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Conserved domains on  [gi|557878626|ref|NP_001273635|]
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ubiquitin-fold modifier 1 isoform 4 [Homo sapiens]

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 ...
 4-64 1.01e-37

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 cd01766:

Pssm-ID: 475130  Cd Length: 75  Bit Score: 119.86  E-value: 1.01e-37
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 557878626  4 VSFKITLTSDPRLPYKVLSVPESTPFTAVLKFAAEEFKVPAATSAIITNDGIGINPAQTAG 64
Cdd:cd01766   1 VTFKITLTSDPKLPFKVLSVPEEAPFTAVLKFAAEEFKVPAATSAIITNDGIGINPAQTAG 61
 
Name Accession Description Interval E-value
Ubl_UFM1 cd01766
ubiquitin-like (Ubl) domain found in ubiquitin fold modifier 1 (UFM1); UFM1 belongs to the ...
 4-64 1.01e-37

ubiquitin-like (Ubl) domain found in ubiquitin fold modifier 1 (UFM1); UFM1 belongs to the ubiquitin-like protein family with similar ubiquitin beta-grasp folds and mechanism of ligation to other proteins. UFM1 is present in nearly all eukaryotic organisms except fungi. Ubiquitin is a protein modifier in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair. The UNF1 cascade has been implicated in endoplasmic reticulum functions, cell cycle control and cell differentiation. The involvement of the UFM1 cascade in diseases is diverse; reports include its involvement in ischemic heart diseases, diabetes, gastric lesions, schizophrenia, hip dysplasia and cancer.


Pssm-ID: 340465  Cd Length: 75  Bit Score: 119.86  E-value: 1.01e-37
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 557878626  4 VSFKITLTSDPRLPYKVLSVPESTPFTAVLKFAAEEFKVPAATSAIITNDGIGINPAQTAG 64
Cdd:cd01766   1 VTFKITLTSDPKLPFKVLSVPEEAPFTAVLKFAAEEFKVPAATSAIITNDGIGINPAQTAG 61
Ufm1 pfam03671
Ubiquitin fold modifier 1 protein; This is a family of short ubiquitin-like proteins, that is ...
 3-64 4.92e-35

Ubiquitin fold modifier 1 protein; This is a family of short ubiquitin-like proteins, that is like neither type-1 or type-2. It is a ubiquitin-fold modifier 1 (Ufm1) that is synthesized in a precursor form of 85 amino-acid residues. In humans the enzyme for Ufm1 is Uba5 and the conjugating enzyme is Ufc1. Prior to activation by Uba5 the extra two amino acids at the C-terminal region of the human pro-Ufm1 protein are removed to expose Gly whose residue is necessary for conjugation to target molecule(s). The mature Ufm1 is conjugated to yet unidentified endogenous proteins,. While Ubiquitin and many Ubls possess the conserved C-terminal di-glycine that is adenylated by each specific E1 or E1-like enzyme, respectively, in an ATP-dependent manner, Ufm1(1-83) possesses a single glycine at its C-terminus, which is followed by a Ser-Cys dipeptide in the precursor form of Ufm1. The C-terminally processed Ufm1(1-83) is specifically activated by Uba5, an E1-like enzyme, and then transferred to its cognate Ufc1, an E2-like enzyme.


Pssm-ID: 397643  Cd Length: 75  Bit Score: 113.29  E-value: 4.92e-35
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 557878626   3 KVSFKITLTSDPRLPYKVLSVPESTPFTAVLKFAAEEFKVPAATSAIITNDGIGINPAQTAG 64
Cdd:pfam03671  1 KVTFKITLTSDPKLPFRVISVPEAAPFTAVLKFAAEEFKVPPATSAIITNDGIGINPAQTAG 62
 
Name Accession Description Interval E-value
Ubl_UFM1 cd01766
ubiquitin-like (Ubl) domain found in ubiquitin fold modifier 1 (UFM1); UFM1 belongs to the ...
 4-64 1.01e-37

ubiquitin-like (Ubl) domain found in ubiquitin fold modifier 1 (UFM1); UFM1 belongs to the ubiquitin-like protein family with similar ubiquitin beta-grasp folds and mechanism of ligation to other proteins. UFM1 is present in nearly all eukaryotic organisms except fungi. Ubiquitin is a protein modifier in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair. The UNF1 cascade has been implicated in endoplasmic reticulum functions, cell cycle control and cell differentiation. The involvement of the UFM1 cascade in diseases is diverse; reports include its involvement in ischemic heart diseases, diabetes, gastric lesions, schizophrenia, hip dysplasia and cancer.


Pssm-ID: 340465  Cd Length: 75  Bit Score: 119.86  E-value: 1.01e-37
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 557878626  4 VSFKITLTSDPRLPYKVLSVPESTPFTAVLKFAAEEFKVPAATSAIITNDGIGINPAQTAG 64
Cdd:cd01766   1 VTFKITLTSDPKLPFKVLSVPEEAPFTAVLKFAAEEFKVPAATSAIITNDGIGINPAQTAG 61
Ufm1 pfam03671
Ubiquitin fold modifier 1 protein; This is a family of short ubiquitin-like proteins, that is ...
 3-64 4.92e-35

Ubiquitin fold modifier 1 protein; This is a family of short ubiquitin-like proteins, that is like neither type-1 or type-2. It is a ubiquitin-fold modifier 1 (Ufm1) that is synthesized in a precursor form of 85 amino-acid residues. In humans the enzyme for Ufm1 is Uba5 and the conjugating enzyme is Ufc1. Prior to activation by Uba5 the extra two amino acids at the C-terminal region of the human pro-Ufm1 protein are removed to expose Gly whose residue is necessary for conjugation to target molecule(s). The mature Ufm1 is conjugated to yet unidentified endogenous proteins,. While Ubiquitin and many Ubls possess the conserved C-terminal di-glycine that is adenylated by each specific E1 or E1-like enzyme, respectively, in an ATP-dependent manner, Ufm1(1-83) possesses a single glycine at its C-terminus, which is followed by a Ser-Cys dipeptide in the precursor form of Ufm1. The C-terminally processed Ufm1(1-83) is specifically activated by Uba5, an E1-like enzyme, and then transferred to its cognate Ufc1, an E2-like enzyme.


Pssm-ID: 397643  Cd Length: 75  Bit Score: 113.29  E-value: 4.92e-35
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 557878626   3 KVSFKITLTSDPRLPYKVLSVPESTPFTAVLKFAAEEFKVPAATSAIITNDGIGINPAQTAG 64
Cdd:pfam03671  1 KVTFKITLTSDPKLPFRVISVPEAAPFTAVLKFAAEEFKVPPATSAIITNDGIGINPAQTAG 62
 
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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