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Conserved domains on  [gi|564358107|ref|XP_006240968|]
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WD repeat-containing protein 18 isoform X3 [Rattus norvegicus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Periplasmic_Binding_Protein_type1 super family cl10011
Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This ...
 135-353 2.77e-36

Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins, the ligands are monosaccharides, including lactose, ribose, fructose, xylose, arabinose, galactose/glucose and other sugars, with a few exceptions. Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has six beta strands while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold.


The actual alignment was detected with superfamily member cd06377:

Pssm-ID: 471960 [Multi-domain]  Cd Length: 373  Bit Score: 134.87  E-value: 2.77e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564358107 135 VLFDMGITSVTMDLAEHHIFCGGSDGSIFQVDLCSRPGPREQSFQPEQN-TGKVFKGHRNQVTCLSVSTDGSILLSGSHD 213
Cdd:cd06377    1 VLKRIGHTVRLGALLPHPWFTRGRAGAALAVDLPTGLLPYNLSLEVVVAaPWARDPASLTRSLCHSVVVQGVAALLAFPQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564358107 214 ESVRLwdvkSKQCVRTVPLKGPVTNAAITLAPPSmlnpefRPSLPLPHFNKHLLGAEHGDEAQGGGLRLQLGLHlqgkEP 293
Cdd:cd06377   81 SRGEL----LQLDFLSAALEIPVVSILRREFPRP------LRSQNPFHLQLDLQSSLESLEDVLVSLLQANSWE----DV 146

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 564358107 294 SYLERLEQLQAALSGYLEKNmlgSQMLPVRVFELEEE-----VRSLRKINRDLFDFSTRIITRPS 353
Cdd:cd06377  147 SLLLCQPWDPTSFLLLWQNN---SQFHLGTVLNLSVLdesdlQRSLQQHLESLKDPSPAIVMFGC 208
WD40 COG2319
WD40 repeat [General function prediction only];
4-242 3.60e-29

WD40 repeat [General function prediction only];


:

Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 116.16  E-value: 3.60e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564358107   4 GPVTCLTTAPNGLYVL-AGIAESIYLWEVSTGNLLVILSRHYQDVSCLKFTGDGSHFVSAGKDCLVLAWSLcsvlqADPS 82
Cdd:COG2319  163 GAVTSVAFSPDGKLLAsGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKLLASGSADGTVRLWDL-----ATGK 237

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564358107  83 RIlaprHVWSQHTLPITDLHCGFGGPmaRVATASLDQTMKLWAISSGDLLLSVLFDMG-ITSVTMDLAEHHIFCGGSDGS 161
Cdd:COG2319  238 LL----RTLTGHSGSVRSVAFSPDGR--LLASGSADGTVRLWDLATGELLRTLTGHSGgVNSVAFSPDGKLLASGSDDGT 311

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564358107 162 IFQVDLcsrpgpreqsfqpeqNTGKV---FKGHRNQVTCLSVSTDGSILLSGSHDESVRLWDVKSKQCVRTVP-LKGPVT 237
Cdd:COG2319  312 VRLWDL---------------ATGKLlrtLTGHTGAVRSVAFSPDGKTLASGSDDGTVRLWDLATGELLRTLTgHTGAVT 376


                 ....*
gi 564358107 238 NAAIT 242
Cdd:COG2319  377 SVAFS 381
 
Name Accession Description Interval E-value
PBP1_iGluR_NMDA_NR3 cd06377
N-terminal leucine-isoleucine-valine-binding protein (LIVBP)-like domain of the NR3 subunit of ...
 135-353 2.77e-36

N-terminal leucine-isoleucine-valine-binding protein (LIVBP)-like domain of the NR3 subunit of NMDA receptor family; N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the NR3 subunit of NMDA receptor family. The ionotropic N-methyl-D-asparate (NMDA) subtype of glutamate receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer composed of two NR1 and two NR2 (A, B, C, and D) or of NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. Among NMDA receptor subtypes, the NR2B subunit containing receptors appear particularly important for pain perception; thus NR2B-selective antagonists may be useful in the treatment of chronic pain.


Pssm-ID: 380600 [Multi-domain]  Cd Length: 373  Bit Score: 134.87  E-value: 2.77e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564358107 135 VLFDMGITSVTMDLAEHHIFCGGSDGSIFQVDLCSRPGPREQSFQPEQN-TGKVFKGHRNQVTCLSVSTDGSILLSGSHD 213
Cdd:cd06377    1 VLKRIGHTVRLGALLPHPWFTRGRAGAALAVDLPTGLLPYNLSLEVVVAaPWARDPASLTRSLCHSVVVQGVAALLAFPQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564358107 214 ESVRLwdvkSKQCVRTVPLKGPVTNAAITLAPPSmlnpefRPSLPLPHFNKHLLGAEHGDEAQGGGLRLQLGLHlqgkEP 293
Cdd:cd06377   81 SRGEL----LQLDFLSAALEIPVVSILRREFPRP------LRSQNPFHLQLDLQSSLESLEDVLVSLLQANSWE----DV 146

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 564358107 294 SYLERLEQLQAALSGYLEKNmlgSQMLPVRVFELEEE-----VRSLRKINRDLFDFSTRIITRPS 353
Cdd:cd06377  147 SLLLCQPWDPTSFLLLWQNN---SQFHLGTVLNLSVLdesdlQRSLQQHLESLKDPSPAIVMFGC 208
WD40 COG2319
WD40 repeat [General function prediction only];
4-242 3.60e-29

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 116.16  E-value: 3.60e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564358107   4 GPVTCLTTAPNGLYVL-AGIAESIYLWEVSTGNLLVILSRHYQDVSCLKFTGDGSHFVSAGKDCLVLAWSLcsvlqADPS 82
Cdd:COG2319  163 GAVTSVAFSPDGKLLAsGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKLLASGSADGTVRLWDL-----ATGK 237

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564358107  83 RIlaprHVWSQHTLPITDLHCGFGGPmaRVATASLDQTMKLWAISSGDLLLSVLFDMG-ITSVTMDLAEHHIFCGGSDGS 161
Cdd:COG2319  238 LL----RTLTGHSGSVRSVAFSPDGR--LLASGSADGTVRLWDLATGELLRTLTGHSGgVNSVAFSPDGKLLASGSDDGT 311

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564358107 162 IFQVDLcsrpgpreqsfqpeqNTGKV---FKGHRNQVTCLSVSTDGSILLSGSHDESVRLWDVKSKQCVRTVP-LKGPVT 237
Cdd:COG2319  312 VRLWDL---------------ATGKLlrtLTGHTGAVRSVAFSPDGKTLASGSDDGTVRLWDLATGELLRTLTgHTGAVT 376


                 ....*
gi 564358107 238 NAAIT 242
Cdd:COG2319  377 SVAFS 381
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 4-244 3.65e-27

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: 108.58  E-value: 3.65e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564358107   4 GPVTCLTTAPNGLYVL-AGIAESIYLWEVSTGNLLVILSRHYQDVSCLKFTGDGSHFVSAGKDCLVLAWSLcsvlqadps 82
Cdd:cd00200   52 GPVRDVAASADGTYLAsGSSDKTIRLWDLETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDV--------- 122

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564358107  83 RILAPRHVWSQHTLPITdlHCGFGGPMARVATASLDQTMKLWAISSGDLLLS-VLFDMGITSVTMDLAEHHIFCGGSDGS 161
Cdd:cd00200  123 ETGKCLTTLRGHTDWVN--SVAFSPDGTFVASSSQDGTIKLWDLRTGKCVATlTGHTGEVNSVAFSPDGEKLLSSSSDGT 200

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564358107 162 IFQVDLcsrpgpreqsfqPEQNTGKVFKGHRNQVTCLSVSTDGSILLSGSHDESVRLWDVKSKQCVRTvpLKGPvTNAAI 241
Cdd:cd00200  201 IKLWDL------------STGKCLGTLRGHENGVNSVAFSPDGYLLASGSEDGTIRVWDLRTGECVQT--LSGH-TNSVT 265


                 ...
gi 564358107 242 TLA 244
Cdd:cd00200  266 SLA 268
WD40_alt pfam14077
Alternative WD40 repeat motif; WD repeats are short subdomains of about 40 amino acids and ...
 306-352 1.36e-22

Alternative WD40 repeat motif; WD repeats are short subdomains of about 40 amino acids and fold into 4 antiparallel beta hairpins. This domain here has been detected on the C-terminus of WD repeat-containing protein 18 during target selection by the Joint Center for Structural Genomics.


Pssm-ID: 433698  Cd Length: 48  Bit Score: 89.07  E-value: 1.36e-22
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 564358107  306 LSGYLEKNMLGSQ-MLPVRVFELEEEVRSLRKINRDLFDFSTRIITRP 352
Cdd:pfam14077   1 MCSTTDKNVLGDQeQLKVRVSELEEEVRTLRKINKDLFDFSTRIITKP 48
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 186-220 6.21e-09

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


Pssm-ID: 197651 [Multi-domain]  Cd Length: 40  Bit Score: 51.16  E-value: 6.21e-09
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 564358107   186 KVFKGHRNQVTCLSVSTDGSILLSGSHDESVRLWD 220
Cdd:smart00320   6 KTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 33-72 7.81e-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: 39.60  E-value: 7.81e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 564358107    33 TGNLLVILSRHYQDVSCLKFTGDGSHFVSAGKDCLVLAWS 72
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 pfam00400
WD domain, G-beta repeat;
34-72 1.43e-03

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 35.78  E-value: 1.43e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 564358107   34 GNLLVILSRHYQDVSCLKFTGDGSHFVSAGKDCLVLAWS 72
Cdd:pfam00400   1 GKLLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
 
Name Accession Description Interval E-value
PBP1_iGluR_NMDA_NR3 cd06377
N-terminal leucine-isoleucine-valine-binding protein (LIVBP)-like domain of the NR3 subunit of ...
 135-353 2.77e-36

N-terminal leucine-isoleucine-valine-binding protein (LIVBP)-like domain of the NR3 subunit of NMDA receptor family; N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the NR3 subunit of NMDA receptor family. The ionotropic N-methyl-D-asparate (NMDA) subtype of glutamate receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer composed of two NR1 and two NR2 (A, B, C, and D) or of NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. Among NMDA receptor subtypes, the NR2B subunit containing receptors appear particularly important for pain perception; thus NR2B-selective antagonists may be useful in the treatment of chronic pain.


Pssm-ID: 380600 [Multi-domain]  Cd Length: 373  Bit Score: 134.87  E-value: 2.77e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564358107 135 VLFDMGITSVTMDLAEHHIFCGGSDGSIFQVDLCSRPGPREQSFQPEQN-TGKVFKGHRNQVTCLSVSTDGSILLSGSHD 213
Cdd:cd06377    1 VLKRIGHTVRLGALLPHPWFTRGRAGAALAVDLPTGLLPYNLSLEVVVAaPWARDPASLTRSLCHSVVVQGVAALLAFPQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564358107 214 ESVRLwdvkSKQCVRTVPLKGPVTNAAITLAPPSmlnpefRPSLPLPHFNKHLLGAEHGDEAQGGGLRLQLGLHlqgkEP 293
Cdd:cd06377   81 SRGEL----LQLDFLSAALEIPVVSILRREFPRP------LRSQNPFHLQLDLQSSLESLEDVLVSLLQANSWE----DV 146

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 564358107 294 SYLERLEQLQAALSGYLEKNmlgSQMLPVRVFELEEE-----VRSLRKINRDLFDFSTRIITRPS 353
Cdd:cd06377  147 SLLLCQPWDPTSFLLLWQNN---SQFHLGTVLNLSVLdesdlQRSLQQHLESLKDPSPAIVMFGC 208
WD40 COG2319
WD40 repeat [General function prediction only];
4-242 3.60e-29

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 116.16  E-value: 3.60e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564358107   4 GPVTCLTTAPNGLYVL-AGIAESIYLWEVSTGNLLVILSRHYQDVSCLKFTGDGSHFVSAGKDCLVLAWSLcsvlqADPS 82
Cdd:COG2319  163 GAVTSVAFSPDGKLLAsGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKLLASGSADGTVRLWDL-----ATGK 237

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564358107  83 RIlaprHVWSQHTLPITDLHCGFGGPmaRVATASLDQTMKLWAISSGDLLLSVLFDMG-ITSVTMDLAEHHIFCGGSDGS 161
Cdd:COG2319  238 LL----RTLTGHSGSVRSVAFSPDGR--LLASGSADGTVRLWDLATGELLRTLTGHSGgVNSVAFSPDGKLLASGSDDGT 311

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564358107 162 IFQVDLcsrpgpreqsfqpeqNTGKV---FKGHRNQVTCLSVSTDGSILLSGSHDESVRLWDVKSKQCVRTVP-LKGPVT 237
Cdd:COG2319  312 VRLWDL---------------ATGKLlrtLTGHTGAVRSVAFSPDGKTLASGSDDGTVRLWDLATGELLRTLTgHTGAVT 376


                 ....*
gi 564358107 238 NAAIT 242
Cdd:COG2319  377 SVAFS 381
WD40 COG2319
WD40 repeat [General function prediction only];
4-242 1.90e-27

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 111.54  E-value: 1.90e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564358107   4 GPVTCLTTAPNGLYVLAGIAE-SIYLWEVSTGNLLVILSRHYQDVSCLKFTGDGSHFVSAGKDCLVLAWSLCSvlqadps 82
Cdd:COG2319   79 AAVLSVAFSPDGRLLASASADgTVRLWDLATGLLLRTLTGHTGAVRSVAFSPDGKTLASGSADGTVRLWDLAT------- 151

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564358107  83 riLAPRHVWSQHTLPITDLHcgF---GgpmARVATASLDQTMKLWAISSGDLLLSVLFDMG-ITSVTMDLAEHHIFCGGS 158
Cdd:COG2319  152 --GKLLRTLTGHSGAVTSVA--FspdG---KLLASGSDDGTVRLWDLATGKLLRTLTGHTGaVRSVAFSPDGKLLASGSA 224

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564358107 159 DGSIFQVDLcsrpgpreqsfqpeqNTGK---VFKGHRNQVTCLSVSTDGSILLSGSHDESVRLWDVKSKQCVRTVP-LKG 234
Cdd:COG2319  225 DGTVRLWDL---------------ATGKllrTLTGHSGSVRSVAFSPDGRLLASGSADGTVRLWDLATGELLRTLTgHSG 289


                 ....*...
gi 564358107 235 PVTNAAIT 242
Cdd:COG2319  290 GVNSVAFS 297
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 4-244 3.65e-27

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: 108.58  E-value: 3.65e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564358107   4 GPVTCLTTAPNGLYVL-AGIAESIYLWEVSTGNLLVILSRHYQDVSCLKFTGDGSHFVSAGKDCLVLAWSLcsvlqadps 82
Cdd:cd00200   52 GPVRDVAASADGTYLAsGSSDKTIRLWDLETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDV--------- 122

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564358107  83 RILAPRHVWSQHTLPITdlHCGFGGPMARVATASLDQTMKLWAISSGDLLLS-VLFDMGITSVTMDLAEHHIFCGGSDGS 161
Cdd:cd00200  123 ETGKCLTTLRGHTDWVN--SVAFSPDGTFVASSSQDGTIKLWDLRTGKCVATlTGHTGEVNSVAFSPDGEKLLSSSSDGT 200

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564358107 162 IFQVDLcsrpgpreqsfqPEQNTGKVFKGHRNQVTCLSVSTDGSILLSGSHDESVRLWDVKSKQCVRTvpLKGPvTNAAI 241
Cdd:cd00200  201 IKLWDL------------STGKCLGTLRGHENGVNSVAFSPDGYLLASGSEDGTIRVWDLRTGECVQT--LSGH-TNSVT 265


                 ...
gi 564358107 242 TLA 244
Cdd:cd00200  266 SLA 268
WD40 COG2319
WD40 repeat [General function prediction only];
3-223 1.09e-25

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 106.53  E-value: 1.09e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564358107   3 PGPVTCLTTAPNGLYVLAGIAE-SIYLWEVSTGNLLVILSRHYQDVSCLKFTGDGSHFVSAGKDCLVLAWSLcsvlqaDP 81
Cdd:COG2319  204 TGAVRSVAFSPDGKLLASGSADgTVRLWDLATGKLLRTLTGHSGSVRSVAFSPDGRLLASGSADGTVRLWDL------AT 277

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564358107  82 SRILaprHVWSQHTLPITDLHCGFGGpmARVATASLDQTMKLWAISSGDLLLSVL-FDMGITSVTMDLAEHHIFCGGSDG 160
Cdd:COG2319  278 GELL---RTLTGHSGGVNSVAFSPDG--KLLASGSDDGTVRLWDLATGKLLRTLTgHTGAVRSVAFSPDGKTLASGSDDG 352

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564358107 161 SifqVDLCSRPGPREqsfqpeqntGKVFKGHRNQVTCLSVSTDGSILLSGSHDESVRLWDVKS 223
Cdd:COG2319  353 T---VRLWDLATGEL---------LRTLTGHTGAVTSVAFSPDGRTLASGSADGTVRLWDLAT 403
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 4-220 1.11e-25

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: 104.34  E-value: 1.11e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564358107   4 GPVTCLTTAPNGLYVLAGIA-ESIYLWEVSTGNLLVILSRHYQDVSCLKFTGDGSHFVSAGKDCLVLAWSLcsvlqadps 82
Cdd:cd00200   94 SYVSSVAFSPDGRILSSSSRdKTIKVWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDL--------- 164

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564358107  83 RILAPRHVWSQHTLPITdlHCGFGGPMARVATASLDQTMKLWAISSGDLLLS-VLFDMGITSVTMDLAEHHIFCGGSDGS 161
Cdd:cd00200  165 RTGKCVATLTGHTGEVN--SVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGTlRGHENGVNSVAFSPDGYLLASGSEDGT 242

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 564358107 162 IFQVDLCSRpgpreqsfqpeqNTGKVFKGHRNQVTCLSVSTDGSILLSGSHDESVRLWD 220
Cdd:cd00200  243 IRVWDLRTG------------ECVQTLSGHTNSVTSLAWSPDGKRLASGSADGTIRIWD 289
WD40_alt pfam14077
Alternative WD40 repeat motif; WD repeats are short subdomains of about 40 amino acids and ...
 306-352 1.36e-22

Alternative WD40 repeat motif; WD repeats are short subdomains of about 40 amino acids and fold into 4 antiparallel beta hairpins. This domain here has been detected on the C-terminus of WD repeat-containing protein 18 during target selection by the Joint Center for Structural Genomics.


Pssm-ID: 433698  Cd Length: 48  Bit Score: 89.07  E-value: 1.36e-22
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 564358107  306 LSGYLEKNMLGSQ-MLPVRVFELEEEVRSLRKINRDLFDFSTRIITRP 352
Cdd:pfam14077   1 MCSTTDKNVLGDQeQLKVRVSELEEEVRTLRKINKDLFDFSTRIITKP 48
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 36-229 1.25e-20

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: 90.47  E-value: 1.25e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564358107  36 LLVILSRHYQDVSCLKFTGDGSHFVSAGKDCLVLAWSLCSVlqaDPSRILaprhvwSQHTLPITDLHCGFGGPmaRVATA 115
Cdd:cd00200    1 LRRTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETG---ELLRTL------KGHTGPVRDVAASADGT--YLASG 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564358107 116 SLDQTMKLWAISSGDlLLSVL--FDMGITSVTMDLAEHHIFCGGSDGSIFQVDLcsrpgpreQSFQPEQntgkVFKGHRN 193
Cdd:cd00200   70 SSDKTIRLWDLETGE-CVRTLtgHTSYVSSVAFSPDGRILSSSSRDKTIKVWDV--------ETGKCLT----TLRGHTD 136

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 564358107 194 QVTCLSVSTDGSILLSGSHDESVRLWDVKSKQCVRT 229
Cdd:cd00200  137 WVNSVAFSPDGTFVASSSQDGTIKLWDLRTGKCVAT 172
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 186-234 5.26e-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: 56.57  E-value: 5.26e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 564358107 186 KVFKGHRNQVTCLSVSTDGSILLSGSHDESVRLWDVKSKQCVRTvpLKG 234
Cdd:cd00200    3 RTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRT--LKG 49
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 186-220 6.21e-09

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


Pssm-ID: 197651 [Multi-domain]  Cd Length: 40  Bit Score: 51.16  E-value: 6.21e-09
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 564358107   186 KVFKGHRNQVTCLSVSTDGSILLSGSHDESVRLWD 220
Cdd:smart00320   6 KTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 pfam00400
WD domain, G-beta repeat;
186-220 1.17e-08

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 50.42  E-value: 1.17e-08
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 564358107  186 KVFKGHRNQVTCLSVSTDGSILLSGSHDESVRLWD 220
Cdd:pfam00400   5 KTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
NBCH_WD40 pfam20426
Neurobeachin beta propeller domain; This entry represents the beta propeller domain found at ...
 175-221 5.70e-06

Neurobeachin beta propeller domain; This entry represents the beta propeller domain found at the C-terminus of neurobeachin-like proteins.


Pssm-ID: 466575 [Multi-domain]  Cd Length: 350  Bit Score: 47.76  E-value: 5.70e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 564358107  175 EQSFQP-EQNTGKVFKG---HRNQVTCLSVSTDGSILLSGSHDESVRLWDV 221
Cdd:pfam20426 103 ENSFQViSLNDGRMVQSirqHKDVVSCVAVTSDGSILATGSYDTTVMVWEV 153
WDR74 cd22857
WD repeat-containing protein 74; WDR74 (WD repeat-containing protein 74) from mammals and ...
 46-225 2.30e-05

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: 45.68  E-value: 2.30e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564358107  46 DVSCLKFTGDGSHFVSAGKDCLVLAWSLcsvlQADPSRIL---APRH--------VWsqhtlpITDLhcGFGGPMA--RV 112
Cdd:cd22857  128 NLLCMRVDPNENYFAFGGKEVELNVWDL----EEKPGKIWrakNVPNdslglrvpVW------VTDL--TFLSKDDhrKI 195

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564358107 113 ATASLDQTMKLWAISSGDL-LLSVLF-DMGITSVTMDLAEHHIFCGGSDGSIFQVDLcsrpgpreqsfqpeqNTGKV--- 187
Cdd:cd22857  196 VTGTGYHQVRLYDTRAQRRpVVSVDFgETPIKAVAEDPDGHTVYVGDTSGDLASIDL---------------RTGKLlgc 260

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 564358107 188 FKGHRN-QVTCLSVSTDGSILLSGSHDESVRLWDVKSKQ 225
Cdd:cd22857  261 FKGKCGgSIRSIARHPELPLIASCGLDRYLRIWDTETRQ 299
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 33-72 7.81e-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: 39.60  E-value: 7.81e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 564358107    33 TGNLLVILSRHYQDVSCLKFTGDGSHFVSAGKDCLVLAWS 72
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 pfam00400
WD domain, G-beta repeat;
34-72 1.43e-03

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 35.78  E-value: 1.43e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 564358107   34 GNLLVILSRHYQDVSCLKFTGDGSHFVSAGKDCLVLAWS 72
Cdd:pfam00400   1 GKLLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 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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