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Conserved domains on  [gi|1443074344|ref|XP_025880666|]
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vacuolar protein-sorting-associated protein 11 homolog isoform X2 [Oryza sativa Japonica Group]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RING-H2_Vps11 cd16688
RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 11 homolog ...
 814-854 2.17e-20

RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 11 homolog (Vps11) and similar proteins; Vps11, also known as RING finger protein 108 (RNF108), is a soluble protein involved in regulation of glycolipid degradation and retrograde toxin transport. It is highly expressed in heart and pancreas. Vps11 associates with Vps16, Vps18, and Vps33 to form a Class C Vps core complex that is required for soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNARE)-mediated membrane fusion at the lysosome-like yeast vacuole. The core complex, together with two additional compartment-specific subunits, forms the tethering complexes HOPS (homotypic vacuole fusion and protein sorting) and CORVET (class C core vacuole/endosome transport). CORVET contains the additional Vps3 and Vps8 subunits. It operates at endosomes, controls traffic into late endosomes and interacts with the Rab5/Vps21-GTP form. HOPS contains the additional Vps39 and Vps41 subunits. It operates at the lysosomal vacuole, controls all traffic from late endosomes into the vacuole and interacts with the Rab7/Ypt7-GTP form. Vps11 is a central scaffold protein upon which both HOPS and CORVET assemble. The HOPS and CORVET complexes disassemble in the absence of Vps11, resulting in massive fragmentation of vacuoles. Vps11 contains a clathrin repeat domain and a C-terminal C3H2C3-type RING-H2 finger. This subfamily also includes Vps11 homologs found in fungi, such as Saccharomyces cerevisiae vacuolar membrane protein Pep5p, also known as carboxypeptidase Y-deficient protein 5, vacuolar morphogenesis protein 1, or vacuolar biogenesis protein END1. Pep5p is essential for vacuolar biogenesis. It associates with Pep3p to form a core Pep3p/Pep5p complex that promotes vesicular docking/fusion reactions in conjunction with SNARE proteins at multiple steps in transport routes to the vacuole.


:

Pssm-ID: 438349 [Multi-domain]  Cd Length: 44  Bit Score: 85.09  E-value: 2.17e-20
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1443074344 814 SKCTTCTFTLDLPAVHFMCMHSFHLRCLGD---NEKECPECAPE 854
Cdd:cd16688     1 TKCSACGSTLDLPSVHFLCGHSFHQHCLEDyeeNDRECPLCAPE 44
VPS11_C pfam12451
Vacuolar protein sorting protein 11 C terminal; This domain family is found in eukaryotes, and ...
 855-897 3.44e-12

Vacuolar protein sorting protein 11 C terminal; This domain family is found in eukaryotes, and is approximately 50 amino acids in length. Vps 11 is one of the evolutionarily conserved class C vacuolar protein sorting genes (c-vps: vps11, vps16, vps18, and vps33), whose products physically associate to form the c-vps protein complex required for vesicle docking and fusion.


:

Pssm-ID: 463590  Cd Length: 44  Bit Score: 61.65  E-value: 3.44e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1443074344 855 YRSVMEAKQKLEHNARDHDLFFRQLRGSKDGFSVVADYFSKGI 897
Cdd:pfam12451   1 NETIRELRRAQEESADQHDLFKSALEESTDRFKVIADYFGRGV 43
Clathrin pfam00637
Region in Clathrin and VPS; Each region is about 140 amino acids long. The regions are ...
 357-473 1.97e-10

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: 59.58  E-value: 1.97e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443074344 357 LEPSYVIQKFLDAKRIYNLTNYLEKLHDRGL-ASKDHTTLLLNCYTKLKDVEKLNHFIKDEDgvgeiKFDVETAIRVCRA 435
Cdd:pfam00637   8 IDVSRVVKLFEKAGLLEELISYLESALKEDSrENPALQTALIELYAKYDDPEELEEFLKKNN-----NYDLEKVAKLCEK 82

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1443074344 436 AGYHEHAMFVAKKAGRHELYLKiLLEDLGRYDEALQYI 473
Cdd:pfam00637  83 ADLYEEAVILYKKIGNWKEAIS-LLKKLGDYKDAIEYA 119
Clathrin super family cl47574
Region in Clathrin and VPS; Each region is about 140 amino acids long. The regions are ...
 651-727 3.25e-04

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.


The actual alignment was detected with superfamily member pfam00637:

Pssm-ID: 459884 [Multi-domain]  Cd Length: 142  Bit Score: 41.86  E-value: 3.25e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1443074344 651 YDVDLALIICNANAFKDGLLFLYEKLKLFKEVISCYKQAHDHEGLIACCKKLgdssqgGDPSLWGDLLKYFSELGED 727
Cdd:pfam00637  71 YDLEKVAKLCEKADLYEEAVILYKKIGNWKEAISLLKKLGDYKDAIEYAVKS------SNPELWEELLEALLDNGRF 141
zf-RVT super family cl16506
zinc-binding in reverse transcriptase; This domain would appear to be a zinc-binding region of ...
 8-32 2.66e-03

zinc-binding in reverse transcriptase; This domain would appear to be a zinc-binding region of a putative reverse transcriptase.


The actual alignment was detected with superfamily member pfam13966:

Pssm-ID: 433612  Cd Length: 84  Bit Score: 37.64  E-value: 2.66e-03
                          10        20
                  ....*....|....*....|....*.
gi 1443074344   8 KCMAP-KIKIFTWRLLMGALPTATRL 32
Cdd:pfam13966  25 KKKAPpKVKFFLWLALRNRLPTADRL 50
 
Name Accession Description Interval E-value
RING-H2_Vps11 cd16688
RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 11 homolog ...
 814-854 2.17e-20

RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 11 homolog (Vps11) and similar proteins; Vps11, also known as RING finger protein 108 (RNF108), is a soluble protein involved in regulation of glycolipid degradation and retrograde toxin transport. It is highly expressed in heart and pancreas. Vps11 associates with Vps16, Vps18, and Vps33 to form a Class C Vps core complex that is required for soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNARE)-mediated membrane fusion at the lysosome-like yeast vacuole. The core complex, together with two additional compartment-specific subunits, forms the tethering complexes HOPS (homotypic vacuole fusion and protein sorting) and CORVET (class C core vacuole/endosome transport). CORVET contains the additional Vps3 and Vps8 subunits. It operates at endosomes, controls traffic into late endosomes and interacts with the Rab5/Vps21-GTP form. HOPS contains the additional Vps39 and Vps41 subunits. It operates at the lysosomal vacuole, controls all traffic from late endosomes into the vacuole and interacts with the Rab7/Ypt7-GTP form. Vps11 is a central scaffold protein upon which both HOPS and CORVET assemble. The HOPS and CORVET complexes disassemble in the absence of Vps11, resulting in massive fragmentation of vacuoles. Vps11 contains a clathrin repeat domain and a C-terminal C3H2C3-type RING-H2 finger. This subfamily also includes Vps11 homologs found in fungi, such as Saccharomyces cerevisiae vacuolar membrane protein Pep5p, also known as carboxypeptidase Y-deficient protein 5, vacuolar morphogenesis protein 1, or vacuolar biogenesis protein END1. Pep5p is essential for vacuolar biogenesis. It associates with Pep3p to form a core Pep3p/Pep5p complex that promotes vesicular docking/fusion reactions in conjunction with SNARE proteins at multiple steps in transport routes to the vacuole.


Pssm-ID: 438349 [Multi-domain]  Cd Length: 44  Bit Score: 85.09  E-value: 2.17e-20
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1443074344 814 SKCTTCTFTLDLPAVHFMCMHSFHLRCLGD---NEKECPECAPE 854
Cdd:cd16688     1 TKCSACGSTLDLPSVHFLCGHSFHQHCLEDyeeNDRECPLCAPE 44
VPS11_C pfam12451
Vacuolar protein sorting protein 11 C terminal; This domain family is found in eukaryotes, and ...
 855-897 3.44e-12

Vacuolar protein sorting protein 11 C terminal; This domain family is found in eukaryotes, and is approximately 50 amino acids in length. Vps 11 is one of the evolutionarily conserved class C vacuolar protein sorting genes (c-vps: vps11, vps16, vps18, and vps33), whose products physically associate to form the c-vps protein complex required for vesicle docking and fusion.


Pssm-ID: 463590  Cd Length: 44  Bit Score: 61.65  E-value: 3.44e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1443074344 855 YRSVMEAKQKLEHNARDHDLFFRQLRGSKDGFSVVADYFSKGI 897
Cdd:pfam12451   1 NETIRELRRAQEESADQHDLFKSALEESTDRFKVIADYFGRGV 43
Clathrin pfam00637
Region in Clathrin and VPS; Each region is about 140 amino acids long. The regions are ...
 357-473 1.97e-10

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: 59.58  E-value: 1.97e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443074344 357 LEPSYVIQKFLDAKRIYNLTNYLEKLHDRGL-ASKDHTTLLLNCYTKLKDVEKLNHFIKDEDgvgeiKFDVETAIRVCRA 435
Cdd:pfam00637   8 IDVSRVVKLFEKAGLLEELISYLESALKEDSrENPALQTALIELYAKYDDPEELEEFLKKNN-----NYDLEKVAKLCEK 82

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1443074344 436 AGYHEHAMFVAKKAGRHELYLKiLLEDLGRYDEALQYI 473
Cdd:pfam00637  83 ADLYEEAVILYKKIGNWKEAIS-LLKKLGDYKDAIEYA 119
Clathrin pfam00637
Region in Clathrin and VPS; Each region is about 140 amino acids long. The regions are ...
 651-727 3.25e-04

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: 41.86  E-value: 3.25e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1443074344 651 YDVDLALIICNANAFKDGLLFLYEKLKLFKEVISCYKQAHDHEGLIACCKKLgdssqgGDPSLWGDLLKYFSELGED 727
Cdd:pfam00637  71 YDLEKVAKLCEKADLYEEAVILYKKIGNWKEAISLLKKLGDYKDAIEYAVKS------SNPELWEELLEALLDNGRF 141
zf-C3H2C3 pfam17122
Zinc-finger;
816-851 7.58e-04

Zinc-finger;


Pssm-ID: 293727  Cd Length: 35  Bit Score: 37.96  E-value: 7.58e-04
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1443074344 816 CTTCTFTLDLPAVHFMCMHSFHLRCLgdNEKECPEC 851
Cdd:pfam17122   1 CDNCGLKLDYPFVHYSCNHSVHTKCV--DPEICPLC 34
CLH smart00299
Clathrin heavy chain repeat homology;
357-473 1.82e-03

Clathrin heavy chain repeat homology;


Pssm-ID: 128594 [Multi-domain]  Cd Length: 140  Bit Score: 39.56  E-value: 1.82e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443074344  357 LEPSYVIQKFLDAKRIYNLTNYLEKLHDRGLASKD-HTTLL-LNCYTKLKDVekLNHFIKDEDgvgeiKFDVETAIRVCR 434
Cdd:smart00299   8 IDVSEVVELFEKRNLLEELIPYLESALKLNSENPAlQTKLIeLYAKYDPQKE--IERLDNKSN-----HYDIEKVGKLCE 80

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 1443074344  435 AAGYHEHAMFVAKKAGRHELYLKILLEDLGRYDEALQYI 473
Cdd:smart00299  81 KAKLYEEAVELYKKDGNFKDAIVTLIEHLGNYEKAIEYF 119
zf-RVT pfam13966
zinc-binding in reverse transcriptase; This domain would appear to be a zinc-binding region of ...
 8-32 2.66e-03

zinc-binding in reverse transcriptase; This domain would appear to be a zinc-binding region of a putative reverse transcriptase.


Pssm-ID: 433612  Cd Length: 84  Bit Score: 37.64  E-value: 2.66e-03
                          10        20
                  ....*....|....*....|....*.
gi 1443074344   8 KCMAP-KIKIFTWRLLMGALPTATRL 32
Cdd:pfam13966  25 KKKAPpKVKFFLWLALRNRLPTADRL 50
 
Name Accession Description Interval E-value
RING-H2_Vps11 cd16688
RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 11 homolog ...
 814-854 2.17e-20

RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 11 homolog (Vps11) and similar proteins; Vps11, also known as RING finger protein 108 (RNF108), is a soluble protein involved in regulation of glycolipid degradation and retrograde toxin transport. It is highly expressed in heart and pancreas. Vps11 associates with Vps16, Vps18, and Vps33 to form a Class C Vps core complex that is required for soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNARE)-mediated membrane fusion at the lysosome-like yeast vacuole. The core complex, together with two additional compartment-specific subunits, forms the tethering complexes HOPS (homotypic vacuole fusion and protein sorting) and CORVET (class C core vacuole/endosome transport). CORVET contains the additional Vps3 and Vps8 subunits. It operates at endosomes, controls traffic into late endosomes and interacts with the Rab5/Vps21-GTP form. HOPS contains the additional Vps39 and Vps41 subunits. It operates at the lysosomal vacuole, controls all traffic from late endosomes into the vacuole and interacts with the Rab7/Ypt7-GTP form. Vps11 is a central scaffold protein upon which both HOPS and CORVET assemble. The HOPS and CORVET complexes disassemble in the absence of Vps11, resulting in massive fragmentation of vacuoles. Vps11 contains a clathrin repeat domain and a C-terminal C3H2C3-type RING-H2 finger. This subfamily also includes Vps11 homologs found in fungi, such as Saccharomyces cerevisiae vacuolar membrane protein Pep5p, also known as carboxypeptidase Y-deficient protein 5, vacuolar morphogenesis protein 1, or vacuolar biogenesis protein END1. Pep5p is essential for vacuolar biogenesis. It associates with Pep3p to form a core Pep3p/Pep5p complex that promotes vesicular docking/fusion reactions in conjunction with SNARE proteins at multiple steps in transport routes to the vacuole.


Pssm-ID: 438349 [Multi-domain]  Cd Length: 44  Bit Score: 85.09  E-value: 2.17e-20
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1443074344 814 SKCTTCTFTLDLPAVHFMCMHSFHLRCLGD---NEKECPECAPE 854
Cdd:cd16688     1 TKCSACGSTLDLPSVHFLCGHSFHQHCLEDyeeNDRECPLCAPE 44
VPS11_C pfam12451
Vacuolar protein sorting protein 11 C terminal; This domain family is found in eukaryotes, and ...
 855-897 3.44e-12

Vacuolar protein sorting protein 11 C terminal; This domain family is found in eukaryotes, and is approximately 50 amino acids in length. Vps 11 is one of the evolutionarily conserved class C vacuolar protein sorting genes (c-vps: vps11, vps16, vps18, and vps33), whose products physically associate to form the c-vps protein complex required for vesicle docking and fusion.


Pssm-ID: 463590  Cd Length: 44  Bit Score: 61.65  E-value: 3.44e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1443074344 855 YRSVMEAKQKLEHNARDHDLFFRQLRGSKDGFSVVADYFSKGI 897
Cdd:pfam12451   1 NETIRELRRAQEESADQHDLFKSALEESTDRFKVIADYFGRGV 43
Clathrin pfam00637
Region in Clathrin and VPS; Each region is about 140 amino acids long. The regions are ...
 357-473 1.97e-10

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: 59.58  E-value: 1.97e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443074344 357 LEPSYVIQKFLDAKRIYNLTNYLEKLHDRGL-ASKDHTTLLLNCYTKLKDVEKLNHFIKDEDgvgeiKFDVETAIRVCRA 435
Cdd:pfam00637   8 IDVSRVVKLFEKAGLLEELISYLESALKEDSrENPALQTALIELYAKYDDPEELEEFLKKNN-----NYDLEKVAKLCEK 82

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1443074344 436 AGYHEHAMFVAKKAGRHELYLKiLLEDLGRYDEALQYI 473
Cdd:pfam00637  83 ADLYEEAVILYKKIGNWKEAIS-LLKKLGDYKDAIEYA 119
Clathrin pfam00637
Region in Clathrin and VPS; Each region is about 140 amino acids long. The regions are ...
 651-727 3.25e-04

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: 41.86  E-value: 3.25e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1443074344 651 YDVDLALIICNANAFKDGLLFLYEKLKLFKEVISCYKQAHDHEGLIACCKKLgdssqgGDPSLWGDLLKYFSELGED 727
Cdd:pfam00637  71 YDLEKVAKLCEKADLYEEAVILYKKIGNWKEAISLLKKLGDYKDAIEYAVKS------SNPELWEELLEALLDNGRF 141
zf-C3H2C3 pfam17122
Zinc-finger;
816-851 7.58e-04

Zinc-finger;


Pssm-ID: 293727  Cd Length: 35  Bit Score: 37.96  E-value: 7.58e-04
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1443074344 816 CTTCTFTLDLPAVHFMCMHSFHLRCLgdNEKECPEC 851
Cdd:pfam17122   1 CDNCGLKLDYPFVHYSCNHSVHTKCV--DPEICPLC 34
CLH smart00299
Clathrin heavy chain repeat homology;
357-473 1.82e-03

Clathrin heavy chain repeat homology;


Pssm-ID: 128594 [Multi-domain]  Cd Length: 140  Bit Score: 39.56  E-value: 1.82e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443074344  357 LEPSYVIQKFLDAKRIYNLTNYLEKLHDRGLASKD-HTTLL-LNCYTKLKDVekLNHFIKDEDgvgeiKFDVETAIRVCR 434
Cdd:smart00299   8 IDVSEVVELFEKRNLLEELIPYLESALKLNSENPAlQTKLIeLYAKYDPQKE--IERLDNKSN-----HYDIEKVGKLCE 80

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 1443074344  435 AAGYHEHAMFVAKKAGRHELYLKILLEDLGRYDEALQYI 473
Cdd:smart00299  81 KAKLYEEAVELYKKDGNFKDAIVTLIEHLGNYEKAIEYF 119
zf-RVT pfam13966
zinc-binding in reverse transcriptase; This domain would appear to be a zinc-binding region of ...
 8-32 2.66e-03

zinc-binding in reverse transcriptase; This domain would appear to be a zinc-binding region of a putative reverse transcriptase.


Pssm-ID: 433612  Cd Length: 84  Bit Score: 37.64  E-value: 2.66e-03
                          10        20
                  ....*....|....*....|....*.
gi 1443074344   8 KCMAP-KIKIFTWRLLMGALPTATRL 32
Cdd:pfam13966  25 KKKAPpKVKFFLWLALRNRLPTADRL 50
RING-H2_Vps cd16484
RING finger, H2 subclass, found in vacuolar protein sorting-associated proteins Vps8, Vps11, ...
 815-851 3.27e-03

RING finger, H2 subclass, found in vacuolar protein sorting-associated proteins Vps8, Vps11, Vps18, Vps41, and similar proteins; This subfamily corresponds to a group of vacuolar protein sorting-associated proteins containing a C-terminal C3H2C3-type RING-H2 finger, which includes Vps8, Vps11, Vps18, and Vps41. Vps11 and Vps18 associate with Vps16 and Vps33 to form a Class C Vps core complex that is required for soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNARE)-mediated membrane fusion at the lysosome-like yeast vacuole. The core complex, together with two additional compartment-specific subunits, forms the tethering complexes HOPS (homotypic vacuole fusion and protein sorting) and CORVET (class C core vacuole/endosome transport). CORVET contains the additional Vps3 and Vps8 subunits. It operates at endosomes, controls traffic into late endosomes and interacts with the Rab5/Vps21-GTP form. HOPS contains the additional Vps39 and Vps41 subunits. It operates at the lysosomal vacuole, controls all traffic from late endosomes into the vacuole and interacts with the Rab7/Ypt7-GTP form.


Pssm-ID: 438147  Cd Length: 48  Bit Score: 36.33  E-value: 3.27e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1443074344 815 KCTTCTF-------TLDLPAVHFMCMHSFHLRCL---GDNEKECPEC 851
Cdd:cd16484     1 KCPICTLplkesdvGANSPVVVFFCGHMFHKFCLpelSMTEAACPIC 47
 
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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