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Conserved domains on  [gi|252019|gb|AAB22649|]
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polyubiquitin, partial [Mus sp.]

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 ...
 1-27 2.12e-08

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 cd01803:

Pssm-ID: 475130 [Multi-domain]  Cd Length: 76  Bit Score: 44.74  E-value: 2.12e-08
                       10        20
               ....*....|....*....|....*..
gi 252019    1 IFVKTLTGKTITLDVEPSVTTKKVKQE 27
Cdd:cd01803  3 IFVKTLTGKTITLEVEPSDTIENVKAK 29
 
Name Accession Description Interval E-value
Ubl_ubiquitin cd01803
ubiquitin-like (Ubl) domain found in ubiquitin; Ubiquitin is a protein modifier in eukaryotes ...
 1-27 2.12e-08

ubiquitin-like (Ubl) domain found in ubiquitin; Ubiquitin is a protein modifier in eukaryotes that is involved in various cellular processes, including transcriptional regulation, cell cycle control, and DNA repair. Ubiquitination is comprised of a cascade of E1, E2 and E3 enzymes that results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. Ubiquitin-like (Ubl) proteins have similar ubiquitin beta-grasp fold and attach to other proteins in a Ubl manner but with biochemically distinct roles. Ubiquitin (Ub)and Ubl proteins conjugate and deconjugate via ligases and peptidases to covalently modify target polypeptides. Ub includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains.


Pssm-ID: 340501 [Multi-domain]  Cd Length: 76  Bit Score: 44.74  E-value: 2.12e-08
                       10        20
               ....*....|....*....|....*..
gi 252019    1 IFVKTLTGKTITLDVEPSVTTKKVKQE 27
Cdd:cd01803  3 IFVKTLTGKTITLEVEPSDTIENVKAK 29
UBI4 COG5272
Ubiquitin [Posttranslational modification, protein turnover, chaperones];
1-26 1.89e-07

Ubiquitin [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 444084 [Multi-domain]  Cd Length: 213  Bit Score: 44.39  E-value: 1.89e-07
                        10        20
                ....*....|....*....|....*.
gi 252019     1 IFVKTLTGKTITLDVEPSVTTKKVKQ 26
Cdd:COG5272   3 IFVKTLTGKTITLEVEPNDTIEAVKA 28
PTZ00044 PTZ00044
ubiquitin; Provisional
 1-26 2.11e-04

ubiquitin; Provisional


Pssm-ID: 185411 [Multi-domain]  Cd Length: 76  Bit Score: 34.80  E-value: 2.11e-04
                        10        20
                ....*....|....*....|....*.
gi 252019     1 IFVKTLTGKTITLDVEPSVTTKKVKQ 26
Cdd:PTZ00044  3 ILIKTLTGKKQSFNFEPDNTVQQVKM 28
ubiquitin pfam00240
Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog) ...
 1-26 6.08e-04

Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog), Nedd8, Elongin B, Rub1, and Parkin. A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites.


Pssm-ID: 459726 [Multi-domain]  Cd Length: 72  Bit Score: 33.30  E-value: 6.08e-04
                         10        20
                 ....*....|....*....|....*.
gi 252019      1 IFVKTLTGKTITLDVEPSVTTKKVKQ 26
Cdd:pfam00240  1 ITVKTLDGKKITLEVDPTDTVLELKE 26
UBQ smart00213
Ubiquitin homologues; Ubiquitin-mediated proteolysis is involved in the regulated turnover of ...
 1-26 1.11e-03

Ubiquitin homologues; Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression


Pssm-ID: 214563 [Multi-domain]  Cd Length: 72  Bit Score: 32.62  E-value: 1.11e-03
                          10        20
                  ....*....|....*....|....*.
gi 252019       1 IFVKTLTGKTITLDVEPSVTTKKVKQ 26
Cdd:smart00213  3 LTVKTLDGKTITLEVKPSDTVSELKE 28
 
Name Accession Description Interval E-value
Ubl_ubiquitin cd01803
ubiquitin-like (Ubl) domain found in ubiquitin; Ubiquitin is a protein modifier in eukaryotes ...
 1-27 2.12e-08

ubiquitin-like (Ubl) domain found in ubiquitin; Ubiquitin is a protein modifier in eukaryotes that is involved in various cellular processes, including transcriptional regulation, cell cycle control, and DNA repair. Ubiquitination is comprised of a cascade of E1, E2 and E3 enzymes that results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. Ubiquitin-like (Ubl) proteins have similar ubiquitin beta-grasp fold and attach to other proteins in a Ubl manner but with biochemically distinct roles. Ubiquitin (Ub)and Ubl proteins conjugate and deconjugate via ligases and peptidases to covalently modify target polypeptides. Ub includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains.


Pssm-ID: 340501 [Multi-domain]  Cd Length: 76  Bit Score: 44.74  E-value: 2.12e-08
                       10        20
               ....*....|....*....|....*..
gi 252019    1 IFVKTLTGKTITLDVEPSVTTKKVKQE 27
Cdd:cd01803  3 IFVKTLTGKTITLEVEPSDTIENVKAK 29
UBI4 COG5272
Ubiquitin [Posttranslational modification, protein turnover, chaperones];
1-26 1.89e-07

Ubiquitin [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 444084 [Multi-domain]  Cd Length: 213  Bit Score: 44.39  E-value: 1.89e-07
                        10        20
                ....*....|....*....|....*.
gi 252019     1 IFVKTLTGKTITLDVEPSVTTKKVKQ 26
Cdd:COG5272   3 IFVKTLTGKTITLEVEPNDTIEAVKA 28
Ubl_AtUPL5_like cd16107
ubiquitin-like (Ubl) domain found in Arabidopsis thaliana ubiquitin-protein ligase 5 (AtUPL5) ...
 1-27 3.90e-05

ubiquitin-like (Ubl) domain found in Arabidopsis thaliana ubiquitin-protein ligase 5 (AtUPL5) and similar proteins; Arabidopsis thaliana AtUPL5, also termed HECT-type E3 ubiquitin transferase UPL5, is an E3 ubiquitin-protein ligase that contains a ubiquitin-like domain (Ubl), a C-type lectin-binding domain, a leucine zipper and a HECT domain. HECT domain containing-ubiquitin-protein ligases have more than one member in different genomes, these proteins have been classified into four sub-families (UPL1/2, UPL3/4, UPL5 and UPL6/7). AtUPL5 fUPL5 regulates leaf senescence in Arabidopsis through degradation of the transcription factor WRKY53.


Pssm-ID: 340524  Cd Length: 70  Bit Score: 36.32  E-value: 3.90e-05
                       10        20
               ....*....|....*....|....*..
gi 252019    1 IFVKTLTGKTITLDVEPSVTTKKVKQE 27
Cdd:cd16107  2 IFVRTYCGKTIVLHAKASDTVESLHQQ 28
Ubl_NEDD8 cd01806
ubiquitin-like (Ubl) domain found in neural precursor cell expressed developmentally ...
 1-26 7.04e-05

ubiquitin-like (Ubl) domain found in neural precursor cell expressed developmentally down-regulated protein 8 (NEDD8) and similar proteins; NEDD8, also termed Neddylin, or RELATED TO UBIQUITIN (RUB/Rub1p) in plant and yeast, is a ubiquitin-like protein that conjugates to nuclear proteins in a manner analogous to ubiquitination and sentrinization. It modifies a family of molecular scaffold proteins called cullins that are responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. NEDD8 deamidation and its inhibition of Cullin-RING ubiquitin ligases (CRLs) activity are responsible for Cycle-inhibiting factor (Cif)/Cif homolog in Burkholderia pseudomallei (CHBP)-induced cytopathic effect. NEDD8 contains a single conserved ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions. Polyubiquitination, signals for a diverse set of cellular events via different isopeptide linkages formed between the C terminus of one ubiquitin (Ub) and the epsilon-amine of K6, K11, K27, K29, K33, K48, or K63 of a second Ub. Ubl NEDD8, contains many of the same lysines (K6, K11, K27, K33, K48) as Ub, where K27 has an role (other than conjugation) in the mechanism of protein neddylation.


Pssm-ID: 340504 [Multi-domain]  Cd Length: 74  Bit Score: 35.83  E-value: 7.04e-05
                       10        20
               ....*....|....*....|....*.
gi 252019    1 IFVKTLTGKTITLDVEPSVTTKKVKQ 26
Cdd:cd01806  1 IKVKTLTGKEIEIDIEPTDKVERIKE 26
PTZ00044 PTZ00044
ubiquitin; Provisional
 1-26 2.11e-04

ubiquitin; Provisional


Pssm-ID: 185411 [Multi-domain]  Cd Length: 76  Bit Score: 34.80  E-value: 2.11e-04
                        10        20
                ....*....|....*....|....*.
gi 252019     1 IFVKTLTGKTITLDVEPSVTTKKVKQ 26
Cdd:PTZ00044  3 ILIKTLTGKKQSFNFEPDNTVQQVKM 28
ubiquitin pfam00240
Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog) ...
 1-26 6.08e-04

Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog), Nedd8, Elongin B, Rub1, and Parkin. A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites.


Pssm-ID: 459726 [Multi-domain]  Cd Length: 72  Bit Score: 33.30  E-value: 6.08e-04
                         10        20
                 ....*....|....*....|....*.
gi 252019      1 IFVKTLTGKTITLDVEPSVTTKKVKQ 26
Cdd:pfam00240  1 ITVKTLDGKKITLEVDPTDTVLELKE 26
UBQ smart00213
Ubiquitin homologues; Ubiquitin-mediated proteolysis is involved in the regulated turnover of ...
 1-26 1.11e-03

Ubiquitin homologues; Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression


Pssm-ID: 214563 [Multi-domain]  Cd Length: 72  Bit Score: 32.62  E-value: 1.11e-03
                          10        20
                  ....*....|....*....|....*.
gi 252019       1 IFVKTLTGKTITLDVEPSVTTKKVKQ 26
Cdd:smart00213  3 LTVKTLDGKTITLEVKPSDTVSELKE 28
Ubl_Rad23 cd01805
ubiquitin-like (Ubl) domain found in the Rad23 protein family; The Rad23 family includes the ...
 1-26 2.90e-03

ubiquitin-like (Ubl) domain found in the Rad23 protein family; The Rad23 family includes the yeast nucleotide excision repair (NER) proteins, Rad23p (in Saccharomyces cerevisiae) and Rhp23p (in Schizosaccharomyces pombe), their mammalian orthologs HR23A and HR23B, and putative DNA repair proteins from plants. Rad23 proteins play dual roles in DNA repair as well as in proteosomal degradation. They have affinity for both the proteasome and ubiquitinylated proteins and participate in translocating polyubiquitinated proteins to the proteasome. Rad23 proteins carry an ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, and two ubiquitin-associated (UBA) domains, as well as a xeroderma pigmentosum group C (XPC) protein-binding domain. The Ubl domain is responsible for the binding to proteasome. The UBA domains are important for binding of ubiquitin (Ub) or multi-ubiquitinated substrates, which suggests Rad23 proteins might be involved in certain pathways of Ub metabolism. Both the Ubl domain and the XPC-binding domain are necessary for efficient NER function of Rad23 proteins.


Pssm-ID: 340503 [Multi-domain]  Cd Length: 72  Bit Score: 31.76  E-value: 2.90e-03
                       10        20
               ....*....|....*....|....*.
gi 252019    1 IFVKTLTGKTITLDVEPSVTTKKVKQ 26
Cdd:cd01805  3 ITFKTLQQQTFEIEVEPSDTVLELKE 28
 
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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