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Conserved domains on  [gi|1907068648|ref|XP_036020426|]
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ubiquitin carboxyl-terminal hydrolase 40 isoform X2 [Mus musculus]

Protein Classification

ubiquitin family protein( domain architecture ID 1000087)

ubiquitin family protein belongs to an diverse class of protein modifier and gene expression regulatory proteins that participate in a number of cellular processes

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Ubl1_cv_Nsp3_N-like super family cl28922
first ubiquitin-like (Ubl) domain located at the N-terminus of coronavirus SARS-CoV ...
 30-95 7.57e-03

first ubiquitin-like (Ubl) domain located at the N-terminus of coronavirus SARS-CoV non-structural protein 3 (Nsp3) and related proteins; This ubiquitin-like (Ubl) domain (Ubl1) is found at the N-terminus of coronavirus Nsp3, a large multi-functional multi-domain protein which is an essential component of the replication/transcription complex (RTC). The functions of Ubl1 in CoVs are related to single-stranded RNA (ssRNA) binding and to interacting with the nucleocapsid (N) protein. SARS-CoV Ubl1 has been shown to bind ssRNA having AUA patterns, and since the 5'-UTR of the SARS-CoV genome has a number of AUA repeats, it may bind there. In mouse hepatitis virus (MHV), this Ubl1 domain binds the cognate N protein. Adjacent to Ubl1 is a Glu-rich acidic region (also referred to as hypervariable region, HVR); Ubl1 together with HVR has been called Nsp3a. Currently, the function of HVR in CoVs is unknown. This model corresponds to one of two Ubl domains in Nsp3; the other is located N-terminal to the papain-like protease (PLpro) and is not represented by this model.


The actual alignment was detected with superfamily member cd17058:

Pssm-ID: 475130  Cd Length: 89  Bit Score: 35.57  E-value: 7.57e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907068648  30 PGAEMDIIVEETLSVRDcLK--------IMLEKSGQQGEI-W-HLRKMDW-CYEaGEPLCEEDATLKELMIRSGDTL 95
Cdd:cd17058    10 DGESLPVVVPQNATVLD-LKkaieryftLKLKREGGTKKIsWkYVWKTYClCFD-GQKLTDDKAKLKDYGIRNGDEL 84
 
Name Accession Description Interval E-value
Ubl_SNRNP25 cd17058
ubiquitin-like (Ubl) domain found in small nuclear ribonucleoprotein U11/U12 subunit 25 ...
 30-95 7.57e-03

ubiquitin-like (Ubl) domain found in small nuclear ribonucleoprotein U11/U12 subunit 25 (SNRNP25) and similar proteins; SNRNP25, also termed U11/U12 small nuclear ribonucleoprotein 25 kDa protein, U11/U12 snRNP 25 kDa protein (U11/U12-25K), or minus-99 protein, is a component of the U11/U12 snRNPs that are part of the U12-type spliceosome. It contains a conserved ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions.


Pssm-ID: 340578  Cd Length: 89  Bit Score: 35.57  E-value: 7.57e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907068648  30 PGAEMDIIVEETLSVRDcLK--------IMLEKSGQQGEI-W-HLRKMDW-CYEaGEPLCEEDATLKELMIRSGDTL 95
Cdd:cd17058    10 DGESLPVVVPQNATVLD-LKkaieryftLKLKREGGTKKIsWkYVWKTYClCFD-GQKLTDDKAKLKDYGIRNGDEL 84
 
Name Accession Description Interval E-value
Ubl_SNRNP25 cd17058
ubiquitin-like (Ubl) domain found in small nuclear ribonucleoprotein U11/U12 subunit 25 ...
 30-95 7.57e-03

ubiquitin-like (Ubl) domain found in small nuclear ribonucleoprotein U11/U12 subunit 25 (SNRNP25) and similar proteins; SNRNP25, also termed U11/U12 small nuclear ribonucleoprotein 25 kDa protein, U11/U12 snRNP 25 kDa protein (U11/U12-25K), or minus-99 protein, is a component of the U11/U12 snRNPs that are part of the U12-type spliceosome. It contains a conserved ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions.


Pssm-ID: 340578  Cd Length: 89  Bit Score: 35.57  E-value: 7.57e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907068648  30 PGAEMDIIVEETLSVRDcLK--------IMLEKSGQQGEI-W-HLRKMDW-CYEaGEPLCEEDATLKELMIRSGDTL 95
Cdd:cd17058    10 DGESLPVVVPQNATVLD-LKkaieryftLKLKREGGTKKIsWkYVWKTYClCFD-GQKLTDDKAKLKDYGIRNGDEL 84
 
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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