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Conserved domains on  [gi|1958790382|ref|XP_038935445|]
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derlin-1 isoform X1 [Rattus norvegicus]

Protein Classification

rhomboid family protein( domain architecture ID 229382)

rhomboid family protein may be a membrane-bound serine protease that catalyzes regulated intramembrane proteolysis, resulting in the release of functional polypeptides from their membrane anchors

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Rhomboid super family cl21536
Rhomboid family; This family contains integral membrane proteins that are related to ...
 1-104 1.18e-45

Rhomboid family; This family contains integral membrane proteins that are related to Drosophila rhomboid protein. Members of this family are found in bacteria and eukaryotes. Rhomboid promotes the cleavage of the membrane-anchored TGF-alpha-like growth factor Spitz, allowing it to activate the Drosophila EGF receptor. Analysis has shown that Rhomboid-1 is an intramembrane serine protease (EC:3.4.21.105). Parasite-encoded rhomboid enzymes are also important for invasion of host cells by Toxoplasma and the malaria parasite.


The actual alignment was detected with superfamily member pfam04511:

Pssm-ID: 451297  Cd Length: 191  Bit Score: 147.50  E-value: 1.18e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958790382   1 MLLFNWICIVITGLAMDMQLLMIPLIMSVLYVWAQLNRDLIVSFWFGTRFKACYLPWVILGFNYIIGGSVINELIGNLVG 80
Cdd:pfam04511  88 MLLFGAVLITIFGLIVDIYFLGQALIAMIVYVWSQRNPDVIVSFWFGLRFQAKYLPWVLLGFSFILGGSVVVDLIGILVG 167

                          90       100
                  ....*....|....*....|....
gi 1958790382  81 HLYFFLMFRYPMDLGGRNFLSTPQ 104
Cdd:pfam04511 168 HIYFFLEDVYPIDLGGKRLLSTPQ 191
 
Name Accession Description Interval E-value
DER1 pfam04511
Der1-like family; The endoplasmic reticulum (ER) of the yeast Saccharomyces cerevisiae ...
 1-104 1.18e-45

Der1-like family; The endoplasmic reticulum (ER) of the yeast Saccharomyces cerevisiae contains of proteolytic system able to selectively degrade misfolded lumenal secretory proteins. For examination of the components involved in this degradation process, mutants were isolated. They could be divided into four complementation groups. The mutations led to stabilization of two different substrates for this process. The mutant classes were called 'der' for 'degradation in the ER'. DER1 was cloned by complementation of the der1-2 mutation. The DER1 gene codes for a novel, hydrophobic protein, that is localized to the ER. Deletion of DER1 abolished degradation of the substrate proteins. The function of the Der1 protein seems to be specifically required for the degradation process associated with the ER. Interestingly this family seems distantly related to the Rhomboid family of membrane peptidases. Suggesting that this family may also mediate degradation of misfolded proteins (Bateman A pers. obs.).


Pssm-ID: 427988  Cd Length: 191  Bit Score: 147.50  E-value: 1.18e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958790382   1 MLLFNWICIVITGLAMDMQLLMIPLIMSVLYVWAQLNRDLIVSFWFGTRFKACYLPWVILGFNYIIGGSVINELIGNLVG 80
Cdd:pfam04511  88 MLLFGAVLITIFGLIVDIYFLGQALIAMIVYVWSQRNPDVIVSFWFGLRFQAKYLPWVLLGFSFILGGSVVVDLIGILVG 167

                          90       100
                  ....*....|....*....|....
gi 1958790382  81 HLYFFLMFRYPMDLGGRNFLSTPQ 104
Cdd:pfam04511 168 HIYFFLEDVYPIDLGGKRLLSTPQ 191
COG5291 COG5291
Predicted membrane protein [Function unknown];
25-103 1.95e-06

Predicted membrane protein [Function unknown];


Pssm-ID: 227611  Cd Length: 313  Bit Score: 45.75  E-value: 1.95e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958790382  25 LIMSVLYVWAQLNRDLIVSFWFGTRFKACYLPWVILGFNYIIGGSV-INELIGNLVGHLYFFLMFRYPMdlGGRNFLSTP 103
Cdd:COG5291   131 FSATITYIWSKRNPRAIIQFFGFISVPGKYLPFILLGFSFLSRRGIsIDDVLGFVVGHLFHYFGDIYPM--IGRDILSTP 208
 
Name Accession Description Interval E-value
DER1 pfam04511
Der1-like family; The endoplasmic reticulum (ER) of the yeast Saccharomyces cerevisiae ...
 1-104 1.18e-45

Der1-like family; The endoplasmic reticulum (ER) of the yeast Saccharomyces cerevisiae contains of proteolytic system able to selectively degrade misfolded lumenal secretory proteins. For examination of the components involved in this degradation process, mutants were isolated. They could be divided into four complementation groups. The mutations led to stabilization of two different substrates for this process. The mutant classes were called 'der' for 'degradation in the ER'. DER1 was cloned by complementation of the der1-2 mutation. The DER1 gene codes for a novel, hydrophobic protein, that is localized to the ER. Deletion of DER1 abolished degradation of the substrate proteins. The function of the Der1 protein seems to be specifically required for the degradation process associated with the ER. Interestingly this family seems distantly related to the Rhomboid family of membrane peptidases. Suggesting that this family may also mediate degradation of misfolded proteins (Bateman A pers. obs.).


Pssm-ID: 427988  Cd Length: 191  Bit Score: 147.50  E-value: 1.18e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958790382   1 MLLFNWICIVITGLAMDMQLLMIPLIMSVLYVWAQLNRDLIVSFWFGTRFKACYLPWVILGFNYIIGGSVINELIGNLVG 80
Cdd:pfam04511  88 MLLFGAVLITIFGLIVDIYFLGQALIAMIVYVWSQRNPDVIVSFWFGLRFQAKYLPWVLLGFSFILGGSVVVDLIGILVG 167

                          90       100
                  ....*....|....*....|....
gi 1958790382  81 HLYFFLMFRYPMDLGGRNFLSTPQ 104
Cdd:pfam04511 168 HIYFFLEDVYPIDLGGKRLLSTPQ 191
COG5291 COG5291
Predicted membrane protein [Function unknown];
25-103 1.95e-06

Predicted membrane protein [Function unknown];


Pssm-ID: 227611  Cd Length: 313  Bit Score: 45.75  E-value: 1.95e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958790382  25 LIMSVLYVWAQLNRDLIVSFWFGTRFKACYLPWVILGFNYIIGGSV-INELIGNLVGHLYFFLMFRYPMdlGGRNFLSTP 103
Cdd:COG5291   131 FSATITYIWSKRNPRAIIQFFGFISVPGKYLPFILLGFSFLSRRGIsIDDVLGFVVGHLFHYFGDIYPM--IGRDILSTP 208
 
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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