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.

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                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1005261230  1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKE-----------------------------ESTLHLVLRLRGG 47
Cdd:cd01803    1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEgippdqqrlifagkqledgrtlsdyniqkESTLHLVLRLRGG 76

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.

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gi 1005261230  1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKE-----------------------------ESTLHLVLRLRGG 47
Cdd:cd01803    1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEgippdqqrlifagkqledgrtlsdyniqkESTLHLVLRLRGG 76

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.

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                 ....*....|....*....|....*....|....*....|....*....
gi 1005261230  3 IFVKTLTGKTITLEVEPSDTIENVKAKIQDKEESTLH-LVLRLRGGIIE 50
Cdd:pfam00240  1 ITVKTLDGKKITLEVDPTDTVLELKEKIAEKEGVPPEqQRLIYSGKVLE 49

ubiquitin; Provisional

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gi 1005261230  1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKE-----------------------------ESTLHLVLRLRGG 47
Cdd:PTZ00044   1 MQILIKTLTGKKQSFNFEPDNTVQQVKMALQEKEgidvkqirliysgkqmsddlklsdykvvpGSTIHMVLQLRGG 76

50S ribosomal protein L40e; Provisional

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                 ....*....|....*....|....*....|....*....|....*..
gi 1005261230 51 PSLRQLAQKYNCDKMICRKCYARLHPRAVNCRkkKCGHTnNLRPKKK 97
Cdd:PRK04136   1 PAKFEEAEKRVFNKKICMRCNARNPWRATKCR--KCGYK-NLRPKAK 44

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1005261230  1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKE-----------------------------ESTLHLVLRLRGG 47
Cdd:cd01803    1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEgippdqqrlifagkqledgrtlsdyniqkESTLHLVLRLRGG 76

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.

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gi 1005261230  3 IFVKTLTGKTITLEVEPSDTIENVKAKIQDKE-----------------------------ESTLHLVLRLRGG 47
Cdd:cd01806    1 IKVKTLTGKEIEIDIEPTDKVERIKERVEEKEgippqqqrlifsgkqmndektaadykiegGSVLHLVLALRGG 74

Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]; Ribosomal protein L40E is part of the Pathway/BioSystem: Archaeal ribosomal proteins

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gi 1005261230 51 PSLRQLAQKYNCDKMICRKCYARLHPRAVNCRkkKCGHTnNLRPKKKVK 99
Cdd:COG1552    2 MAKFEEAEKRRLNKKICMRCGARNPIRATRCR--KCGYK-NLRPKKKER 47

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

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gi 1005261230   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEE 35
Cdd:smart00213  1 IELTVKTLDGKTITLEVKPSDTVSELKEKIAELTG 35

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.

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                 ....*....|....*....|....*....|...
gi 1005261230  2 QIFVKTLTGKTITLEVEPSDTIENVKAKIQDKE 34
Cdd:cd16107    1 QIFVRTYCGKTIVLHAKASDTVESLHQQIEART 33

ubiquitin-like (Ubl) domain found in ubiquitin and ubiquitin-like Ubl proteins; Ubiquitin-like (Ubl) proteins have a similar ubiquitin (Ub) beta-grasp fold and attach to other proteins in a Ubl manner but with biochemically distinct roles. Ub and Ubl proteins conjugate and deconjugate via ligases and peptidases to covalently modify target polypeptides. Some Ubl domains have adaptor roles in Ub-signaling by mediating protein-protein interaction. Prokaryotic sulfur carrier proteins are Ub-related proteins that can be activated in an ATP-dependent manner. 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. One of these seven lysine residues (K27, Ub numbering) is conserved in this Ubl_ubiquitin_like family. K27-linked Ub chains are versatile and can be recognized by several downstream receptor proteins. K27 has roles beyond chain linkage, such as in Ubl NEDD8 (which contains many of the same lysines (K6, K11, K27, K33, K48) as Ub) where K27 has a role (other than conjugation) in the mechanism of protein neddylation.

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                 ....*....|....*....|....*....|..
gi 1005261230  3 IFVKTLTGKTITLEVEPSDTIENVKAKIQDKE 34
Cdd:cd17039    1 ITVKTLDGKTYTVEVDPDDTVADLKEKIEEKT 32

ubiquitin-like (Ubl) domain 2 found in leukocyte antigen F (HLA-F) adjacent transcript 10 (FAT10) and similar proteins; FAT10, also termed ubiquitin D (UBD), or diubiquitin, is a cytokine-inducible ubiquitin-like (Ubl) modifer that is highly expressed in the thymus, and targets substrates covalently for 26S proteasomal degradation. It is also associated with cancer development, antigen processing and antimicrobial defense, chromosomal stability and cell cycle regulation. FAT10 is presented on immune cells and under the inflammatory conditions, is synergistically induced by interferon gamma (IFNgamma) and tumor necrosis factor (TNFalpha) in the non-immune (liver parenchymal) cells. FAT10 contains two Ubl domains. The family corresponds to the second Ubl domain of FAT10. Some family members contain only one Ubl domain.

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                 ....*....|....*....|....*....|...
gi 1005261230  1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDK 33
Cdd:cd17053    1 LTVNSKLLTGTVHTLQVSRSTTVAQVKAMIEDQ 33

UV excision repair protein Rad23; All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]

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gi 1005261230   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQD 32
Cdd:TIGR00601   1 MTLTFKTLQQQKFKIDMEPDETVKELKEKIEA 32

ubiquitin-like (Ubl) domain found in plant TBP-associated factors (TAFs) and similar proteins; TAFs, also termed transcription initiation factor TFIID subunits, or TAFII250 subunits, are components of the TFIID complex, a multisubunit protein complex involved in promoter recognition and essential for mediating regulation of RNA polymerase transcription. TAFs is the core scaffold of the TFIID complex, which is comprised of the TATA binding protein (TBP) and 12-15 TAFs. TAFs contain a ubiquitin-like (Ubl) domain and a Bromo domain.

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                 ....*....|....*....|....*....|...
gi 1005261230  1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDK 33
Cdd:cd17064    1 MKVIVKSLGGKGSLLRVDASETLESLKGKASKK 33

ubiquitin-like (Ubl) domain 1 found in interferon-stimulated gene 15 (ISG15) and similar proteins; ISG15, also termed interferon-induced 15 kDa protein, or interferon-induced 17 kDa protein (IP17), or ubiquitin cross-reactive protein (UCRP), is an antiviral interferon-induced ubiquitin-like protein (Ubl) that upon viral infection, modifies cellular and viral proteins by mechanisms similar to ubiquitination. Although ISG15 has properties similar to those of other Ubl molecules, it is a unique member of the Ubl superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system. ISG15 contains two tandem Ubl domains with a beta-grasp Ubl fold. This family corresponds to the first Ubl domain.

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gi 1005261230  1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDK 33
Cdd:cd01792    1 WDLTVKMLTGNEFQVSVSPSMTVSELKAQITQK 33

Beta-grasp ubiquitin-like fold; Ubiquitin is a protein modifier that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair in eukaryotes. The ubiquitination process comprises 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 proteins have similar ubiquitin beta-grasp fold and attach to other proteins in a ubiquitin-like manner but with biochemically distinct roles. Ubiquitin and ubiquitin-like proteins conjugate and deconjugate via ligases and peptidases to covalently modify target polypeptides. Some other ubiquitin-like domains have adaptor roles in ubiquitin-signaling by mediating protein-protein interaction. In addition to Ubiquitin-like (Ubl) domain, Ras-associating (RA) domain, F0/F1 sub-domain of FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, TGS (ThrRS, GTPase and SpoT) domain, Ras-binding domain (RBD), Ubiquitin regulatory domain X (UBX), Dublecortin-like domain, and RING finger- and WD40-associated ubiquitin-like (RAWUL) domain have beta-grasp ubiquitin-like folds, and are included in this superfamily.

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                 ....*....|....*....|....*....|..
gi 1005261230  3 IFVKTLTGKTITLEVEPSDTIENVKAKIQDKE 34
Cdd:cd00196    1 VKVETPSLKKIVVAVPPSTTLRQVLEKVAKRI 32