------GEKLLSSSSDGTIK 202
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1809665845 502 LWTTKNNKPLYSFEDNADYVYDVMWSPtHPALFACVDGMGRLDLWNLNNDTEVPTASisvEGNPALNRVRWTHSGREIAV 581
Cdd:cd00200   203 LWDLSTGKCLGTLRGHENGVNSVAFSP-DGYLLASGSEDGTIRVWDLRTGECVQTLS---GHTNSVTSLAWSPDGKRLAS 278
                         330
                  ....*....|.
gi 1809665845 582 GDSEGQIVIYD 592
Cdd:cd00200   279 GSADGTIRIWD 289
Dynein_IC2 pfam11540
Cytoplasmic dynein 1 intermediate chain 2; Intermediate chain IC 2 forms part of the complex ...
127-157 1.01e-13

Cytoplasmic dynein 1 intermediate chain 2; Intermediate chain IC 2 forms part of the complex cytoplasmic dynein 1 along with a heavy chain (HC), two light intermediate chains (LICs) and three light chains (LCs). The complex is responsible for hydrolysing ATP to generate force toward the minus end of microtubules. IC binds to the HC via the N terminal binding domain on the HC and ICs contain binding sites for the LCs. The ICs are responsible for binding to kinetochores and the Golgi apparatus through an interaction with the p150Glued subunit of dynactin which is another complex.


Pssm-ID: 463291  Cd Length: 31  Bit Score: 65.26  E-value: 1.01e-13
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1809665845 127 RGPIKLGMAKITQVDFPPREIVTYTKETQTP 157
Cdd:pfam11540   1 RKPPRLSVSKVQETDIPPKETVTYSKETQTP 31
PLN00181 PLN00181
protein SPA1-RELATED; Provisional
493-599 1.08e-03

protein SPA1-RELATED; Provisional


Pssm-ID: 177776 [Multi-domain]  Cd Length: 793  Bit Score: 42.00  E-value: 1.08e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1809665845 493 TSSFDWTVKLWTTKNNKPLYSFEDNADYVYDVMWSPTHPALFACVDGMGRLDLWNLNNDTEVPTasISVEGNPALNRVRw 572
Cdd:PLN00181  550 SSNFEGVVQVWDVARSQLVTEMKEHEKRVWSIDYSSADPTLLASGSDDGSVKLWSINQGVSIGT--IKTKANICCVQFP- 626
                          90       100
                  ....*....|....*....|....*..
gi 1809665845 573 THSGREIAVGDSEGQIVIYDVGEIAVP 599
Cdd:PLN00181  627 SESGRSLAFGSADHKVYYYDLRNPKLP 653
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
466-503 2.51e-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: 36.14  E-value: 2.51e-03
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 1809665845  466 FEGHQGPITGIHCHaavgavDFSHLFVTSSFDWTVKLW 503
Cdd:smart00320   8 LKGHTGPVTSVAFS------PDGKYLASGSDDGTIKLW 39
 
Name Accession Description Interval E-value
WD40 COG2319
WD40 repeat [General function prediction only];
303-593 3.00e-16

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 81.11  E-value: 3.00e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1809665845 303 PDGVALVWNMKYKKTTPEYVFHcQSAVMSATFakfHPN--LVVGGTYSGQIVLWDNRSNKrtpvQRTPLSAaaHTHPVYC 380
Cdd:COG2319    98 ADGTVRLWDLATGLLLRTLTGH-TGAVRSVAF---SPDgkTLASGSADGTVRLWDLATGK----LLRTLTG--HSGAVTS 167
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1809665845 381 VNVvgTQNAHNLISISTDGKICSWSLDmlshpqdSMELVHK-QSKAVAVTSMSF-PVGDVnnFVVGSEEGSVytacR--H 456
Cdd:COG2319   168 VAF--SPDGKLLASGSDDGTVRLWDLA-------TGKLLRTlTGHTGAVRSVAFsPDGKL--LASGSADGTV----RlwD 232
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1809665845 457 GSKAGISEMFEGHQGPITgihchaavgAVDFS---HLFVTSSFDWTVKLWTTKNNKPLYSFEDNADYVYDVMWSPThPAL 533
Cdd:COG2319   233 LATGKLLRTLTGHSGSVR---------SVAFSpdgRLLASGSADGTVRLWDLATGELLRTLTGHSGGVNSVAFSPD-GKL 302
                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1809665845 534 FACVDGMGRLDLWNLNNDTEVPTASISVEgnpALNRVRWTHSGREIAVGDSEGQIVIYDV 593
Cdd:COG2319   303 LASGSDDGTVRLWDLATGKLLRTLTGHTG---AVRSVAFSPDGKTLASGSDDGTVRLWDL 359
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
270-592 4.27e-16

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: 79.30  E-value: 4.27e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1809665845 270 WSKHR-VVSCLDWSSQYPELLVASYnnnedaphepDGVALVWNMKYKKTTPEYVFHcQSAVMSATFAKFHPNLVVGGtYS 348
Cdd:cd00200     5 LKGHTgGVTCVAFSPDGKLLATGSG----------DGTIKVWDLETGELLRTLKGH-TGPVRDVAASADGTYLASGS-SD 72
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1809665845 349 GQIVLWDNRSNKRTpvqRTplsAAAHTHPVYCVNVvgTQNAHNLISISTDGKICSWSLDmlshpqdsmelvhkqsKAVAV 428
Cdd:cd00200    73 KTIRLWDLETGECV---RT---LTGHTSYVSSVAF--SPDGRILSSSSRDKTIKVWDVE----------------TGKCL 128
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1809665845 429 TSMSFPVGDVNNFVVGSEEGSVYTACRHG-------SKAGISEMFEGHQGPITGIHCHAAvgavdfSHLFVTSSFDWTVK 501
Cdd:cd00200   129 TTLRGHTDWVNSVAFSPDGTFVASSSQDGtiklwdlRTGKCVATLTGHTGEVNSVAFSPD------GEKLLSSSSDGTIK 202
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1809665845 502 LWTTKNNKPLYSFEDNADYVYDVMWSPtHPALFACVDGMGRLDLWNLNNDTEVPTASisvEGNPALNRVRWTHSGREIAV 581
Cdd:cd00200   203 LWDLSTGKCLGTLRGHENGVNSVAFSP-DGYLLASGSEDGTIRVWDLRTGECVQTLS---GHTNSVTSLAWSPDGKRLAS 278
                         330
                  ....*....|.
gi 1809665845 582 GDSEGQIVIYD 592
Cdd:cd00200   279 GSADGTIRIWD 289
WD40 COG2319
WD40 repeat [General function prediction only];
304-593 1.41e-15

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 79.18  E-value: 1.41e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1809665845 304 DGVALVWNMKYKKTTPEYVFHcQSAVMSATFakfHPN--LVVGGTYSGQIVLWDNRSNKRTPVQRtplsaaAHTHPVYCV 381
Cdd:COG2319   141 DGTVRLWDLATGKLLRTLTGH-SGAVTSVAF---SPDgkLLASGSDDGTVRLWDLATGKLLRTLT------GHTGAVRSV 210
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1809665845 382 NVvgTQNAHNLISISTDGKICSWSLDmlshpqdSMELVHK-QSKAVAVTSMSF-PVGDVnnFVVGSEEGSVY------TA 453
Cdd:COG2319   211 AF--SPDGKLLASGSADGTVRLWDLA-------TGKLLRTlTGHSGSVRSVAFsPDGRL--LASGSADGTVRlwdlatGE 279
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1809665845 454 CRHgskagiseMFEGHQGPITgihchaavgAVDFS---HLFVTSSFDWTVKLWTTKNNKPLYSFEDNADYVYDVMWSPTH 530
Cdd:COG2319   280 LLR--------TLTGHSGGVN---------SVAFSpdgKLLASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAFSPDG 342
                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1809665845 531 PALFACVDGmGRLDLWNLNNDTEVPTASisvEGNPALNRVRWTHSGREIAVGDSEGQIVIYDV 593
Cdd:COG2319   343 KTLASGSDD-GTVRLWDLATGELLRTLT---GHTGAVTSVAFSPDGRTLASGSADGTVRLWDL 401
WD40 COG2319
WD40 repeat [General function prediction only];
304-612 7.12e-15

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 76.87  E-value: 7.12e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1809665845 304 DGVALVWNMKYKKTTPEYVFHcQSAVMSATFAkFHPNLVVGGTYSGQIVLWDNRSNKRTPVQRtplsaaAHTHPVYCVNV 383
Cdd:COG2319    57 DLTLLLLDAAAGALLATLLGH-TAAVLSVAFS-PDGRLLASASADGTVRLWDLATGLLLRTLT------GHTGAVRSVAF 128
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1809665845 384 vgTQNAHNLISISTDGKICSWSLDmlshpqDSMELVHKQSKAVAVTSMSF-PVGDVnnFVVGSEEGSVYTACRHGSKAGI 462
Cdd:COG2319   129 --SPDGKTLASGSADGTVRLWDLA------TGKLLRTLTGHSGAVTSVAFsPDGKL--LASGSDDGTVRLWDLATGKLLR 198
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1809665845 463 SemFEGHQGPITgihchaavgAVDFS---HLFVTSSFDWTVKLWTTKNNKPLYSFEDNADYVYDVMWSPTHPALfACVDG 539
Cdd:COG2319   199 T--LTGHTGAVR---------SVAFSpdgKLLASGSADGTVRLWDLATGKLLRTLTGHSGSVRSVAFSPDGRLL-ASGSA 266
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1809665845 540 MGRLDLWNLNNDTEVPTASisvEGNPALNRVRWTHSGREIAVGDSEGQIVIYDV----------GEIAVPRNDEWARFGR 609
Cdd:COG2319   267 DGTVRLWDLATGELLRTLT---GHSGGVNSVAFSPDGKLLASGSDDGTVRLWDLatgkllrtltGHTGAVRSVAFSPDGK 343

                  ...
gi 1809665845 610 TLA 612
Cdd:COG2319   344 TLA 346
Dynein_IC2 pfam11540
Cytoplasmic dynein 1 intermediate chain 2; Intermediate chain IC 2 forms part of the complex ...
127-157 1.01e-13

Cytoplasmic dynein 1 intermediate chain 2; Intermediate chain IC 2 forms part of the complex cytoplasmic dynein 1 along with a heavy chain (HC), two light intermediate chains (LICs) and three light chains (LCs). The complex is responsible for hydrolysing ATP to generate force toward the minus end of microtubules. IC binds to the HC via the N terminal binding domain on the HC and ICs contain binding sites for the LCs. The ICs are responsible for binding to kinetochores and the Golgi apparatus through an interaction with the p150Glued subunit of dynactin which is another complex.


Pssm-ID: 463291  Cd Length: 31  Bit Score: 65.26  E-value: 1.01e-13
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1809665845 127 RGPIKLGMAKITQVDFPPREIVTYTKETQTP 157
Cdd:pfam11540   1 RKPPRLSVSKVQETDIPPKETVTYSKETQTP 31
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
428-593 3.93e-12

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: 67.36  E-value: 3.93e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1809665845 428 VTSMSFpVGDVNNFVVGSEEGSVYTACRHGSKAGISemFEGHQGPITGIHCHAavgavdFSHLFVTSSFDWTVKLWTTKN 507
Cdd:cd00200    12 VTCVAF-SPDGKLLATGSGDGTIKVWDLETGELLRT--LKGHTGPVRDVAASA------DGTYLASGSSDKTIRLWDLET 82
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1809665845 508 NKPLYSFEDNADYVYDVMWSPTHPALFAC-VDgmGRLDLWNLNNDTEVptasISVEGNPA-LNRVRWTHSGREIAVGDSE 585
Cdd:cd00200    83 GECVRTLTGHTSYVSSVAFSPDGRILSSSsRD--KTIKVWDVETGKCL----TTLRGHTDwVNSVAFSPDGTFVASSSQD 156

                  ....*...
gi 1809665845 586 GQIVIYDV 593
Cdd:cd00200   157 GTIKLWDL 164
WD40 COG2319
WD40 repeat [General function prediction only];
304-550 1.22e-11

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 66.86  E-value: 1.22e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1809665845 304 DGVALVWNMKYKKTTPEYVFHcQSAVMSATFAkfhPN--LVVGGTYSGQIVLWDNRSNKrtpvQRTPLSAaaHTHPVYCV 381
Cdd:COG2319   183 DGTVRLWDLATGKLLRTLTGH-TGAVRSVAFS---PDgkLLASGSADGTVRLWDLATGK----LLRTLTG--HSGSVRSV 252
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1809665845 382 NVvgTQNAHNLISISTDGKICSWSLD------MLSHPQDsmelvhkqskavAVTSMSF-PVGDVnnFVVGSEEGSVY--- 451
Cdd:COG2319   253 AF--SPDGRLLASGSADGTVRLWDLAtgellrTLTGHSG------------GVNSVAFsPDGKL--LASGSDDGTVRlwd 316
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1809665845 452 ---TACRHGskagisemFEGHQGPITgihchaavgAVDFS---HLFVTSSFDWTVKLWTTKNNKPLYSFEDNADYVYDVM 525
Cdd:COG2319   317 latGKLLRT--------LTGHTGAVR---------SVAFSpdgKTLASGSDDGTVRLWDLATGELLRTLTGHTGAVTSVA 379
                         250       260
                  ....*....|....*....|....*
gi 1809665845 526 WSPTHPALfACVDGMGRLDLWNLNN 550
Cdd:COG2319   380 FSPDGRTL-ASGSADGTVRLWDLAT 403
PLN00181 PLN00181
protein SPA1-RELATED; Provisional
493-599 1.08e-03

protein SPA1-RELATED; Provisional


Pssm-ID: 177776 [Multi-domain]  Cd Length: 793  Bit Score: 42.00  E-value: 1.08e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1809665845 493 TSSFDWTVKLWTTKNNKPLYSFEDNADYVYDVMWSPTHPALFACVDGMGRLDLWNLNNDTEVPTasISVEGNPALNRVRw 572
Cdd:PLN00181  550 SSNFEGVVQVWDVARSQLVTEMKEHEKRVWSIDYSSADPTLLASGSDDGSVKLWSINQGVSIGT--IKTKANICCVQFP- 626
                          90       100
                  ....*....|....*....|....*..
gi 1809665845 573 THSGREIAVGDSEGQIVIYDVGEIAVP 599
Cdd:PLN00181  627 SESGRSLAFGSADHKVYYYDLRNPKLP 653
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
466-503 2.51e-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: 36.14  E-value: 2.51e-03
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 1809665845  466 FEGHQGPITGIHCHaavgavDFSHLFVTSSFDWTVKLW 503
Cdd:smart00320   8 LKGHTGPVTSVAFS------PDGKYLASGSDDGTIKLW 39
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH