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Conserved domains on  [gi|971825952|ref|NP_001305320|]
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U3 small nucleolar RNA-associated protein 4 homolog isoform 2 [Homo sapiens]

Protein Classification

WD40 repeat domain-containing protein( domain architecture ID 11455410)

WD40 repeat domain-containing protein similar to 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
PubMed:  10322433|8090199
SCOP:  4002744

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
WD40 COG2319
WD40 repeat [General function prediction only];
19-467 8.93e-26

WD40 repeat [General function prediction only];


:

Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 110.00  E-value: 8.93e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971825952  19 GPIWSMAASPSGSQLLVGCEDGSVKLFQITPDKIQfeRNFDRQKSRILSLSWHPSGTHIAAGSIDY-ISVFDVKSGSAVH 97
Cdd:COG2319   79 AAVLSVAFSPDGRLLASASADGTVRLWDLATGLLL--RTLTGHTGAVRSVAFSPDGKTLASGSADGtVRLWDLATGKLLR 156

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971825952  98 KMIVDRQYmgvskrkciVWGVAFLSDG-TIISVDSAGKVQFWDSATGTLVKSHLIANADVQSIAVADQEDSFVVGTAEGT 176
Cdd:COG2319  157 TLTGHSGA---------VTSVAFSPDGkLLASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKLLASGSADGT 227

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971825952 177 VfhfQLVPVTSNssekQWVRTkpFQHHTHDVRTVAHSP--TALISGGTDthlvfrplmekvevknydaalrkitfphrcl 254
Cdd:COG2319  228 V---RLWDLATG----KLLRT--LTGHSGSVRSVAFSPdgRLLASGSAD------------------------------- 267

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971825952 255 iscskkrqlllfqfaHHLELWRlgstVATGKNGDTLplsknadhllhlktKGPENIICScispcgswiaystvsrfflyr 334
Cdd:COG2319  268 ---------------GTVRLWD----LATGELLRTL--------------TGHSGGVNS--------------------- 293

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971825952 335 lnyehdnislkrvskmpaflrsalqILFSEDSTKLFVASNQGALHIVQLSGGsfKHLHAFQPQSGTVEAmclLAVSPDGN 414
Cdd:COG2319  294 -------------------------VAFSPDGKLLASGSDDGTVRLWDLATG--KLLRTLTGHTGAVRS---VAFSPDGK 343

                        410       420       430       440       450
                 ....*....|....*....|....*....|....*....|....*....|...
gi 971825952 415 WLAASGTSAGVHVYNVKQLKLHCTVPAYNFPVTAMAIAPNTNNLVIAHSDQQV 467
Cdd:COG2319  344 TLASGSDDGTVRLWDLATGELLRTLTGHTGAVTSVAFSPDGRTLASGSADGTV 396
 
Name Accession Description Interval E-value
WD40 COG2319
WD40 repeat [General function prediction only];
19-467 8.93e-26

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 110.00  E-value: 8.93e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971825952  19 GPIWSMAASPSGSQLLVGCEDGSVKLFQITPDKIQfeRNFDRQKSRILSLSWHPSGTHIAAGSIDY-ISVFDVKSGSAVH 97
Cdd:COG2319   79 AAVLSVAFSPDGRLLASASADGTVRLWDLATGLLL--RTLTGHTGAVRSVAFSPDGKTLASGSADGtVRLWDLATGKLLR 156

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971825952  98 KMIVDRQYmgvskrkciVWGVAFLSDG-TIISVDSAGKVQFWDSATGTLVKSHLIANADVQSIAVADQEDSFVVGTAEGT 176
Cdd:COG2319  157 TLTGHSGA---------VTSVAFSPDGkLLASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKLLASGSADGT 227

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971825952 177 VfhfQLVPVTSNssekQWVRTkpFQHHTHDVRTVAHSP--TALISGGTDthlvfrplmekvevknydaalrkitfphrcl 254
Cdd:COG2319  228 V---RLWDLATG----KLLRT--LTGHSGSVRSVAFSPdgRLLASGSAD------------------------------- 267

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971825952 255 iscskkrqlllfqfaHHLELWRlgstVATGKNGDTLplsknadhllhlktKGPENIICScispcgswiaystvsrfflyr 334
Cdd:COG2319  268 ---------------GTVRLWD----LATGELLRTL--------------TGHSGGVNS--------------------- 293

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971825952 335 lnyehdnislkrvskmpaflrsalqILFSEDSTKLFVASNQGALHIVQLSGGsfKHLHAFQPQSGTVEAmclLAVSPDGN 414
Cdd:COG2319  294 -------------------------VAFSPDGKLLASGSDDGTVRLWDLATG--KLLRTLTGHTGAVRS---VAFSPDGK 343

                        410       420       430       440       450
                 ....*....|....*....|....*....|....*....|....*....|...
gi 971825952 415 WLAASGTSAGVHVYNVKQLKLHCTVPAYNFPVTAMAIAPNTNNLVIAHSDQQV 467
Cdd:COG2319  344 TLASGSDDGTVRLWDLATGELLRTLTGHTGAVTSVAFSPDGRTLASGSADGTV 396
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 3-223 7.51e-17

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: 81.23  E-value: 7.51e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971825952   3 YDLQALNIKYAMDAFGGPIWSMAASPSGsQLLVGC-EDGSVKLFQITPDKIQFErnFDRQKSRILSLSWHPSGTHIAAGS 81
Cdd:cd00200   78 WDLETGECVRTLTGHTSYVSSVAFSPDG-RILSSSsRDKTIKVWDVETGKCLTT--LRGHTDWVNSVAFSPDGTFVASSS 154

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971825952  82 ID-YISVFDVKSGSAVHkmivdrQYMGvskRKCIVWGVAFLSDG-TIISVDSAGKVQFWDSATGTLVKSHLIANADVQSI 159
Cdd:cd00200  155 QDgTIKLWDLRTGKCVA------TLTG---HTGEVNSVAFSPDGeKLLSSSSDGTIKLWDLSTGKCLGTLRGHENGVNSV 225

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 971825952 160 AVADQEDSFVVGTAEGTVFHFQLvpvtsnsseKQWVRTKPFQHHTHDVRTVAHSPTA--LISGGTD 223
Cdd:cd00200  226 AFSPDGYLLASGSEDGTIRVWDL---------RTGECVQTLSGHTNSVTSLAWSPDGkrLASGSAD 282
ANAPC4_WD40 pfam12894
Anaphase-promoting complex subunit 4 WD40 domain; Apc4 contains an N-terminal propeller-shaped ...
 24-119 2.32e-06

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


Pssm-ID: 403945 [Multi-domain]  Cd Length: 91  Bit Score: 46.12  E-value: 2.32e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971825952   24 MAASPSGSQLLVGCEDGSVKLFQITPDKIqFERNFDRQKSRILSLSWHPSGTHIAAGSID-YISVFDVKSGSAVHKMIVd 102
Cdd:pfam12894   1 MSWCPTMDLIALATEDGELLLHRLNWQRV-WTLSPDKEDLEVTSLAWRPDGKLLAVGYSDgTVRLLDAENGKIVHHFSA- 78

                          90
                  ....*....|....*..
gi 971825952  103 rqymGVSKRKCIVWGVA 119
Cdd:pfam12894  79 ----GSDLITCLGWGEN 91
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 19-45 4.92e-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: 34.98  E-value: 4.92e-03
                           10        20
                   ....*....|....*....|....*..
gi 971825952    19 GPIWSMAASPSGSQLLVGCEDGSVKLF 45
Cdd:smart00320  13 GPVTSVAFSPDGKYLASGSDDGTIKLW 39
 
Name Accession Description Interval E-value
WD40 COG2319
WD40 repeat [General function prediction only];
19-467 8.93e-26

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 110.00  E-value: 8.93e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971825952  19 GPIWSMAASPSGSQLLVGCEDGSVKLFQITPDKIQfeRNFDRQKSRILSLSWHPSGTHIAAGSIDY-ISVFDVKSGSAVH 97
Cdd:COG2319   79 AAVLSVAFSPDGRLLASASADGTVRLWDLATGLLL--RTLTGHTGAVRSVAFSPDGKTLASGSADGtVRLWDLATGKLLR 156

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971825952  98 KMIVDRQYmgvskrkciVWGVAFLSDG-TIISVDSAGKVQFWDSATGTLVKSHLIANADVQSIAVADQEDSFVVGTAEGT 176
Cdd:COG2319  157 TLTGHSGA---------VTSVAFSPDGkLLASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKLLASGSADGT 227

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971825952 177 VfhfQLVPVTSNssekQWVRTkpFQHHTHDVRTVAHSP--TALISGGTDthlvfrplmekvevknydaalrkitfphrcl 254
Cdd:COG2319  228 V---RLWDLATG----KLLRT--LTGHSGSVRSVAFSPdgRLLASGSAD------------------------------- 267

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971825952 255 iscskkrqlllfqfaHHLELWRlgstVATGKNGDTLplsknadhllhlktKGPENIICScispcgswiaystvsrfflyr 334
Cdd:COG2319  268 ---------------GTVRLWD----LATGELLRTL--------------TGHSGGVNS--------------------- 293

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971825952 335 lnyehdnislkrvskmpaflrsalqILFSEDSTKLFVASNQGALHIVQLSGGsfKHLHAFQPQSGTVEAmclLAVSPDGN 414
Cdd:COG2319  294 -------------------------VAFSPDGKLLASGSDDGTVRLWDLATG--KLLRTLTGHTGAVRS---VAFSPDGK 343

                        410       420       430       440       450
                 ....*....|....*....|....*....|....*....|....*....|...
gi 971825952 415 WLAASGTSAGVHVYNVKQLKLHCTVPAYNFPVTAMAIAPNTNNLVIAHSDQQV 467
Cdd:COG2319  344 TLASGSDDGTVRLWDLATGELLRTLTGHTGAVTSVAFSPDGRTLASGSADGTV 396
WD40 COG2319
WD40 repeat [General function prediction only];
3-323 2.81e-24

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 105.38  E-value: 2.81e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971825952   3 YDLQALNIKYAMDAFGGPIWSMAASPSGSQLLVGCEDGSVKLFQITPDKIQfeRNFDRQKSRILSLSWHPSGTHIAAGSI 82
Cdd:COG2319  105 WDLATGLLLRTLTGHTGAVRSVAFSPDGKTLASGSADGTVRLWDLATGKLL--RTLTGHSGAVTSVAFSPDGKLLASGSD 182

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971825952  83 DY-ISVFDVKSGSAVHKMIVDRQYmgvskrkciVWGVAFLSDG-TIISVDSAGKVQFWDSATGTLVKSHLIANADVQSIA 160
Cdd:COG2319  183 DGtVRLWDLATGKLLRTLTGHTGA---------VRSVAFSPDGkLLASGSADGTVRLWDLATGKLLRTLTGHSGSVRSVA 253

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971825952 161 VADQEDSFVVGTAEGTVFHFQLvpvtsnsSEKQWVRTkpFQHHTHDVRTVAHSP--TALISGGTDTHLvfrplmeKVevk 238
Cdd:COG2319  254 FSPDGRLLASGSADGTVRLWDL-------ATGELLRT--LTGHSGGVNSVAFSPdgKLLASGSDDGTV-------RL--- 314

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971825952 239 nYDAALRKITFPHRcliscskkrqlllfqfAHHLELWRL-----GSTVATGKNGDTLPLSKNADHLLHLKTKGPENIICS 313
Cdd:COG2319  315 -WDLATGKLLRTLT----------------GHTGAVRSVafspdGKTLASGSDDGTVRLWDLATGELLRTLTGHTGAVTS 377

                        330
                 ....*....|.
gi 971825952 314 -CISPCGSWIA 323
Cdd:COG2319  378 vAFSPDGRTLA 388
WD40 COG2319
WD40 repeat [General function prediction only];
3-177 1.42e-20

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 94.21  E-value: 1.42e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971825952   3 YDLQALNIKYAMDAFGGPIWSMAASPSGSQLLVGCEDGSVKLFQITPDKIQfeRNFDRQKSRILSLSWHPSGTHIAAGSI 82
Cdd:COG2319  231 WDLATGKLLRTLTGHSGSVRSVAFSPDGRLLASGSADGTVRLWDLATGELL--RTLTGHSGGVNSVAFSPDGKLLASGSD 308

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971825952  83 DY-ISVFDVKSGSAVHkmivdrqymGVSKRKCIVWGVAFLSDG-TIISVDSAGKVQFWDSATGTLVKSHLIANADVQSIA 160
Cdd:COG2319  309 DGtVRLWDLATGKLLR---------TLTGHTGAVRSVAFSPDGkTLASGSDDGTVRLWDLATGELLRTLTGHTGAVTSVA 379

                        170
                 ....*....|....*..
gi 971825952 161 VADQEDSFVVGTAEGTV 177
Cdd:COG2319  380 FSPDGRTLASGSADGTV 396
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 3-223 7.51e-17

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: 81.23  E-value: 7.51e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971825952   3 YDLQALNIKYAMDAFGGPIWSMAASPSGsQLLVGC-EDGSVKLFQITPDKIQFErnFDRQKSRILSLSWHPSGTHIAAGS 81
Cdd:cd00200   78 WDLETGECVRTLTGHTSYVSSVAFSPDG-RILSSSsRDKTIKVWDVETGKCLTT--LRGHTDWVNSVAFSPDGTFVASSS 154

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971825952  82 ID-YISVFDVKSGSAVHkmivdrQYMGvskRKCIVWGVAFLSDG-TIISVDSAGKVQFWDSATGTLVKSHLIANADVQSI 159
Cdd:cd00200  155 QDgTIKLWDLRTGKCVA------TLTG---HTGEVNSVAFSPDGeKLLSSSSDGTIKLWDLSTGKCLGTLRGHENGVNSV 225

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 971825952 160 AVADQEDSFVVGTAEGTVFHFQLvpvtsnsseKQWVRTKPFQHHTHDVRTVAHSPTA--LISGGTD 223
Cdd:cd00200  226 AFSPDGYLLASGSEDGTIRVWDL---------RTGECVQTLSGHTNSVTSLAWSPDGkrLASGSAD 282
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 19-226 1.72e-15

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: 77.38  E-value: 1.72e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971825952  19 GPIWSMAASPSGSQLLVGCEDGSVKLFQITPDkiQFERNFDRQKSRILSLSWHPSGTHIAAGSIDY-ISVFDVKSGSAVH 97
Cdd:cd00200   10 GGVTCVAFSPDGKLLATGSGDGTIKVWDLETG--ELLRTLKGHTGPVRDVAASADGTYLASGSSDKtIRLWDLETGECVR 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971825952  98 KMIVDRQYmgvskrkciVWGVAFLSDGTIISVDSA-GKVQFWDSATGTLVKSHLIANADVQSIAVaDQEDSFVV-GTAEG 175
Cdd:cd00200   88 TLTGHTSY---------VSSVAFSPDGRILSSSSRdKTIKVWDVETGKCLTTLRGHTDWVNSVAF-SPDGTFVAsSSQDG 157

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 971825952 176 TVFHFqlvpvtsNSSEKQWVRTkpFQHHTHDVRTVAHSPTA--LISGGTDTHL 226
Cdd:cd00200  158 TIKLW-------DLRTGKCVAT--LTGHTGEVNSVAFSPDGekLLSSSSDGTI 201
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 19-228 4.29e-15

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: 76.22  E-value: 4.29e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971825952  19 GPIWSMAASPSGSQLLVGCEDGSVKLFQItpDKIQFERNFDRQKSRILSLSWHPSGTHIAAGSIDY-ISVFDVKSGSAVH 97
Cdd:cd00200   52 GPVRDVAASADGTYLASGSSDKTIRLWDL--ETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKtIKVWDVETGKCLT 129

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971825952  98 KMivdrqymgvSKRKCIVWGVAFLSDGTIISVDSA-GKVQFWDSATGTLVKSHLIANADVQSIAVADQEDSFVVGTAEGT 176
Cdd:cd00200  130 TL---------RGHTDWVNSVAFSPDGTFVASSSQdGTIKLWDLRTGKCVATLTGHTGEVNSVAFSPDGEKLLSSSSDGT 200

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 971825952 177 VFHFQLvpvtsnsSEKQWVRTkpFQHHTHDVRTVAHSPTA--LISGGTDTHLVF 228
Cdd:cd00200  201 IKLWDL-------STGKCLGT--LRGHENGVNSVAFSPDGylLASGSEDGTIRV 245
WD40 COG2319
WD40 repeat [General function prediction only];
3-142 4.32e-15

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 77.64  E-value: 4.32e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971825952   3 YDLQALNIKYAMDAFGGPIWSMAASPSGSQLLVGCEDGSVKLFQITPDKIQfeRNFDRQKSRILSLSWHPSGTHIAAGSI 82
Cdd:COG2319  273 WDLATGELLRTLTGHSGGVNSVAFSPDGKLLASGSDDGTVRLWDLATGKLL--RTLTGHTGAVRSVAFSPDGKTLASGSD 350

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 971825952  83 D-YISVFDVKSGSAVHKmivdrqYMGVSKRkciVWGVAFLSDG-TIISVDSAGKVQFWDSAT 142
Cdd:COG2319  351 DgTVRLWDLATGELLRT------LTGHTGA---VTSVAFSPDGrTLASGSADGTVRLWDLAT 403
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 3-139 1.02e-09

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: 60.04  E-value: 1.02e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971825952   3 YDLQALNIKYAMDAFGGPIWSMAASPSGSQLLVGCEDGSVKLFQItpDKIQFERNFDRQKSRILSLSWHPSGTHIAAGSI 82
Cdd:cd00200  162 WDLRTGKCVATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDL--STGKCLGTLRGHENGVNSVAFSPDGYLLASGSE 239

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 971825952  83 DY-ISVFDVKSGSaVHKMIVdrqymGVSKRkciVWGVAFLSDG-TIISVDSAGKVQFWD 139
Cdd:cd00200  240 DGtIRVWDLRTGE-CVQTLS-----GHTNS---VTSLAWSPDGkRLASGSADGTIRIWD 289
ANAPC4_WD40 pfam12894
Anaphase-promoting complex subunit 4 WD40 domain; Apc4 contains an N-terminal propeller-shaped ...
 24-119 2.32e-06

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


Pssm-ID: 403945 [Multi-domain]  Cd Length: 91  Bit Score: 46.12  E-value: 2.32e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971825952   24 MAASPSGSQLLVGCEDGSVKLFQITPDKIqFERNFDRQKSRILSLSWHPSGTHIAAGSID-YISVFDVKSGSAVHKMIVd 102
Cdd:pfam12894   1 MSWCPTMDLIALATEDGELLLHRLNWQRV-WTLSPDKEDLEVTSLAWRPDGKLLAVGYSDgTVRLLDAENGKIVHHFSA- 78

                          90
                  ....*....|....*..
gi 971825952  103 rqymGVSKRKCIVWGVA 119
Cdd:pfam12894  79 ----GSDLITCLGWGEN 91
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 339-464 1.40e-04

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: 44.25  E-value: 1.40e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971825952 339 HDNISLKRVSKMPAFLRSALQILFSEDSTKLFVASNQGALHIVQLSGGSFKHLhaFQPQSGTVEAMCllaVSPDGNWLAA 418
Cdd:cd00200  120 WDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDLRTGKCVAT--LTGHTGEVNSVA---FSPDGEKLLS 194

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 971825952 419 SGTSAGVHVYNVKQLKLHCTVPAYNFPVTAMAIAPNTNNLVIAHSD 464
Cdd:cd00200  195 SSSDGTIKLWDLSTGKCLGTLRGHENGVNSVAFSPDGYLLASGSED 240
YncE COG3391
DNA-binding beta-propeller fold protein YncE [General function prediction only];
351-461 5.19e-04

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


Pssm-ID: 442618 [Multi-domain]  Cd Length: 237  Bit Score: 41.99  E-value: 5.19e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971825952 351 PAFLRSALQILFSEDSTKLFVA-SNQGALHIVQLSGGsfKHLHAFQPQSGTVEamclLAVSPDGNWL-AASGTSAGVHVY 428
Cdd:COG3391   64 AAAVADADGADAGADGRRLYVAnSGSGRVSVIDLATG--KVVATIPVGGGPRG----LAVDPDGGRLyVADSGNGRVSVI 137

                         90       100       110
                 ....*....|....*....|....*....|...
gi 971825952 429 NVKQLKLHCTVPAYNFPvTAMAIAPNTNNLVIA 461
Cdd:COG3391  138 DTATGKVVATIPVGAGP-HGIAVDPDGKRLYVA 169
TolB COG0823
Periplasmic component TolB of the Tol biopolymer transport system [Intracellular trafficking, ...
 304-424 4.00e-03

Periplasmic component TolB of the Tol biopolymer transport system [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 440585 [Multi-domain]  Cd Length: 158  Bit Score: 38.50  E-value: 4.00e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971825952 304 TKGPENIICSCISPCGSWIAYSTVS--RFFLYRLNYEHDNIslKRVSKMPAFLRSALqilFSEDSTKLFVASNQG---AL 378
Cdd:COG0823   27 TNSPGIDTSPAWSPDGRRIAFTSDRggGPQIYVVDADGGEP--RRLTFGGGYNASPS---WSPDGKRLAFVSRSDgrfDI 101

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 971825952 379 HIVQLSGGSFKHL--HAFQPqsgtveamcllAVSPDGNWLAASGTSAG 424
Cdd:COG0823  102 YVLDLDGGAPRRLtdGPGSP-----------SWSPDGRRIVFSSDRGG 138
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 362-507 4.87e-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: 4.87e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971825952 362 FSEDSTKLFVASNQGALHIVQLSGGSFkhLHAFQPQSGTVEAmclLAVSPDGNWLAASGTSAGVHVYNVKQLKLHCTVPA 441
Cdd:cd00200   17 FSPDGKLLATGSGDGTIKVWDLETGEL--LRTLKGHTGPVRD---VAASADGTYLASGSSDKTIRLWDLETGECVRTLTG 91

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 971825952 442 YNFPVTAMAIAPNTNNLVIAHSDQQVFEYSIPDKQYtdwsrtVQKQGFHHLWlqrdtpITHISFHP 507
Cdd:cd00200   92 HTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKC------LTTLRGHTDW------VNSVAFSP 145
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 19-45 4.92e-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: 34.98  E-value: 4.92e-03
                           10        20
                   ....*....|....*....|....*..
gi 971825952    19 GPIWSMAASPSGSQLLVGCEDGSVKLF 45
Cdd:smart00320  13 GPVTSVAFSPDGKYLASGSDDGTIKLW 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.
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