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Conserved domains on  [gi|1831520193|ref|NP_001367568|]
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Vacuolar protein sorting-associated protein 41 homolog [Caenorhabditis elegans]

Protein Classification

WD40 and CLH domain-containing protein( domain architecture ID 11457046)

protein containing domains WD40, CLH, and RING_Ubox

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CLH smart00299
Clathrin heavy chain repeat homology;
621-755 5.11e-29

Clathrin heavy chain repeat homology;


:

Pssm-ID: 128594 [Multi-domain]  Cd Length: 140  Bit Score: 112.75  E-value: 5.11e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1831520193  621 LLDNADSVEPSFVMEKI--GRQPKLQLAYLTKLMSRN-EGTEFADKAVQLYAEYDQKKLLPFL-RKNANYNVNKARKLCS 696
Cdd:smart00299   1 LLEVSDPIDVSEVVELFekRNLLEELIPYLESALKLNsENPALQTKLIELYAKYDPQKEIERLdNKSNHYDIEKVGKLCE 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1831520193  697 DKGYIEETIYLLAKSGNHYDAVKMMVREYRNMEKVIDYCKDQNDPDLWIHLLGVVAEFP 755
Cdd:smart00299  81 KAKLYEEAVELYKKDGNFKDAIVTLIEHLGNYEKAIEYFVKQNNPELWAEVLKALLDKP 139
RING_Ubox super family cl17238
RING finger (Really Interesting New Gene) domain and U-box domain superfamily; The RING finger ...
 838-893 4.27e-03

RING finger (Really Interesting New Gene) domain and U-box domain superfamily; The RING finger is a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc. It is defined by the "cross-brace" motif that chelates zinc atoms by eight amino acid residues, typically Cys or His, arranged in a characteristic spacing. Canonical RING motifs have been categorized into two major subclasses, RING-HC (C3HC4-type) and RING-H2 (C3H2C3-type), according to their Cys/His content. There are also many variants of RING fingers: some have different Cys/His patterns while some lack a single Cys or His residue at typical Zn ligand positions (the fourth or eighth zinc ligand is prevalently exchanged for an Asp, which can indeed chelate Zn in a RING finger as well). C4C4-, C3HC3D-, C2H2C4-, and C3HC5-type RING fingers are closely related to RING-HC fingers. In contrast, C4HC3- (RING-CH alias RINGv), C3H3C2-, C3H2C2D-, C3DHC3-, and C4HC2H-type RING fingers are more closely related to RING-H2 fingers. However, not all RING finger-containing proteins display regular RING finger features, and the RING finger family has turned out to be multifarious. The degenerate RING fingers of the Siz/PIAS RING (SP-RING) family proteins and sporulation protein RMD5, are characterized by lacking the second, fifth, and sixth Zn2+ ion-coordinating residues. They bind only one Zn2+ ion. On the other hand, the RING fingers of the human APC11 and RBX1 proteins can bind a third Zn atom since they harbor four additional Zn ligands. U-box is a modified form of the RING finger domain that lacks metal chelating Cys and His residues. It resembles the cross-brace RING structure consisting of three beta-sheets and a single alpha-helix, which would be stabilized by salt bridges instead of chelated metal ions. U-box proteins are widely distributed among eukaryotic organisms and show a higher prevalence in plants than in other organisms. RING finger/U-box-containing proteins are a group of diverse proteins with a variety of cellular functions, including oncogenesis, development, viral replication, signal transduction, the cell cycle and apoptosis. Many of them are ubiquitin-protein ligases (E3s) that serve as scaffolds for binding to ubiquitin-conjugating enzymes (E2s, also referred to as ubiquitin carrier proteins or UBCs) in close proximity to substrate proteins, which enable efficient transfer of ubiquitin from E2 to the substrates.


The actual alignment was detected with superfamily member cd16687:

Pssm-ID: 473075  Cd Length: 54  Bit Score: 36.27  E-value: 4.27e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1831520193 838 RCSLCAQIIINSNQETTkkfsdIKVFKCGHIFHLAC-----STSEMERRqsiEEGLCIACS 893
Cdd:cd16687     2 SCCICLKPYKRREDNDE-----VIVFSCGHAYHSTClrskgSGVVTDGQ---ERWTCYLCN 54
HRD1 super family cl34953
HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein ...
 791-883 9.60e-03

HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones];


The actual alignment was detected with superfamily member COG5243:

Pssm-ID: 227568 [Multi-domain]  Cd Length: 491  Bit Score: 39.57  E-value: 9.60e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1831520193 791 LDKLLVDYTNHAELQQCCYDstLNDLNVLTQGLISAADESVsvnivsrCSLCAQIIINSNQETTKKFSDIKVFK--CGHI 868
Cdd:COG5243   251 FYALFRRIREHARFRRATKD--LNAMYPTATEEQLTNSDRT-------CTICMDEMFHPDHEPLPRGLDMTPKRlpCGHI 321

                          90
                  ....*....|....*
gi 1831520193 869 FHLACSTSEMERRQS 883
Cdd:COG5243   322 LHLHCLKNWLERQQT 336
 
Name Accession Description Interval E-value
CLH smart00299
Clathrin heavy chain repeat homology;
621-755 5.11e-29

Clathrin heavy chain repeat homology;


Pssm-ID: 128594 [Multi-domain]  Cd Length: 140  Bit Score: 112.75  E-value: 5.11e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1831520193  621 LLDNADSVEPSFVMEKI--GRQPKLQLAYLTKLMSRN-EGTEFADKAVQLYAEYDQKKLLPFL-RKNANYNVNKARKLCS 696
Cdd:smart00299   1 LLEVSDPIDVSEVVELFekRNLLEELIPYLESALKLNsENPALQTKLIELYAKYDPQKEIERLdNKSNHYDIEKVGKLCE 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1831520193  697 DKGYIEETIYLLAKSGNHYDAVKMMVREYRNMEKVIDYCKDQNDPDLWIHLLGVVAEFP 755
Cdd:smart00299  81 KAKLYEEAVELYKKDGNFKDAIVTLIEHLGNYEKAIEYFVKQNNPELWAEVLKALLDKP 139
Clathrin pfam00637
Region in Clathrin and VPS; Each region is about 140 amino acids long. The regions are ...
 640-744 6.71e-15

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: 72.67  E-value: 6.71e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1831520193 640 QPKLQLAYLTKLMSRNEgteFADKAVQ-----LYAEYDQ-KKLLPFLRKNANYNVNKARKLCSDKGYIEETIYLLAKSGN 713
Cdd:pfam00637  22 LLEELISYLESALKEDS---RENPALQtalieLYAKYDDpEELEEFLKKNNNYDLEKVAKLCEKADLYEEAVILYKKIGN 98

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1831520193 714 HYDAVKMMVREyRNMEKVIDYCKDQNDPDLW 744
Cdd:pfam00637  99 WKEAISLLKKL-GDYKDAIEYAVKSSNPELW 128
RING-H2_Vps8 cd16687
RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 8 (Vps8) and ...
 838-893 4.27e-03

RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 8 (Vps8) and similar proteins; Vps8 is the Rab-specific subunit of the endosomal tethering complex CORVET (class C core vacuole/endosome transport) that also includes Vps3 and a Class C Vps core complex composed of Vps11, Vps16, Vps18, and Vps33. CORVET operates at endosomes, controls traffic into late endosomes, and interacts with the Rab5/Vps21-GTP form. The CORVET-specific Vps3 and Vps8 subunits belong to the class D Vps. They form a subcomplex that interact with Rab5/Vps21, and is critical for localization and function of the CORVET tethering complex on endosomes. Vps8 contains an N-terminal WD40 repeat and a C-terminal C3H2C3-type RING-H2 finger.


Pssm-ID: 438348  Cd Length: 54  Bit Score: 36.27  E-value: 4.27e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1831520193 838 RCSLCAQIIINSNQETTkkfsdIKVFKCGHIFHLAC-----STSEMERRqsiEEGLCIACS 893
Cdd:cd16687     2 SCCICLKPYKRREDNDE-----VIVFSCGHAYHSTClrskgSGVVTDGQ---ERWTCYLCN 54
HRD1 COG5243
HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein ...
 791-883 9.60e-03

HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 227568 [Multi-domain]  Cd Length: 491  Bit Score: 39.57  E-value: 9.60e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1831520193 791 LDKLLVDYTNHAELQQCCYDstLNDLNVLTQGLISAADESVsvnivsrCSLCAQIIINSNQETTKKFSDIKVFK--CGHI 868
Cdd:COG5243   251 FYALFRRIREHARFRRATKD--LNAMYPTATEEQLTNSDRT-------CTICMDEMFHPDHEPLPRGLDMTPKRlpCGHI 321

                          90
                  ....*....|....*
gi 1831520193 869 FHLACSTSEMERRQS 883
Cdd:COG5243   322 LHLHCLKNWLERQQT 336
 
Name Accession Description Interval E-value
CLH smart00299
Clathrin heavy chain repeat homology;
621-755 5.11e-29

Clathrin heavy chain repeat homology;


Pssm-ID: 128594 [Multi-domain]  Cd Length: 140  Bit Score: 112.75  E-value: 5.11e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1831520193  621 LLDNADSVEPSFVMEKI--GRQPKLQLAYLTKLMSRN-EGTEFADKAVQLYAEYDQKKLLPFL-RKNANYNVNKARKLCS 696
Cdd:smart00299   1 LLEVSDPIDVSEVVELFekRNLLEELIPYLESALKLNsENPALQTKLIELYAKYDPQKEIERLdNKSNHYDIEKVGKLCE 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1831520193  697 DKGYIEETIYLLAKSGNHYDAVKMMVREYRNMEKVIDYCKDQNDPDLWIHLLGVVAEFP 755
Cdd:smart00299  81 KAKLYEEAVELYKKDGNFKDAIVTLIEHLGNYEKAIEYFVKQNNPELWAEVLKALLDKP 139
Clathrin pfam00637
Region in Clathrin and VPS; Each region is about 140 amino acids long. The regions are ...
 640-744 6.71e-15

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: 72.67  E-value: 6.71e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1831520193 640 QPKLQLAYLTKLMSRNEgteFADKAVQ-----LYAEYDQ-KKLLPFLRKNANYNVNKARKLCSDKGYIEETIYLLAKSGN 713
Cdd:pfam00637  22 LLEELISYLESALKEDS---RENPALQtalieLYAKYDDpEELEEFLKKNNNYDLEKVAKLCEKADLYEEAVILYKKIGN 98

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1831520193 714 HYDAVKMMVREyRNMEKVIDYCKDQNDPDLW 744
Cdd:pfam00637  99 WKEAISLLKKL-GDYKDAIEYAVKSSNPELW 128
RING-H2_Vps8 cd16687
RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 8 (Vps8) and ...
 838-893 4.27e-03

RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 8 (Vps8) and similar proteins; Vps8 is the Rab-specific subunit of the endosomal tethering complex CORVET (class C core vacuole/endosome transport) that also includes Vps3 and a Class C Vps core complex composed of Vps11, Vps16, Vps18, and Vps33. CORVET operates at endosomes, controls traffic into late endosomes, and interacts with the Rab5/Vps21-GTP form. The CORVET-specific Vps3 and Vps8 subunits belong to the class D Vps. They form a subcomplex that interact with Rab5/Vps21, and is critical for localization and function of the CORVET tethering complex on endosomes. Vps8 contains an N-terminal WD40 repeat and a C-terminal C3H2C3-type RING-H2 finger.


Pssm-ID: 438348  Cd Length: 54  Bit Score: 36.27  E-value: 4.27e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1831520193 838 RCSLCAQIIINSNQETTkkfsdIKVFKCGHIFHLAC-----STSEMERRqsiEEGLCIACS 893
Cdd:cd16687     2 SCCICLKPYKRREDNDE-----VIVFSCGHAYHSTClrskgSGVVTDGQ---ERWTCYLCN 54
HRD1 COG5243
HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein ...
 791-883 9.60e-03

HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 227568 [Multi-domain]  Cd Length: 491  Bit Score: 39.57  E-value: 9.60e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1831520193 791 LDKLLVDYTNHAELQQCCYDstLNDLNVLTQGLISAADESVsvnivsrCSLCAQIIINSNQETTKKFSDIKVFK--CGHI 868
Cdd:COG5243   251 FYALFRRIREHARFRRATKD--LNAMYPTATEEQLTNSDRT-------CTICMDEMFHPDHEPLPRGLDMTPKRlpCGHI 321

                          90
                  ....*....|....*
gi 1831520193 869 FHLACSTSEMERRQS 883
Cdd:COG5243   322 LHLHCLKNWLERQQT 336
 
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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