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Conserved domains on  [gi|114199475|ref|NP_055211|]
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vacuolar protein sorting-associated protein 41 homolog isoform 1 [Homo sapiens]

Protein Classification

vacuolar protein sorting-associated protein 41 homolog( domain architecture ID 12201336)

vacuolar protein sorting-associated protein 41 homolog (Vps41) is a protein involved in trafficking of proteins from the late Golgi to the vacuole

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CLH smart00299
Clathrin heavy chain repeat homology;
571-708 7.69e-31

Clathrin heavy chain repeat homology;


:

Pssm-ID: 128594 [Multi-domain]  Cd Length: 140  Bit Score: 118.15  E-value: 7.69e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114199475   571 LLDNEDKISIKKVVEELEDR--PELQHVYLHKLFKRDHhKGQRYHEKQISLYAEYDRPNLLPFL-RDSTHCPLEKALEIC 647
Cdd:smart00299   1 LLEVSDPIDVSEVVELFEKRnlLEELIPYLESALKLNS-ENPALQTKLIELYAKYDPQKEIERLdNKSNHYDIEKVGKLC 79

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 114199475   648 QQRNFVEETVYLLSRMGNSRSALKMIMEELHDVDKAIEFAKEQDDGELWEDLILYSIDKPP 708
Cdd:smart00299  80 EKAKLYEEAVELYKKDGNFKDAIVTLIEHLGNYEKAIEYFVKQNNPELWAEVLKALLDKPR 140
RING-H2_Vps41 cd16690
RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 41 (Vps41) and ...
 787-841 5.04e-25

RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 41 (Vps41) and similar proteins; Vps41, also known as S53, is a protein involved in trafficking of proteins from the late Golgi to the vacuole. It interacts with caspase-8, suggesting a potential role of Vps41 beyond lysosomal trafficking. It has been identified as a potential therapeutic target for human Parkinson's disease (PD). Vps41 and the soluble N-ethylmaleimide-sensitive factor attachment protein receptors protein VAMP7 are specifically involved in the fusion of the trans-Golgi network-derived lysosome-associated membrane protein carriers with late endosomes. Vps41 is a specific subunit of the lysosomal tethering complex HOPS (homotypic vacuole fusion and protein sorting) that also includes Vps39 and a Class C Vps core complex composed of Vps11, Vps16, Vps18, and Vps33. HOPS operates at the lysosomal vacuole, controls all traffic from late endosomes into the vacuole and interacts with the Rab7/Ypt7-GTP form. The HOPS-specific Vps39 and Vps41 subunits belong to the class B Vps. They form a subcomplex that interacts with Rab7/Ypt7 and is are required for homotypic and heterotypic late endosome fusion. Vps41 contains an N-terminal WD40 repeat, one or two clathrin repeats and a C3H2C3-type RING-H2 finger domain close to its C-terminus.


:

Pssm-ID: 438351  Cd Length: 51  Bit Score: 98.20  E-value: 5.04e-25
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 114199475 787 EENICESCLSPILPSDAAKPFSVVVFHCRHMFHKECLPMPSMnsaaQFCNICSAK 841
Cdd:cd16690    1 EEQICEACHRPLLVSDLRKAFNVVVFFCRHAFHEDCLPAQNV----EFCNICSAQ 51
 
Name Accession Description Interval E-value
CLH smart00299
Clathrin heavy chain repeat homology;
571-708 7.69e-31

Clathrin heavy chain repeat homology;


Pssm-ID: 128594 [Multi-domain]  Cd Length: 140  Bit Score: 118.15  E-value: 7.69e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114199475   571 LLDNEDKISIKKVVEELEDR--PELQHVYLHKLFKRDHhKGQRYHEKQISLYAEYDRPNLLPFL-RDSTHCPLEKALEIC 647
Cdd:smart00299   1 LLEVSDPIDVSEVVELFEKRnlLEELIPYLESALKLNS-ENPALQTKLIELYAKYDPQKEIERLdNKSNHYDIEKVGKLC 79

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 114199475   648 QQRNFVEETVYLLSRMGNSRSALKMIMEELHDVDKAIEFAKEQDDGELWEDLILYSIDKPP 708
Cdd:smart00299  80 EKAKLYEEAVELYKKDGNFKDAIVTLIEHLGNYEKAIEYFVKQNNPELWAEVLKALLDKPR 140
Clathrin pfam00637
Region in Clathrin and VPS; Each region is about 140 amino acids long. The regions are ...
 571-710 2.06e-27

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: 108.11  E-value: 2.06e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114199475  571 LLDNEDKISIKKVVEELEDR--PELQHVYLHKLFKRDHHKGQRYHEKQISLYAEYDRP-NLLPFLRDSTHCPLEKALEIC 647
Cdd:pfam00637   1 LIESTDPIDVSRVVKLFEKAglLEELISYLESALKEDSRENPALQTALIELYAKYDDPeELEEFLKKNNNYDLEKVAKLC 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 114199475  648 QQRNFVEETVYLLSRMGNSRSALKMImEELHDVDKAIEFAKEQDDGELWEDLILYSIDKPPFI 710
Cdd:pfam00637  81 EKADLYEEAVILYKKIGNWKEAISLL-KKLGDYKDAIEYAVKSSNPELWEELLEALLDNGRFE 142
RING-H2_Vps41 cd16690
RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 41 (Vps41) and ...
 787-841 5.04e-25

RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 41 (Vps41) and similar proteins; Vps41, also known as S53, is a protein involved in trafficking of proteins from the late Golgi to the vacuole. It interacts with caspase-8, suggesting a potential role of Vps41 beyond lysosomal trafficking. It has been identified as a potential therapeutic target for human Parkinson's disease (PD). Vps41 and the soluble N-ethylmaleimide-sensitive factor attachment protein receptors protein VAMP7 are specifically involved in the fusion of the trans-Golgi network-derived lysosome-associated membrane protein carriers with late endosomes. Vps41 is a specific subunit of the lysosomal tethering complex HOPS (homotypic vacuole fusion and protein sorting) that also includes Vps39 and a Class C Vps core complex composed of Vps11, Vps16, Vps18, and Vps33. HOPS operates at the lysosomal vacuole, controls all traffic from late endosomes into the vacuole and interacts with the Rab7/Ypt7-GTP form. The HOPS-specific Vps39 and Vps41 subunits belong to the class B Vps. They form a subcomplex that interacts with Rab7/Ypt7 and is are required for homotypic and heterotypic late endosome fusion. Vps41 contains an N-terminal WD40 repeat, one or two clathrin repeats and a C3H2C3-type RING-H2 finger domain close to its C-terminus.


Pssm-ID: 438351  Cd Length: 51  Bit Score: 98.20  E-value: 5.04e-25
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 114199475 787 EENICESCLSPILPSDAAKPFSVVVFHCRHMFHKECLPMPSMnsaaQFCNICSAK 841
Cdd:cd16690    1 EEQICEACHRPLLVSDLRKAFNVVVFFCRHAFHEDCLPAQNV----EFCNICSAQ 51
 
Name Accession Description Interval E-value
CLH smart00299
Clathrin heavy chain repeat homology;
571-708 7.69e-31

Clathrin heavy chain repeat homology;


Pssm-ID: 128594 [Multi-domain]  Cd Length: 140  Bit Score: 118.15  E-value: 7.69e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114199475   571 LLDNEDKISIKKVVEELEDR--PELQHVYLHKLFKRDHhKGQRYHEKQISLYAEYDRPNLLPFL-RDSTHCPLEKALEIC 647
Cdd:smart00299   1 LLEVSDPIDVSEVVELFEKRnlLEELIPYLESALKLNS-ENPALQTKLIELYAKYDPQKEIERLdNKSNHYDIEKVGKLC 79

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 114199475   648 QQRNFVEETVYLLSRMGNSRSALKMIMEELHDVDKAIEFAKEQDDGELWEDLILYSIDKPP 708
Cdd:smart00299  80 EKAKLYEEAVELYKKDGNFKDAIVTLIEHLGNYEKAIEYFVKQNNPELWAEVLKALLDKPR 140
Clathrin pfam00637
Region in Clathrin and VPS; Each region is about 140 amino acids long. The regions are ...
 571-710 2.06e-27

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: 108.11  E-value: 2.06e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114199475  571 LLDNEDKISIKKVVEELEDR--PELQHVYLHKLFKRDHHKGQRYHEKQISLYAEYDRP-NLLPFLRDSTHCPLEKALEIC 647
Cdd:pfam00637   1 LIESTDPIDVSRVVKLFEKAglLEELISYLESALKEDSRENPALQTALIELYAKYDDPeELEEFLKKNNNYDLEKVAKLC 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 114199475  648 QQRNFVEETVYLLSRMGNSRSALKMImEELHDVDKAIEFAKEQDDGELWEDLILYSIDKPPFI 710
Cdd:pfam00637  81 EKADLYEEAVILYKKIGNWKEAISLL-KKLGDYKDAIEYAVKSSNPELWEELLEALLDNGRFE 142
RING-H2_Vps41 cd16690
RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 41 (Vps41) and ...
 787-841 5.04e-25

RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 41 (Vps41) and similar proteins; Vps41, also known as S53, is a protein involved in trafficking of proteins from the late Golgi to the vacuole. It interacts with caspase-8, suggesting a potential role of Vps41 beyond lysosomal trafficking. It has been identified as a potential therapeutic target for human Parkinson's disease (PD). Vps41 and the soluble N-ethylmaleimide-sensitive factor attachment protein receptors protein VAMP7 are specifically involved in the fusion of the trans-Golgi network-derived lysosome-associated membrane protein carriers with late endosomes. Vps41 is a specific subunit of the lysosomal tethering complex HOPS (homotypic vacuole fusion and protein sorting) that also includes Vps39 and a Class C Vps core complex composed of Vps11, Vps16, Vps18, and Vps33. HOPS operates at the lysosomal vacuole, controls all traffic from late endosomes into the vacuole and interacts with the Rab7/Ypt7-GTP form. The HOPS-specific Vps39 and Vps41 subunits belong to the class B Vps. They form a subcomplex that interacts with Rab7/Ypt7 and is are required for homotypic and heterotypic late endosome fusion. Vps41 contains an N-terminal WD40 repeat, one or two clathrin repeats and a C3H2C3-type RING-H2 finger domain close to its C-terminus.


Pssm-ID: 438351  Cd Length: 51  Bit Score: 98.20  E-value: 5.04e-25
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 114199475 787 EENICESCLSPILPSDAAKPFSVVVFHCRHMFHKECLPMPSMnsaaQFCNICSAK 841
Cdd:cd16690    1 EEQICEACHRPLLVSDLRKAFNVVVFFCRHAFHEDCLPAQNV----EFCNICSAQ 51
RING-H2_Vps cd16484
RING finger, H2 subclass, found in vacuolar protein sorting-associated proteins Vps8, Vps11, ...
 790-839 3.29e-16

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: 72.92  E-value: 3.29e-16
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 114199475 790 ICESCLSPILPSDAAKPFSVVVFHCRHMFHKECLPMPSMNsaAQFCNICS 839
Cdd:cd16484    1 KCPICTLPLKESDVGANSPVVVFFCGHMFHKFCLPELSMT--EAACPICL 48
RING-H2_Pep3p-like cd16462
RING finger, H2 subclass, found in Saccharomyces cerevisiae vacuolar membrane protein PEP3 ...
 791-823 3.65e-03

RING finger, H2 subclass, found in Saccharomyces cerevisiae vacuolar membrane protein PEP3 (Pep3p) and similar proteins; Pep3p, also known as carboxypeptidase Y-deficient protein 3, vacuolar morphogenesis protein 8, vacuolar protein sorting-associated protein 18 (Vps18p), or vacuolar protein-targeting protein 18, is a vacuolar membrane protein that affects late Golgi functions required for vacuolar protein sorting and efficient alpha-factor prohormone maturation. It is required for vacuolar biogenesis and for trafficking of hydrolase precursors to the vacuole. The disruption of PEP3 may cause hypersensitivity to heat shock and ethanol stresses, probably due to disappearance of normal vacuoles. As a component of the homotypic fusion and vacuole protein sorting (HOPS) and class C core vacuole/endosome tethering (CORVET) complexes, its overexpression shortens lag phase but does not alter growth rate in Saccharomyces cerevisiae exposed to acetic acid stress. Moreover, Pep3p forms the Class C Vps protein complex (C-Vps complex) with Pep5p (also known as Vps11), Vps16, and Vps33, and is necessary for trafficking of hydrolase precursors to the vacuole by promoting vesicular docking reactions with SNARE proteins. Pep3p contains a C3H2C3-type RING-H2 finger at the C-terminus.


Pssm-ID: 438125 [Multi-domain]  Cd Length: 50  Bit Score: 36.12  E-value: 3.65e-03
                         10        20        30
                 ....*....|....*....|....*....|...
gi 114199475 791 CESCLSPILpsdaAKPFsvVVFHCRHMFHKECL 823
Cdd:cd16462    3 CAVCGRPLL----TRQF--YVFPCQHAFHADCL 29
 
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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