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Conserved domains on  [gi|429242105|ref|NP_593409|]
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HOPS complex subunit Vps41 [Schizosaccharomyces pombe]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CLH super family cl46917
Clathrin heavy chain repeat homology;
625-712 1.42e-14

Clathrin heavy chain repeat homology;


The actual alignment was detected with superfamily member smart00299:

Pssm-ID: 128594 [Multi-domain]  Cd Length: 140  Bit Score: 71.54  E-value: 1.42e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429242105   625 AEFDRKRFFDFLVNT-QCYSLDHAAQICKQYNYLDELVYILGRMGNNKEALMLIINELLDIGRAIRYVKEQADRELWDDL 703
Cdd:smart00299  52 AKYDPQKEIERLDNKsNHYDIEKVGKLCEKAKLYEEAVELYKKDGNFKDAIVTLIEHLGNYEKAIEYFVKQNNPELWAEV 131


                   ....*....
gi 429242105   704 ISYSLDKPE 712
Cdd:smart00299 132 LKALLDKPR 140
WD40 super family cl29593
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 44-204 6.65e-08

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.


The actual alignment was detected with superfamily member cd00200:

Pssm-ID: 475233 [Multi-domain]  Cd Length: 289  Bit Score: 55.03  E-value: 6.65e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429242105  44 ISACAIS--KEHFFFGSHNGAIYIY-QKNGILLRKMILHSASVVDLSVDLESENLASCSMDGKMIISNITTRE--TTVHD 118
Cdd:cd00200   12 VTCVAFSpdGKLLATGSGDGTIKVWdLETGELLRTLKGHTGPVRDVAASADGTYLASGSSDKTIRLWDLETGEcvRTLTG 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429242105 119 FKRPLLSVAIDPyystrsSRQVLSGGRAGKVVLSEKGWLGNKDTVLQADCGAVY--KISWYTTYIAWASDLG-ITVYSTE 195
Cdd:cd00200   92 HTSYVSSVAFSP------DGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNsvAFSPDGTFVASSSQDGtIKLWDLR 165


                 ....*....
gi 429242105 196 FGKVLGRLE 204
Cdd:cd00200  166 TGKCVATLT 174
 
Name Accession Description Interval E-value
CLH smart00299
Clathrin heavy chain repeat homology;
625-712 1.42e-14

Clathrin heavy chain repeat homology;


Pssm-ID: 128594 [Multi-domain]  Cd Length: 140  Bit Score: 71.54  E-value: 1.42e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429242105   625 AEFDRKRFFDFLVNT-QCYSLDHAAQICKQYNYLDELVYILGRMGNNKEALMLIINELLDIGRAIRYVKEQADRELWDDL 703
Cdd:smart00299  52 AKYDPQKEIERLDNKsNHYDIEKVGKLCEKAKLYEEAVELYKKDGNFKDAIVTLIEHLGNYEKAIEYFVKQNNPELWAEV 131


                   ....*....
gi 429242105   704 ISYSLDKPE 712
Cdd:smart00299 132 LKALLDKPR 140
Clathrin pfam00637
Region in Clathrin and VPS; Each region is about 140 amino acids long. The regions are ...
 628-714 1.66e-13

Region in Clathrin and VPS; Each region is about 140 amino acids long. The regions are composed of multiple alpha helical repeats. They occur in the arm region of the Clathrin heavy chain.


Pssm-ID: 459884 [Multi-domain]  Cd Length: 142  Bit Score: 68.44  E-value: 1.66e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429242105  628 DRKRFFDFLVNTQCYSLDHAAQICKQYNYLDELVYILGRMGNNKEALMLIiNELLDIGRAIRYVKEQADRELWDDLISYS 707
Cdd:pfam00637  57 DPEELEEFLKKNNNYDLEKVAKLCEKADLYEEAVILYKKIGNWKEAISLL-KKLGDYKDAIEYAVKSSNPELWEELLEAL 135


                  ....*..
gi 429242105  708 LDKPEFI 714
Cdd:pfam00637 136 LDNGRFE 142
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 44-204 6.65e-08

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: 55.03  E-value: 6.65e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429242105  44 ISACAIS--KEHFFFGSHNGAIYIY-QKNGILLRKMILHSASVVDLSVDLESENLASCSMDGKMIISNITTRE--TTVHD 118
Cdd:cd00200   12 VTCVAFSpdGKLLATGSGDGTIKVWdLETGELLRTLKGHTGPVRDVAASADGTYLASGSSDKTIRLWDLETGEcvRTLTG 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429242105 119 FKRPLLSVAIDPyystrsSRQVLSGGRAGKVVLSEKGWLGNKDTVLQADCGAVY--KISWYTTYIAWASDLG-ITVYSTE 195
Cdd:cd00200   92 HTSYVSSVAFSP------DGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNsvAFSPDGTFVASSSQDGtIKLWDLR 165


                 ....*....
gi 429242105 196 FGKVLGRLE 204
Cdd:cd00200  166 TGKCVATLT 174
WD40 COG2319
WD40 repeat [General function prediction only];
41-204 1.69e-05

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 47.98  E-value: 1.69e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429242105  41 NDTISACAISK--EHFFFGSHNGAIYIYQ-KNGILLRKMILHSASVVDLSVDLESENLASCSMDGKMIISNITTRE--TT 115
Cdd:COG2319  162 SGAVTSVAFSPdgKLLASGSDDGTVRLWDlATGKLLRTLTGHTGAVRSVAFSPDGKLLASGSADGTVRLWDLATGKllRT 241

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429242105 116 VHDFKRPLLSVAIDPyystrSSRQVLSGGRAGKVVLsekgW---LGNKDTVLQADCGAVYKISWYT--TYIAWASDLG-I 189
Cdd:COG2319  242 LTGHSGSVRSVAFSP-----DGRLLASGSADGTVRL----WdlaTGELLRTLTGHSGGVNSVAFSPdgKLLASGSDDGtV 312

                        170
                 ....*....|....*
gi 429242105 190 TVYSTEFGKVLGRLE 204
Cdd:COG2319  313 RLWDLATGKLLRTLT 327
 
Name Accession Description Interval E-value
CLH smart00299
Clathrin heavy chain repeat homology;
625-712 1.42e-14

Clathrin heavy chain repeat homology;


Pssm-ID: 128594 [Multi-domain]  Cd Length: 140  Bit Score: 71.54  E-value: 1.42e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429242105   625 AEFDRKRFFDFLVNT-QCYSLDHAAQICKQYNYLDELVYILGRMGNNKEALMLIINELLDIGRAIRYVKEQADRELWDDL 703
Cdd:smart00299  52 AKYDPQKEIERLDNKsNHYDIEKVGKLCEKAKLYEEAVELYKKDGNFKDAIVTLIEHLGNYEKAIEYFVKQNNPELWAEV 131


                   ....*....
gi 429242105   704 ISYSLDKPE 712
Cdd:smart00299 132 LKALLDKPR 140
Clathrin pfam00637
Region in Clathrin and VPS; Each region is about 140 amino acids long. The regions are ...
 628-714 1.66e-13

Region in Clathrin and VPS; Each region is about 140 amino acids long. The regions are composed of multiple alpha helical repeats. They occur in the arm region of the Clathrin heavy chain.


Pssm-ID: 459884 [Multi-domain]  Cd Length: 142  Bit Score: 68.44  E-value: 1.66e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429242105  628 DRKRFFDFLVNTQCYSLDHAAQICKQYNYLDELVYILGRMGNNKEALMLIiNELLDIGRAIRYVKEQADRELWDDLISYS 707
Cdd:pfam00637  57 DPEELEEFLKKNNNYDLEKVAKLCEKADLYEEAVILYKKIGNWKEAISLL-KKLGDYKDAIEYAVKSSNPELWEELLEAL 135


                  ....*..
gi 429242105  708 LDKPEFI 714
Cdd:pfam00637 136 LDNGRFE 142
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 44-204 6.65e-08

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: 55.03  E-value: 6.65e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429242105  44 ISACAIS--KEHFFFGSHNGAIYIY-QKNGILLRKMILHSASVVDLSVDLESENLASCSMDGKMIISNITTRE--TTVHD 118
Cdd:cd00200   12 VTCVAFSpdGKLLATGSGDGTIKVWdLETGELLRTLKGHTGPVRDVAASADGTYLASGSSDKTIRLWDLETGEcvRTLTG 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429242105 119 FKRPLLSVAIDPyystrsSRQVLSGGRAGKVVLSEKGWLGNKDTVLQADCGAVY--KISWYTTYIAWASDLG-ITVYSTE 195
Cdd:cd00200   92 HTSYVSSVAFSP------DGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNsvAFSPDGTFVASSSQDGtIKLWDLR 165


                 ....*....
gi 429242105 196 FGKVLGRLE 204
Cdd:cd00200  166 TGKCVATLT 174
WD40 COG2319
WD40 repeat [General function prediction only];
41-204 1.69e-05

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 47.98  E-value: 1.69e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429242105  41 NDTISACAISK--EHFFFGSHNGAIYIYQ-KNGILLRKMILHSASVVDLSVDLESENLASCSMDGKMIISNITTRE--TT 115
Cdd:COG2319  162 SGAVTSVAFSPdgKLLASGSDDGTVRLWDlATGKLLRTLTGHTGAVRSVAFSPDGKLLASGSADGTVRLWDLATGKllRT 241

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429242105 116 VHDFKRPLLSVAIDPyystrSSRQVLSGGRAGKVVLsekgW---LGNKDTVLQADCGAVYKISWYT--TYIAWASDLG-I 189
Cdd:COG2319  242 LTGHSGSVRSVAFSP-----DGRLLASGSADGTVRL----WdlaTGELLRTLTGHSGGVNSVAFSPdgKLLASGSDDGtV 312

                        170
                 ....*....|....*
gi 429242105 190 TVYSTEFGKVLGRLE 204
Cdd:COG2319  313 RLWDLATGKLLRTLT 327
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 27-198 8.92e-05

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: 45.40  E-value: 8.92e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429242105  27 IYERITEKFQGCFM--NDTISACAISKEHFF--FGSHNGAIYIYQ-KNGILLRKMILHSASVVDLSVDLESENLASCSMD 101
Cdd:cd00200  119 VWDVETGKCLTTLRghTDWVNSVAFSPDGTFvaSSSQDGTIKLWDlRTGKCVATLTGHTGEVNSVAFSPDGEKLLSSSSD 198

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429242105 102 GKMIISNITTRET--TVHDFKRPLLSVAIDPyystrSSRQVLSGGRAGKVvlseKGW---LGNKDTVLQADCGAVYKISW 176
Cdd:cd00200  199 GTIKLWDLSTGKClgTLRGHENGVNSVAFSP-----DGYLLASGSEDGTI----RVWdlrTGECVQTLSGHTNSVTSLAW 269

                        170       180
                 ....*....|....*....|..
gi 429242105 177 yttyiawaSDLGITVYSTEFGK 198
Cdd:cd00200  270 --------SPDGKRLASGSADG 283
 
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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