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 71987570  1 MVFVKTLH-RTLFLEVAANEDVLSIKQKIEAAEGIPAEEQRLCYAAR 46
Cdd:cd16107  1 QIFVRTYCgKTIVLHAKASDTVESLHQQIEARTGIPSLEQRLIFGGR 47

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 71987570  1 MVFVKTLH-RTLFLEVAANEDVLSIKQKIEAAEGIPAEEQRLCYAAR 46
Cdd:cd16107  1 QIFVRTYCgKTIVLHAKASDTVESLHQQIEARTGIPSLEQRLIFGGR 47

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 71987570    2 VFVKTLH-RTLFLEVAANEDVLSIKQKIEAAEGIPAEEQRLCYAAR 46
Cdd:pfam00240  1 ITVKTLDgKKITLEVDPTDTVLELKEKIAEKEGVPPEQQRLIYSGK 46

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 71987570     4 VKTLHRTLF-LEVAANEDVLSIKQKIEAAEG---IPAEEQRLCYAAR 46
Cdd:TIGR00601   5 FKTLQQQKFkIDMEPDETVKELKEKIEAEQGkdaYPVAQQKLIYSGK 51

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 71987570  1 MVFVKTLH-RTLFLEVAANEDVLSIKQKIEAAEGIPAEEQRLCYAAR 46
Cdd:cd16107  1 QIFVRTYCgKTIVLHAKASDTVESLHQQIEARTGIPSLEQRLIFGGR 47

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 71987570    2 VFVKTLH-RTLFLEVAANEDVLSIKQKIEAAEGIPAEEQRLCYAAR 46
Cdd:pfam00240  1 ITVKTLDgKKITLEVDPTDTVLELKEKIAEKEGVPPEQQRLIYSGK 46

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 71987570  2 VFVKTLH-RTLFLEVAANEDVLSIKQKIEAAEGIPAEEQRLCYAAR 46
Cdd:cd01803  3 IFVKTLTgKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGK 48

ubiquitin-like (Ubl) domain found in ubiquitin-like protein FUBI and similar proteins; FUBI is a pro-apoptotic regulatory gene FAU encoding ubiquitin-like protein with ribosomal protein S30 as a C-terminal extension. FUBI functions as a tumor suppressor protein that may be involved in the ATP-dependent proteolytic activity of ubiquitin. The N-terminal ubiquitin-like (Ubl) domain of FUBI has the beta-grasp Ubl fold, and it may act as a substitute or an inhibitor of ubiquitin or one of ubiquitin's close relatives UCRP, FAT10, and Nedd8.

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               ....*....|....*....|....*....|....
gi 71987570 13 LEVAANEDVLSIKQKIEAAEGIPAEEQRLCYAAR 46
Cdd:cd01793 13 LEVSGNETVADIKAHIAALEGIAVEDQVLLYAGA 46

ubiquitin-like (Ubl) domain found in Saccharomyces cerevisiae proteasome interacting protein Dsk2p and similar proteins; The family contains several fungal multiubiquitin receptors, including Saccharomyces cerevisiae Dsk2p and Schizosaccharomyces pombe Dph1p, both of which have been characterized as shuttle proteins transporting ubiquitinated substrates destined for degradation from the E3 ligase to the 26S proteasome. They interact with the proteasome through their N-terminal ubiquitin-like domain (Ubl) and with ubiquitin (Ub) through their C-terminal Ub-associated domain (UBA). S. cerevisiae Dsk2p is a nuclear-enriched protein that may involve in the ubiquitin-proteasome proteolytic pathway through interacting with K48-linked polyubiquitin and the proteasome. Moreover, it has been implicated in spindle pole duplication through assisting in Cdc31 assembly into the new spindle pole body (SPB). S. pombe Dph1p is an ubiquitin (Ub0 receptor working in concert with the class V myosin, Myo52, to target the degradation of the S. pombe CLIP-170 homolog, Tip1. It also can protect Ub chains against disassembly by deubiquitinating enzymes.

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               ....*....|....*....|....*....|....
gi 71987570 13 LEVAANEDVLSIKQKIEAAEGIPAEEQRLCYAAR 46
Cdd:cd16106 15 VEVEPDATVLELKELIAEKSDIPAEQQRLIYKGK 48

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.

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               ....*....|....*....|....*....|....*....|....*..
gi 71987570  2 VFVKTLHRTLF-LEVAANEDVLSIKQKIEAAEG-IPAEEQRLCYAAR 46
Cdd:cd01805  3 ITFKTLQQQTFeIEVEPSDTVLELKEKIEQEQGdFPASGQKLIYSGK 49

ubiquitin-like (Ubl) domain found in Sacsin and similar proteins; Sacsin, also termed DnaJ homolog subfamily C member 29 (DNAJC29), is encoded by SACS gene that is highly expressed in the brain. Mutations in SACS can cause the neurodegenerative disease autosomal recessive spastic ataxia of Charlevoix Saguenay (ARSACS) which is characterized by early-onset spastic ataxia. Sacsin is a modular protein that is localized on the mitochondrial surface and possibaly required for normal mitochondrial network organization. Sacsin knockdown resulted in a reduction in cells expressing plyglutamine-expanded ataxin-1, which correlated with a loss of cells with large nuclear ataxin-1 incusions. At the N-terminus, sacsin contains a ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, which can interact with the proteasome. At the C-terminus, sacsin harbors a protein-protein interaction J-domain followed by an higher eukaryotes and prokaryotes nucleotide-binding (HEPN) domain. The J-domain is typically associated with DnaJ-like co-chaperones involved in regulation of the Hsp70 heat shock system.

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               ....*....|....*....|....*....|....*....
gi 71987570  8 HRTLflEVAANEDVLSIKQKIEAAEGIPAEEQRLCYAAR 46
Cdd:cd17049 14 CRTF--EVPPSAAVRDIKELIYEETDFPVSEQQLWHNGK 50

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 71987570     4 VKTLHRTLF-LEVAANEDVLSIKQKIEAAEG---IPAEEQRLCYAAR 46
Cdd:TIGR00601   5 FKTLQQQKFkIDMEPDETVKELKEKIEAEQGkdaYPVAQQKLIYSGK 51