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Conserved domains on  [gi|398366023|ref|NP_014915|]
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Ytm1p [Saccharomyces cerevisiae S288C]

Protein Classification

WD repeat WDR12/YTM1 family ribosome biogenesis protein( domain architecture ID 10548159)

WD repeat WDR12/YTM1 family ribosome biogenesis protein is required for maturation of ribosomal RNAs and the formation of the ribosome

CATH:  2.130.10.10
Gene Ontology:  GO:0042254|GO:0005515
PubMed:  10322433|18448671|17353269|18925368|8090199|21468892|29026209|30069656
SCOP:  4002744

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 103-451 1.55e-56

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: 189.08  E-value: 1.55e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366023 103 EDWVSSLDVGDGSKHIISGSYDGIVRTWDLSGN-VQKQYSGHSGPIRAVKYISN-TRLVSAGNDRTLRLWktknddlklt 180
Cdd:cd00200    9 TGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGeLLRTLKGHTGPVRDVAASADgTYLASGSSDKTIRLW---------- 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366023 181 sqqqaqeddddevNIEDGKTLAILEGHKAPVVSIDVSDNSRIL-SASYDNSIGFWstiykemtvvdpleDINNPNNKISt 259
Cdd:cd00200   79 -------------DLETGECVRTLTGHTSYVSSVAFSPDGRILsSSSRDKTIKVW--------------DVETGKCLTT- 130

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366023 260 aarkrrkltmkdgtirrraplslLESHTAPVEQVIFdSTDNTVGYSVSQDHTIKTWDLVTARCIDTRTTSYS-LLSIAQL 338
Cdd:cd00200  131 -----------------------LRGHTDWVNSVAF-SPDGTFVASSSQDGTIKLWDLRTGKCVATLTGHTGeVNSVAFS 186

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366023 339 STLNLLACGSSARHITLHDPRVGASSKvtqqQLIGHKNFVSSLDTCPeNEYILCSGSHDGTVKVWDVRSTSPMYTITred 418
Cdd:cd00200  187 PDGEKLLSSSSDGTIKLWDLSTGKCLG----TLRGHENGVNSVAFSP-DGYLLASGSEDGTIRVWDLRTGECVQTLS--- 258

                        330       340       350
                 ....*....|....*....|....*....|....
gi 398366023 419 ksvqkGVNDKVFAVKWAEKVG-IISAGQDKKIQI 451
Cdd:cd00200  259 -----GHTNSVTSLAWSPDGKrLASGSADGTIRI 287
NLE pfam08154
NLE (NUC135) domain; This domain is located N terminal to WD40 repeats. It is found in the ...
 8-72 2.82e-23

NLE (NUC135) domain; This domain is located N terminal to WD40 repeats. It is found in the microtubule-associated protein Swiss:Q12024.


:

Pssm-ID: 462380  Cd Length: 66  Bit Score: 92.59  E-value: 2.82e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 398366023    8 VKIRFFTREKDelLHVQDTPMYAPISLKRYGLSEIVNHLLGSE---KPVPFDFLIEGELLRTSLHDYL 72
Cdd:pfam08154   1 VQVRFVTKEGE--LAVPGTPLDVPVSLTRYQLSELVNSLLKNEeleKPVPFDFLINGEFLRTSLEEHL 66
 
Name Accession Description Interval E-value
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 103-451 1.55e-56

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: 189.08  E-value: 1.55e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366023 103 EDWVSSLDVGDGSKHIISGSYDGIVRTWDLSGN-VQKQYSGHSGPIRAVKYISN-TRLVSAGNDRTLRLWktknddlklt 180
Cdd:cd00200    9 TGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGeLLRTLKGHTGPVRDVAASADgTYLASGSSDKTIRLW---------- 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366023 181 sqqqaqeddddevNIEDGKTLAILEGHKAPVVSIDVSDNSRIL-SASYDNSIGFWstiykemtvvdpleDINNPNNKISt 259
Cdd:cd00200   79 -------------DLETGECVRTLTGHTSYVSSVAFSPDGRILsSSSRDKTIKVW--------------DVETGKCLTT- 130

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366023 260 aarkrrkltmkdgtirrraplslLESHTAPVEQVIFdSTDNTVGYSVSQDHTIKTWDLVTARCIDTRTTSYS-LLSIAQL 338
Cdd:cd00200  131 -----------------------LRGHTDWVNSVAF-SPDGTFVASSSQDGTIKLWDLRTGKCVATLTGHTGeVNSVAFS 186

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366023 339 STLNLLACGSSARHITLHDPRVGASSKvtqqQLIGHKNFVSSLDTCPeNEYILCSGSHDGTVKVWDVRSTSPMYTITred 418
Cdd:cd00200  187 PDGEKLLSSSSDGTIKLWDLSTGKCLG----TLRGHENGVNSVAFSP-DGYLLASGSEDGTIRVWDLRTGECVQTLS--- 258

                        330       340       350
                 ....*....|....*....|....*....|....
gi 398366023 419 ksvqkGVNDKVFAVKWAEKVG-IISAGQDKKIQI 451
Cdd:cd00200  259 -----GHTNSVTSLAWSPDGKrLASGSADGTIRI 287
WD40 COG2319
WD40 repeat [General function prediction only];
103-407 5.76e-40

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 148.14  E-value: 5.76e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366023 103 EDWVSSLDVGDGSKHIISGSYDGIVRTWDL-SGNVQKQYSGHSGPIRAVKYISN-TRLVSAGNDRTLRLWktknddlklt 180
Cdd:COG2319  120 TGAVRSVAFSPDGKTLASGSADGTVRLWDLaTGKLLRTLTGHSGAVTSVAFSPDgKLLASGSDDGTVRLW---------- 189

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366023 181 sqqqaqeddddevNIEDGKTLAILEGHKAPVVSIDVS-DNSRILSASYDNSIGFWSTiykemTVVDPLEDINNPNNKIST 259
Cdd:COG2319  190 -------------DLATGKLLRTLTGHTGAVRSVAFSpDGKLLASGSADGTVRLWDL-----ATGKLLRTLTGHSGSVRS 251

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366023 260 AA--RKRRKL--TMKDGTIR-----RRAPLSLLESHTAPVEQVIFdSTDNTVGYSVSQDHTIKTWDLVTARCIDTRT-TS 329
Cdd:COG2319  252 VAfsPDGRLLasGSADGTVRlwdlaTGELLRTLTGHSGGVNSVAF-SPDGKLLASGSDDGTVRLWDLATGKLLRTLTgHT 330

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 398366023 330 YSLLSIAQLSTLNLLACGSSARHITLHDPRVGASSKVtqqqLIGHKNFVSSLDTCPENEYILcSGSHDGTVKVWDVRS 407
Cdd:COG2319  331 GAVRSVAFSPDGKTLASGSDDGTVRLWDLATGELLRT----LTGHTGAVTSVAFSPDGRTLA-SGSADGTVRLWDLAT 403
NLE pfam08154
NLE (NUC135) domain; This domain is located N terminal to WD40 repeats. It is found in the ...
 8-72 2.82e-23

NLE (NUC135) domain; This domain is located N terminal to WD40 repeats. It is found in the microtubule-associated protein Swiss:Q12024.


Pssm-ID: 462380  Cd Length: 66  Bit Score: 92.59  E-value: 2.82e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 398366023    8 VKIRFFTREKDelLHVQDTPMYAPISLKRYGLSEIVNHLLGSE---KPVPFDFLIEGELLRTSLHDYL 72
Cdd:pfam08154   1 VQVRFVTKEGE--LAVPGTPLDVPVSLTRYQLSELVNSLLKNEeleKPVPFDFLINGEFLRTSLEEHL 66
PTZ00420 PTZ00420
coronin; Provisional
 272-451 5.04e-07

coronin; Provisional


Pssm-ID: 240412 [Multi-domain]  Cd Length: 568  Bit Score: 51.87  E-value: 5.04e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366023 272 GTIR-----RRAPLSLLESHTAPVEQVIFDSTDNTVGYSVSQDHTIKTWDLvtarcidtrttsysllsiaqlstlnllac 346
Cdd:PTZ00420  54 GAIRlenqmRKPPVIKLKGHTSSILDLQFNPCFSEILASGSEDLTIRVWEI----------------------------- 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366023 347 gssaRHitlHDPRVgASSKVTQQQLIGHKNFVSSLDTCPENEYILCSGSHDGTVKVWDvrstspmytITREDKSVQKGVN 426
Cdd:PTZ00420 105 ----PH---NDESV-KEIKDPQCILKGHKKKISIIDWNPMNYYIMCSSGFDSFVNIWD---------IENEKRAFQINMP 167

                        170       180
                 ....*....|....*....|....*.
gi 398366023 427 DKVFAVKWAEKVGIISAG-QDKKIQI 451
Cdd:PTZ00420 168 KKLSSLKWNIKGNLLSGTcVGKHMHI 193
WD40 pfam00400
WD domain, G-beta repeat;
368-404 1.11e-05

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 42.33  E-value: 1.11e-05
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 398366023  368 QQQLIGHKNFVSSLDTCPENEYILcSGSHDGTVKVWD 404
Cdd:pfam00400   4 LKTLEGHTGSVTSLAFSPDGKLLA-SGSDDGTVKVWD 39
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 369-404 2.00e-05

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


Pssm-ID: 197651 [Multi-domain]  Cd Length: 40  Bit Score: 41.53  E-value: 2.00e-05
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 398366023   369 QQLIGHKNFVSSLDTCPENEYILcSGSHDGTVKVWD 404
Cdd:smart00320   6 KTLKGHTGPVTSVAFSPDGKYLA-SGSDDGTIKLWD 40
 
Name Accession Description Interval E-value
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 103-451 1.55e-56

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: 189.08  E-value: 1.55e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366023 103 EDWVSSLDVGDGSKHIISGSYDGIVRTWDLSGN-VQKQYSGHSGPIRAVKYISN-TRLVSAGNDRTLRLWktknddlklt 180
Cdd:cd00200    9 TGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGeLLRTLKGHTGPVRDVAASADgTYLASGSSDKTIRLW---------- 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366023 181 sqqqaqeddddevNIEDGKTLAILEGHKAPVVSIDVSDNSRIL-SASYDNSIGFWstiykemtvvdpleDINNPNNKISt 259
Cdd:cd00200   79 -------------DLETGECVRTLTGHTSYVSSVAFSPDGRILsSSSRDKTIKVW--------------DVETGKCLTT- 130

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366023 260 aarkrrkltmkdgtirrraplslLESHTAPVEQVIFdSTDNTVGYSVSQDHTIKTWDLVTARCIDTRTTSYS-LLSIAQL 338
Cdd:cd00200  131 -----------------------LRGHTDWVNSVAF-SPDGTFVASSSQDGTIKLWDLRTGKCVATLTGHTGeVNSVAFS 186

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366023 339 STLNLLACGSSARHITLHDPRVGASSKvtqqQLIGHKNFVSSLDTCPeNEYILCSGSHDGTVKVWDVRSTSPMYTITred 418
Cdd:cd00200  187 PDGEKLLSSSSDGTIKLWDLSTGKCLG----TLRGHENGVNSVAFSP-DGYLLASGSEDGTIRVWDLRTGECVQTLS--- 258

                        330       340       350
                 ....*....|....*....|....*....|....
gi 398366023 419 ksvqkGVNDKVFAVKWAEKVG-IISAGQDKKIQI 451
Cdd:cd00200  259 -----GHTNSVTSLAWSPDGKrLASGSADGTIRI 287
WD40 COG2319
WD40 repeat [General function prediction only];
103-407 5.76e-40

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 148.14  E-value: 5.76e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366023 103 EDWVSSLDVGDGSKHIISGSYDGIVRTWDL-SGNVQKQYSGHSGPIRAVKYISN-TRLVSAGNDRTLRLWktknddlklt 180
Cdd:COG2319  120 TGAVRSVAFSPDGKTLASGSADGTVRLWDLaTGKLLRTLTGHSGAVTSVAFSPDgKLLASGSDDGTVRLW---------- 189

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366023 181 sqqqaqeddddevNIEDGKTLAILEGHKAPVVSIDVS-DNSRILSASYDNSIGFWSTiykemTVVDPLEDINNPNNKIST 259
Cdd:COG2319  190 -------------DLATGKLLRTLTGHTGAVRSVAFSpDGKLLASGSADGTVRLWDL-----ATGKLLRTLTGHSGSVRS 251

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366023 260 AA--RKRRKL--TMKDGTIR-----RRAPLSLLESHTAPVEQVIFdSTDNTVGYSVSQDHTIKTWDLVTARCIDTRT-TS 329
Cdd:COG2319  252 VAfsPDGRLLasGSADGTVRlwdlaTGELLRTLTGHSGGVNSVAF-SPDGKLLASGSDDGTVRLWDLATGKLLRTLTgHT 330

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 398366023 330 YSLLSIAQLSTLNLLACGSSARHITLHDPRVGASSKVtqqqLIGHKNFVSSLDTCPENEYILcSGSHDGTVKVWDVRS 407
Cdd:COG2319  331 GAVRSVAFSPDGKTLASGSDDGTVRLWDLATGELLRT----LTGHTGAVTSVAFSPDGRTLA-SGSADGTVRLWDLAT 403
WD40 COG2319
WD40 repeat [General function prediction only];
104-451 8.45e-39

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 145.05  E-value: 8.45e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366023 104 DWVSSLDVGDGSKHIISGSYDGIVRTWDL-SGNVQKQYSGHSGPIRAVKYISN-TRLVSAGNDRTLRLWktknddlklts 181
Cdd:COG2319   79 AAVLSVAFSPDGRLLASASADGTVRLWDLaTGLLLRTLTGHTGAVRSVAFSPDgKTLASGSADGTVRLW----------- 147

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366023 182 qqqaqeddddevNIEDGKTLAILEGHKAPVVSIDVS-DNSRILSASYDNSIGFWSTIYKEM--TVVDPLEDIN----NPN 254
Cdd:COG2319  148 ------------DLATGKLLRTLTGHSGAVTSVAFSpDGKLLASGSDDGTVRLWDLATGKLlrTLTGHTGAVRsvafSPD 215

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366023 255 NK-ISTAARkrrkltmkDGTIR-----RRAPLSLLESHTAPVEQVIFdSTDNTVGYSVSQDHTIKTWDLVTARCIDTRTT 328
Cdd:COG2319  216 GKlLASGSA--------DGTVRlwdlaTGKLLRTLTGHSGSVRSVAF-SPDGRLLASGSADGTVRLWDLATGELLRTLTG 286

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366023 329 -SYSLLSIAQLSTLNLLACGSSARHITLHDPRVGAsskvTQQQLIGHKNFVSSLDTCPENEYILcSGSHDGTVKVWDVRS 407
Cdd:COG2319  287 hSGGVNSVAFSPDGKLLASGSDDGTVRLWDLATGK----LLRTLTGHTGAVRSVAFSPDGKTLA-SGSDDGTVRLWDLAT 361

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....*.
gi 398366023 408 TSPMYTITredksvqkGVNDKVFAVKWAEKvG--IISAGQDKKIQI 451
Cdd:COG2319  362 GELLRTLT--------GHTGAVTSVAFSPD-GrtLASGSADGTVRL 398
NLE pfam08154
NLE (NUC135) domain; This domain is located N terminal to WD40 repeats. It is found in the ...
 8-72 2.82e-23

NLE (NUC135) domain; This domain is located N terminal to WD40 repeats. It is found in the microtubule-associated protein Swiss:Q12024.


Pssm-ID: 462380  Cd Length: 66  Bit Score: 92.59  E-value: 2.82e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 398366023    8 VKIRFFTREKDelLHVQDTPMYAPISLKRYGLSEIVNHLLGSE---KPVPFDFLIEGELLRTSLHDYL 72
Cdd:pfam08154   1 VQVRFVTKEGE--LAVPGTPLDVPVSLTRYQLSELVNSLLKNEeleKPVPFDFLINGEFLRTSLEEHL 66
WD40 COG2319
WD40 repeat [General function prediction only];
106-451 7.95e-22

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 96.90  E-value: 7.95e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366023 106 VSSLDVGDGSKHIISGSYDGIVRTWDLSGNVQKQYSGHSGPIRAVKYISN-TRLVSAGNDRTLRLWktknddlkltsqqq 184
Cdd:COG2319   40 ASLAASPDGARLAAGAGDLTLLLLDAAAGALLATLLGHTAAVLSVAFSPDgRLLASASADGTVRLW-------------- 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366023 185 aqeddddevNIEDGKTLAILEGHKAPVVSIDVS-DNSRILSASYDNSIGFWSTiykemtvvdpledinnpnnkistaark 263
Cdd:COG2319  106 ---------DLATGLLLRTLTGHTGAVRSVAFSpDGKTLASGSADGTVRLWDL--------------------------- 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366023 264 rrkltmKDGTIRRRaplslLESHTAPVEQVIFdSTDNTVGYSVSQDHTIKTWDLVTARCIDTrttsysllsiaqlstlnl 343
Cdd:COG2319  150 ------ATGKLLRT-----LTGHSGAVTSVAF-SPDGKLLASGSDDGTVRLWDLATGKLLRT------------------ 199

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366023 344 lacgssarhitlhdprvgasskvtqqqLIGHKNFVSSLDTCPENEYILcSGSHDGTVKVWDVRSTSPMYTITredksvqk 423
Cdd:COG2319  200 ---------------------------LTGHTGAVRSVAFSPDGKLLA-SGSADGTVRLWDLATGKLLRTLT-------- 243

                        330       340       350
                 ....*....|....*....|....*....|
gi 398366023 424 GVNDKVFAVKWAEKvG--IISAGQDKKIQI 451
Cdd:COG2319  244 GHSGSVRSVAFSPD-GrlLASGSADGTVRL 272
WD40 COG2319
WD40 repeat [General function prediction only];
102-174 1.83e-11

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 65.70  E-value: 1.83e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 398366023 102 NEDWVSSLDVGDGSKHIISGSYDGIVRTWDLSGNVQKQ-YSGHSGPIRAVKYISN-TRLVSAGNDRTLRLWKTKN 174
Cdd:COG2319  329 HTGAVRSVAFSPDGKTLASGSDDGTVRLWDLATGELLRtLTGHTGAVTSVAFSPDgRTLASGSADGTVRLWDLAT 403
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 101-171 5.66e-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: 56.96  E-value: 5.66e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 398366023 101 SNEDWVSSLDVGDGSKHIISGSYDGIVRTWDL-SGNVQKQYSGHSGPIRAVKYI-SNTRLVSAGNDRTLRLWK 171
Cdd:cd00200  217 GHENGVNSVAFSPDGYLLASGSEDGTIRVWDLrTGECVQTLSGHTNSVTSLAWSpDGKRLASGSADGTIRIWD 289
PTZ00420 PTZ00420
coronin; Provisional
 272-451 5.04e-07

coronin; Provisional


Pssm-ID: 240412 [Multi-domain]  Cd Length: 568  Bit Score: 51.87  E-value: 5.04e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366023 272 GTIR-----RRAPLSLLESHTAPVEQVIFDSTDNTVGYSVSQDHTIKTWDLvtarcidtrttsysllsiaqlstlnllac 346
Cdd:PTZ00420  54 GAIRlenqmRKPPVIKLKGHTSSILDLQFNPCFSEILASGSEDLTIRVWEI----------------------------- 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366023 347 gssaRHitlHDPRVgASSKVTQQQLIGHKNFVSSLDTCPENEYILCSGSHDGTVKVWDvrstspmytITREDKSVQKGVN 426
Cdd:PTZ00420 105 ----PH---NDESV-KEIKDPQCILKGHKKKISIIDWNPMNYYIMCSSGFDSFVNIWD---------IENEKRAFQINMP 167

                        170       180
                 ....*....|....*....|....*.
gi 398366023 427 DKVFAVKWAEKVGIISAG-QDKKIQI 451
Cdd:PTZ00420 168 KKLSSLKWNIKGNLLSGTcVGKHMHI 193
WD40 pfam00400
WD domain, G-beta repeat;
368-404 1.11e-05

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 42.33  E-value: 1.11e-05
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 398366023  368 QQQLIGHKNFVSSLDTCPENEYILcSGSHDGTVKVWD 404
Cdd:pfam00400   4 LKTLEGHTGSVTSLAFSPDGKLLA-SGSDDGTVKVWD 39
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 369-404 2.00e-05

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


Pssm-ID: 197651 [Multi-domain]  Cd Length: 40  Bit Score: 41.53  E-value: 2.00e-05
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 398366023   369 QQLIGHKNFVSSLDTCPENEYILcSGSHDGTVKVWD 404
Cdd:smart00320   6 KTLKGHTGPVTSVAFSPDGKYLA-SGSDDGTIKLWD 40
Nup160 pfam11715
Nucleoporin Nup120/160; Nup120 is conserved from fungi to plants to humans, and is homologous ...
 269-409 7.74e-05

Nucleoporin Nup120/160; Nup120 is conserved from fungi to plants to humans, and is homologous with the Nup160 of vertebrates. The nuclear core complex, or NPC, mediates macromolecular transport across the nuclear envelope. Deletion of the NUP120 gene causes clustering of NPCs at one side of the nuclear envelope, moderate nucleolar fragmentation and slower cell growth. The vertebrate NPC is estimated to contain between 30 and 60 different proteins. most of which are not known. Two important ones in creating the nucleoporin basket are Nup98 and Nup153, and Nup120, in conjunction with Nup 133, interacts with these two and itself plays a role in mRNA export. Nup160, Nup133, Nup96, and Nup107 are all targets of phosphorylation. The phosphorylation sites are clustered mainly at the N-terminal regions of these proteins, which are predicted to be natively disordered. The entire Nup107-160 sub-complex is stable throughout the cell cycle, thus it seems unlikely that phosphorylation affects interactions within the Nup107-160 sub-complex, but rather that it regulates the association of the sub-complex with the NPC and other proteins.


Pssm-ID: 432020 [Multi-domain]  Cd Length: 540  Bit Score: 45.15  E-value: 7.74e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366023  269 MKDGTIRRRAPLSLLESHTAPVeqvIFDSTDNTVGYSVSQDHTIKTWDLVTARCIDTRTtsysllsiaqLSTLNLLACGS 348
Cdd:pfam11715 206 LADPTIRYSGSSVALSLSAAPA---VTTVGGQNFLFTLSLDHTLRVWDLLTGKCLATID----------LLDLELPQDSS 272

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 398366023  349 SARHItlhDPrvgasskvtqqqliGHKNFVSSLDTCPENEYILCSGSHDGTVKVWDVRSTS 409
Cdd:pfam11715 273 SWLTL---DP--------------APSSLIRVSGSFRAYLVLTYSPSSNGQFKFWKVKSND 316
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 197-235 1.43e-04

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


Pssm-ID: 197651 [Multi-domain]  Cd Length: 40  Bit Score: 39.22  E-value: 1.43e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 398366023   197 DGKTLAILEGHKAPVVSIDVS-DNSRILSASYDNSIGFWS 235
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAFSpDGKYLASGSDDGTIKLWD 40
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 133-171 1.81e-04

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


Pssm-ID: 197651 [Multi-domain]  Cd Length: 40  Bit Score: 38.83  E-value: 1.81e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 398366023   133 SGNVQKQYSGHSGPIRAVKYISN-TRLVSAGNDRTLRLWK 171
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAFSPDgKYLASGSDDGTIKLWD 40
PLN00181 PLN00181
protein SPA1-RELATED; Provisional
 274-415 5.06e-04

protein SPA1-RELATED; Provisional


Pssm-ID: 177776 [Multi-domain]  Cd Length: 793  Bit Score: 42.77  E-value: 5.06e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366023 274 IRRRAPLSLLESHTAPVEQVIFDSTDNTVGYSVSQDHTIKTWDLVTARCIDTRTTSYSLLSIAQLS-TLNLLACGSSARH 352
Cdd:PLN00181 562 VARSQLVTEMKEHEKRVWSIDYSSADPTLLASGSDDGSVKLWSINQGVSIGTIKTKANICCVQFPSeSGRSLAFGSADHK 641

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 398366023 353 ITLHDPRvgaSSKVTQQQLIGHKNFVSSLDTCpeNEYILCSGSHDGTVKVWDVRST------SPMYTIT 415
Cdd:PLN00181 642 VYYYDLR---NPKLPLCTMIGHSKTVSYVRFV--DSSTLVSSSTDNTLKLWDLSMSisgineTPLHSFM 705
WD40 pfam00400
WD domain, G-beta repeat;
198-235 1.03e-03

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 36.55  E-value: 1.03e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 398366023  198 GKTLAILEGHKAPVVSIDVSDNSR-ILSASYDNSIGFWS 235
Cdd:pfam00400   1 GKLLKTLEGHTGSVTSLAFSPDGKlLASGSDDGTVKVWD 39
WD40 pfam00400
WD domain, G-beta repeat;
134-170 1.75e-03

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 36.17  E-value: 1.75e-03
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 398366023  134 GNVQKQYSGHSGPIRAVKYISN-TRLVSAGNDRTLRLW 170
Cdd:pfam00400   1 GKLLKTLEGHTGSVTSLAFSPDgKLLASGSDDGTVKVW 38
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 103-131 7.87e-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: 34.21  E-value: 7.87e-03
                           10        20
                   ....*....|....*....|....*....
gi 398366023   103 EDWVSSLDVGDGSKHIISGSYDGIVRTWD 131
Cdd:smart00320  12 TGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 pfam00400
WD domain, G-beta repeat;
103-131 9.91e-03

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 33.86  E-value: 9.91e-03
                          10        20
                  ....*....|....*....|....*....
gi 398366023  103 EDWVSSLDVGDGSKHIISGSYDGIVRTWD 131
Cdd:pfam00400  11 TGSVTSLAFSPDGKLLASGSDDGTVKVWD 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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