ubiquitin-like (Ubl) domain found in transmembrane and ubiquitin-like domain-containing protein 2 (TMUB2); TMUB2 is composed of an uncharacterized transmembrane domain and a ubiquitin-like (Ubl) domain-containing protein that shows high sequence similarity to TMUB1; the latter is highly expressed in the nervous system and is involved in the termination of liver regeneration.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1212983113 153 LITVRLKFLNDTEELAVARPEDTVGALKSKYFPGQESQMKLIYQGRLLQDPARTLRSLNITDNCVIHCHRS 223
Cdd:cd17132     1 LITVRLKFLNDTEEVAVVRPEDTIGFLKSKYFPGQEQQMKLIYQGQLLQDPARTLRSLNITDNCVIHCHRS 71

ubiquitin-like (Ubl) domain found in transmembrane and ubiquitin-like domain-containing protein 2 (TMUB2); TMUB2 is composed of an uncharacterized transmembrane domain and a ubiquitin-like (Ubl) domain-containing protein that shows high sequence similarity to TMUB1; the latter is highly expressed in the nervous system and is involved in the termination of liver regeneration.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1212983113 153 LITVRLKFLNDTEELAVARPEDTVGALKSKYFPGQESQMKLIYQGRLLQDPARTLRSLNITDNCVIHCHRS 223
Cdd:cd17132     1 LITVRLKFLNDTEEVAVVRPEDTIGFLKSKYFPGQEQQMKLIYQGQLLQDPARTLRSLNITDNCVIHCHRS 71

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

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                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1212983113  154 ITVRLKFLNDTEELAVARPEDTVGALKSKYFPGQESQM---KLIYQGRLLQDpARTLRSLNITDNCVIHCH 221
Cdd:smart00213   1 IELTVKTLDGKTITLEVKPSDTVSELKEKIAELTGIPPeqqRLIYKGKVLED-DRTLADYGIQDGSTIHLV 70

ubiquitin-like (Ubl) domain found in transmembrane and ubiquitin-like domain-containing protein 2 (TMUB2); TMUB2 is composed of an uncharacterized transmembrane domain and a ubiquitin-like (Ubl) domain-containing protein that shows high sequence similarity to TMUB1; the latter is highly expressed in the nervous system and is involved in the termination of liver regeneration.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1212983113 153 LITVRLKFLNDTEELAVARPEDTVGALKSKYFPGQESQMKLIYQGRLLQDPARTLRSLNITDNCVIHCHRS 223
Cdd:cd17132     1 LITVRLKFLNDTEEVAVVRPEDTIGFLKSKYFPGQEQQMKLIYQGQLLQDPARTLRSLNITDNCVIHCHRS 71

ubiquitin-like (Ubl) domain found in transmembrane and ubiquitin-like domain-containing proteins TMUB1, TMUB2, and similar proteins; TMUB1, also termed dendritic cell-derived ubiquitin-like protein (DULP), or hepatocyte odd protein shuttling protein, or ubiquitin-like protein SB144, or HOPS, is highly expressed in the nervous system. It is involved in the termination of liver regeneration and plays a negative role in interleukin-6-induced hepatocyte proliferation. The overexpression of Tmub1 has been shown to play a role in the inhibition of cell proliferation. TMUB1 has been implicated in the regulation of locomotor activity and wakefulness in mice, perhaps acting through its interaction with CAMLG. It also facilitates the recycling of AMPA receptors into synaptic membrane in cultured primary neurons. TMUB1 contains transmembrane domains and a ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold. TMUB2 is an uncharacterized transmembrane domain and Ubl domain-containing protein that shows high sequence similarity to TMUB1.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1212983113 153 LITVRLKFLNDTEELAVARPEDTVGALKSKYFPG---QESQMKLIYQGRLLQDPARTLRSLNITDNCVIHCHRS 223
Cdd:cd17057     1 TITIRLKFLNETERVVYARPEDTVGDFKRRHFPDelaQGKRVRLIYQGQLLRDDSRTLSSYGIQDGSVIHCHIS 74

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

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1212983113  154 ITVRLKFLNDTEELAVARPEDTVGALKSKYFPGQESQM---KLIYQGRLLQDpARTLRSLNITDNCVIHCH 221
Cdd:smart00213   1 IELTVKTLDGKTITLEVKPSDTVSELKEKIAELTGIPPeqqRLIYKGKVLED-DRTLADYGIQDGSTIHLV 70

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 1212983113 156 VRLKFL-NDTEELAVArPEDTVGALKSK------YFPgqESQMKLIYQGRLLQDpARTLRSLNITDN 215
Cdd:cd01805     3 ITFKTLqQQTFEIEVE-PSDTVLELKEKieqeqgDFP--ASGQKLIYSGKVLKD-DKTLSEYNIKEK 65

ubiquitin-like (Ubl) domain found in eukaryotic protein linking integrin-associated protein (IAP, also known as CD47) with cytoskeleton (PLIC) proteins; The PLIC proteins (or ubiquilins) family contains human homologs of the yeast ubiquitin-like (Ubl) Dsk2 protein, PLIC-1 (also termed ubiquilin-1), PLIC-2 (also termed ubiquilin-2, or Chap1), PLIC-3 (also termed ubiquilin-3) and PLIC-4 (also termed ubiquilin-4, ataxin-1 interacting ubiquitin-like protein, A1Up, connexin43-interacting protein of 75 kDa, or CIP75), and mouse PLIC proteins. They are ubiquitin (Ub)-binding adaptor proteins involved in all protein degradation pathways through delivering ubiquitinated substrates to proteasomes. They also promote autophagy-dependent cell survival during nutrient starvation. PLIC-1 regulates the function of the thrombospondin receptor CD47 and G protein signaling. It plays a role in TLR4-mediated signaling through interacting with the Toll/interleukin-1 receptor (TIR) domain of TLR4. It also inhibits the TLR3-Trif antiviral pathway by reducing the abundance of Trif. Moreover, PLIC-1 binds to gamma-aminobutyric acid receptors (GABAARs) and modulates the Ub-dependent, proteasomal degradation of GABAARs. Furthermore, PLIC-1 acts as a molecular chaperone regulating amyloid precursor protein (APP) biosynthesis, trafficking, and degradation by stimulating K63-linked polyubiquitination of lysine 688 in the APP intracellular domain. In addition, PLIC-1 is involved in the protein aggregation-stress pathway via associating with the Ub-interacting motif (UIM) proteins ataxin 3, HSJ1a, and epidermal growth factor substrate 15 (EPS15). PLIC-2 is a protein that binds the ATPase domain of the HSP70-like Stch protein. It functions as a negative regulator of G protein-coupled receptor (GPCR) endocytosis. It also involved in amyotrophic lateral sclerosis (ALS)-related dementia. PLIC-3 is encoded by UbiquilinN3, a testis-specific gene. It shows high sequence similarity with the Xenopus protein XDRP1, a nuclear phosphoprotein that binds to the N-terminus of cyclin A and inhibits Ca2+-induced degradation of cyclin A, but not cyclin B. PLIC-4 is an ubiquitin-like (Ubl) nuclear protein that interacts with ataxin-1 and further links ataxin-1 with the chaperone and Ub-proteasome pathways. It also binds to the non-ubiquitinated gap junction protein connexin43 (Cx43) and regulates the turnover of Cx43 through the proteasomal pathway. PLIC proteins contain an N-terminal Ubl domain that is responsible for the binding of Ub-interacting motifs (UIMs) expressed by proteasomes and endocytic adaptors, and C-terminal Ub-associated (UBA) domain that interacts with Ub chains present on proteins destined for proteasomal degradation. In addition, mammalian PLIC2 proteins have an extra collagen-like motif region, which is absent in other PLIC proteins and the yeast Dsk2 protein.

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gi 1212983113 153 LITVRLKFLNDTEELAVArPEDTVGALK---SKYFPGQESQMKLIYQGRLLQDPaRTLRSLNITDNCVIH 219
Cdd:cd01808     2 IIKVTVKTPKEKEDFEVP-EDSSVKEFKeeiSKKFKAPVEQLVLIFAGKILKDQ-DTLSQHGIKDGLTVH 69

ubiquitin-like (Ubl) domain found in the eukaryotic Ddi1 family; The eukaryotic Ddi1 family, including yeast aspartyl protease DNA-damage inducible 1 (Ddi1) and Ddi1-like proteins from vertebrates and other eukaryotes, has been characterized by containing an N-terminal ubiquitin-like (Ubl) domain and a conserved retroviral aspartyl-protease-like domain (RVP) that is important in cell-cycle control. Yeast Ddi1 and many family members also contain a C-terminal ubiquitin-association (UBA) domain, however, Ddi1-like proteins from all vertebrates lack the UBA domain. Ddi1, also termed v-SNARE-master 1 (Vsm1), is an ubiquitin receptor involved in the cell cycle and late secretory pathway in Saccharomyces cerevisiae. It functions as an UBA-Ubl shuttle protein that is required for the proteasome to enable ubiquitin-dependent degradation of its ligands. For instance, Ddi1 plays an essential role in the final stages of proteasomal degradation of Ho endonuclease and of its cognate FBP, Ufo1. Moreover, Ddi1 and its associated protein Rad23p play a cooperative role as negative regulators in yeast PHO pathway. This family also includes mammalian regulatory solute carrier protein family 1 member 1 (RSC1A1), also termed transporter regulator RS1 (RS1), which mediates transcriptional and post-transcriptional regulation of Na(+)-D-glucose cotransporter SGLT1. Ddi1-like proteins play a significant role in cell cycle control, growth control, and trafficking in yeast and may play a crucial role in embryogenesis in higher eukaryotes.

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gi 1212983113 188 ESQMKLIYQGRLLQDPARTLRSLNITDNCVI 218
Cdd:cd01796    39 AAEQVLLHNGQPLTDDKKTLEALGLKDGDLL 69