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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1142696096   1 MKVTVMT-GDEQIVTLDVDRDESVENLKALLEVETRVPLRQQQIHFNGKEMQNTEK-LSAAGVQDGDLVMM 69
Cdd:cd01796     1 MKLTVTTeDDDRLFSLEVSPDMTLEDLKALCEAETGIPAAEQVLLHNGQPLTDDKKtLEALGLKDGDLLLL 71

Aspartyl protease; This family of eukaryotic aspartyl proteases have a fold similar to retroviral proteases which implies they function proteolytically during regulated protein turnover.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1142696096 172 QKGIDENWEAALEHNPEAFARVVMLYVDMEVNGVPLKAFVDSGAQSTIISKSCAERCGLLRLLDQRFRGIAVGVGQSEIL 251
Cdd:pfam09668   1 QENIDENLEHAMEHHPEVFGRVTMLYINCEINGVPVKAFVDSGAQTSIMSPRCAERCGIMRLVDTRFAGIAKGVGTARIL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1142696096 252 GRIHVAPIKIGNIFYPCSFTVLDAPNMEFLFGLDMLRKHQCMID 295
Cdd:pfam09668  81 GRIHMADVKIGGLFLPCSFSVIEGQDMDLLLGLDMLKRHQCCID 124

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1142696096   3 VTVMTGDEQIVTLDVDRDESVENLKALLEVETRVPLRQQQIHFNGKEMQNTEKLSAAGVQDGDLVMM 69
Cdd:pfam00240   1 ITVKTLDGKKITLEVDPTDTVLELKEKIAEKEGVPPEQQRLIYSGKVLEDDQTLGEYGIEDGSTIHL 67

UBA domain found in Saccharomyces cerevisiae DNA-damage response protein Ddi1 and similar proteins; Ddi1, also called v-SNARE-master 1 (Vsm1), is a ubiquitin receptor involved in regulation of the cell cycle and late secretory pathway in Saccharomyces cerevisiae. It functions as a ubiquitin association domain (UBA)- ubiquitin-like-domain (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. Ddi1 contains an N-terminal UBL domain and a C-terminal UBA domain. It also harbors a central retroviral aspartyl-protease-like domain (RVP) which may be important in cell-cycle control. At this point, Ddi1 may function proteolytically during regulated protein turnover in the cell. This family also includes mammalian regulatory solute carrier protein family 1 member 1 (RSC1A1), also called transporter regulator RS1 (RS1) which mediates transcriptional and post-transcriptional regulation of Na(+)-D-glucose cotransporter SGLT1.

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1142696096 371 EAKVTKLVELGFDRASVTQALKLFNGNEEQAAAFLF 406
Cdd:cd14309     1 EEKIAQLMDLGFSREEAIQALEATNGNVELAASLLF 36

Predicted aspartyl protease [General function prediction only];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1142696096 197 YVDMEVNGVPLKAFVDSGAQSTIISKSCAERCGlLRLLDQRFRGIAVGVGQSEILGRIHVAPIKIGNI-FYPCSFTVLDA 275
Cdd:COG3577    43 VVEGTINGQPVRFLVDTGASTVVLSESDARRLG-LDPEDLGRPVRVQTANGVVRAARVRLDSVRIGGItLRNVRAVVLPG 121

                          90
                  ....*....|....*..
gi 1142696096 276 PNMEF-LFGLDMLRKHQ 291
Cdd:COG3577   122 GELDDgLLGMSFLGRLD 138

clan AA aspartic protease, TIGR02281 family; This family consists of predicted aspartic proteases, typically from 180 to 230 amino acids in length, in MEROPS clan AA. This model describes the well-conserved 121-residue C-terminal region. The poorly conserved, variable length N-terminal region usually contains a predicted transmembrane helix. Sequences in the seed alignment and those scoring above the trusted cutoff are Proteobacterial; homologs scroing between trusted and noise are found in Pyrobaculum aerophilum str. IM2 (archaeal), Pirellula sp. (Planctomycetes), and Nostoc sp. PCC 7120 (Cyanobacteria). [Protein fate, Degradation of proteins, peptides, and glycopeptides]

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1142696096 197 YVDMEVNGVPLKAFVDSGAQSTIISKSCAERCGLLRLLDQRFRGIAVGVGQSEIlGRIHVAPIKIGNIF 265
Cdd:TIGR02281  13 YATGRVNGRNVRFLVDTGATSVALNEEDAQRLGLDLNRLGYTVTVSTANGQIKA-ARVTLDRVAIGGIV 80

Aspartyl protease; This family of eukaryotic aspartyl proteases have a fold similar to retroviral proteases which implies they function proteolytically during regulated protein turnover.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1142696096 172 QKGIDENWEAALEHNPEAFARVVMLYVDMEVNGVPLKAFVDSGAQSTIISKSCAERCGLLRLLDQRFRGIAVGVGQSEIL 251
Cdd:pfam09668   1 QENIDENLEHAMEHHPEVFGRVTMLYINCEINGVPVKAFVDSGAQTSIMSPRCAERCGIMRLVDTRFAGIAKGVGTARIL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1142696096 252 GRIHVAPIKIGNIFYPCSFTVLDAPNMEFLFGLDMLRKHQCMID 295
Cdd:pfam09668  81 GRIHMADVKIGGLFLPCSFSVIEGQDMDLLLGLDMLKRHQCCID 124

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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1142696096   1 MKVTVMT-GDEQIVTLDVDRDESVENLKALLEVETRVPLRQQQIHFNGKEMQNTEK-LSAAGVQDGDLVMM 69
Cdd:cd01796     1 MKLTVTTeDDDRLFSLEVSPDMTLEDLKALCEAETGIPAAEQVLLHNGQPLTDDKKtLEALGLKDGDLLLL 71

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1142696096   3 VTVMTGDEQIVTLDVDRDESVENLKALLEVETRVPLRQQQIHFNGKEMQNTEKLSAAGVQDGDLVMMF 70
Cdd:cd17039     1 ITVKTLDGKTYTVEVDPDDTVADLKEKIEEKTGIPVEQQRLIYNGKELKDDKTLSDYGIKDGSTIHLV 68

Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to 230 amino acids in length, in MEROPS clan AA. This model describes the well-conserved 121-residue C-terminal region. The poorly conserved, variable length N-terminal region usually contains a predicted transmembrane helix.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1142696096 198 VDMEVNGVPLKAFVDSGAQSTIISKSCAERCGlLRLLDQRFRGIAVGVGQSEILGRIHVAPIKIGNI-FYPCSFTVLDAP 276
Cdd:pfam13650   1 VPVTINGKPVRFLVDTGASGTVISPSLAERLG-LKVRGLAYTVRVSTAGGRVSAARVRLDSLRLGGLtLENVPALVLDLG 79

                          90
                  ....*....|
gi 1142696096 277 NM-EFLFGLD 285
Cdd:pfam13650  80 DLiDGLLGMD 89

UBA domain found in Saccharomyces cerevisiae DNA-damage response protein Ddi1 and similar proteins; Ddi1, also called v-SNARE-master 1 (Vsm1), is a ubiquitin receptor involved in regulation of the cell cycle and late secretory pathway in Saccharomyces cerevisiae. It functions as a ubiquitin association domain (UBA)- ubiquitin-like-domain (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. Ddi1 contains an N-terminal UBL domain and a C-terminal UBA domain. It also harbors a central retroviral aspartyl-protease-like domain (RVP) which may be important in cell-cycle control. At this point, Ddi1 may function proteolytically during regulated protein turnover in the cell. This family also includes mammalian regulatory solute carrier protein family 1 member 1 (RSC1A1), also called transporter regulator RS1 (RS1) which mediates transcriptional and post-transcriptional regulation of Na(+)-D-glucose cotransporter SGLT1.

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1142696096 371 EAKVTKLVELGFDRASVTQALKLFNGNEEQAAAFLF 406
Cdd:cd14309     1 EEKIAQLMDLGFSREEAIQALEATNGNVELAASLLF 36

NRIP_C; putative nuclear receptor interacting protein; Proteins in this family have been described as probable nuclear receptor interacting proteins. The C-terminal domain of this family is homologous to the retroviral aspartyl protease domain. The domain is structurally related to one lobe of the pepsin molecule. The conserved active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1142696096 198 VDMEVNGVPLKAFVDSGAQSTIISKSCAERCGLL-RLLDQRFRGIAVGVGQS-EILGRIHVAPIKIGNIFYPCSFTVLDA 275
Cdd:cd05480     1 VSCQCAGKELRALVDTGCQYNLISAACLDRLGLKeRVLKAKAEEEAPSLPTSvKVIGQIERLVLQLGQLTVECSAQVVDD 80

                          90       100
                  ....*....|....*....|.
gi 1142696096 276 PNMEFLFGLDMLRKHQCMIDL 296
Cdd:cd05480    81 NEKNFSLGLQTLKSLKCVINL 101

ubiquitin-like (Ubl) domain found in BAG family molecular chaperone regulator 1 (BAG1) and similar proteins; BAG1, also termed Bcl-2-associated athanogene 1, or HAP, is a multifunctional protein involved in a variety of cellular functions such as apoptosis, transcription, and proliferative pathways, as well as in cell signaling and differentiation. It delivers chaperone-recognized unfolded substrates to the proteasome for degradation. BAG1 functions as a co-chaperone for Hsp70/Hsc70 to increase Hsp70 foldase activity. It also suppresses apoptosis and enhances neuronal differentiation. As an anti-apoptotic factor, BAG1 interacts with tau and regulates its proteasomal degradation. It also binds to BCR-ABL with a high affinity, and directly routes immature BCR-ABL for proteasomal degradation. It acts as a potential therapeutic target in Parkinson's disease. It also modulates huntingtin toxicity, aggregation, degradation, and subcellular distribution, suggesting a role in Huntington's disease. There are at least four isoforms of Bag1 protein that are formed by alternative initiation of translation within a common mRNA. BAG1 contains an N-terminal ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, and a C-terminal BAG domain.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1142696096   1 MKVTVMTGDEQ---IVTLDVDRDESVENLKALLEVETRVPLRQQQIHFNGKEMQNTEK-LSAAGVQDGDLVMM 69
Cdd:cd01812     1 LTVTVIHGSNKhtiELPSQDEDEPTLQDLAEAIEEVTGVPVENQKLIFKGKSLKDPEQpLSALGVKNGSKIML 73

ubiquitin-like (Ubl) domain found in ubiquitin-like proteins UBL4A and similar proteins; UBL4A, also termed GdX, is a ubiquitously expressed ubiquitin-like (Ubl) protein that forms a complex with partner proteins and participates in the protein processing through endoplasmic reticulum (ER), acting as a chaperone. As a key component of the BCL2-associated athanogene 6 (BAG6) chaperone complex, UBL4A plays a role in mediating DNA damage signaling and cell death. UBL4A also regulates insulin-induced Akt plasma membrane translocation through promotion of Arp2/3-dependent actin branching. Moreover, UBL4A specifically stabilizes the TC45/STAT3 association and promotes dephosphorylation of STAT3 to repress tumorigenesis. UBL4B is testis-specific, and encoded by an X-derived retrogene Ubl4b, which is specifically expressed in post-meiotic germ cells in mammals. As a germ cell-specific cytoplasmic protein, UBL4B is not present in somatic cells. Moreover, UBL4B is present in elongated spermatids, but not in spermatocytes and round spermatids, suggesting its function is restricted to late spermiogenesis. The function of UBL4A may be compensated by either UBL4B or other Ubl proteins in normal conditions. Both UBL4A and UBL4B contain a conserved Ubl domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1142696096   1 MKVTVMTGDEQIVTLDVDRDESVENLKALLEVETRVPLRQQQIHFNGKEMQNTEKLSAAGVQDGDLVMMF 70
Cdd:cd01807     1 MLITVKILQGKECTIEVSPTESVLTVKQLVAEQLNVPVSQQRLVFKGKTLADEHSLSDYSIGPGSKIHLV 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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1142696096   1 MKVTVMTGDEQIVTLDVDRDESVENLKALLEVETRV-PLRQQQIHFNGKEMQNTEKLSAAGVQDGD-LVMM 69
Cdd:cd01805     1 MKITFKTLQQQTFEIEVEPSDTVLELKEKIEQEQGDfPASGQKLIYSGKVLKDDKTLSEYNIKEKDfVVVM 71

Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a single domain of the two-domain eukaryotic aspartyl proteases.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1142696096 202 VNGVPLKAFVDSGAQSTIISKSCAERCGLLR-LLDQRFRgIAVGVGQSEILGRIHVA-PIKIGNIFYPCSFTVLDAPNME 279
Cdd:pfam08284  26 VNSIPATVLFDSGATHSFISHAFVGKLKLPVeSLSNPLC-IETPTGGSVTTNLICPScPIEIQGISFLADLILLDMKDLD 104

                          90
                  ....*....|....*.
gi 1142696096 280 FLFGLDMLRKHQCMID 295
Cdd:pfam08284 105 VILGMDWLSKNKANID 120

ubiquitin-like (Ubl) domain found in ubiquitin carboxyl-terminal hydrolase 14 (USP14) and similar proteins; USP14 (EC 3.4.19.12), also termed deubiquitinating enzyme 14, or ubiquitin thioesterase 14, or ubiquitin-specific-processing protease 14, or ubiquitin carboxyl-terminal hydrolase 14, is a component of proteasome regulatory subunit 19S that regulates deubiquitinated proteins entering inside the proteasome core 20S, which plays an inhibitory role in protein degradation. USP14 is also associated with various signal transduction pathways and tumorigenesis, and thus plays an essential role in the development of various types of cancer. Moreover, USP14 mediates the development of cardiac hypertrophy by promoting GSK-3beta phosphorylation, suggesting a role in cardiac hypertrophy treatment. USP14 contains an N-terminal ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, and a C-terminal ubiquitin-specific protease (USP) domain.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1142696096   2 KVTVMTGDEQIVTLDVDRDESVENLKALLEVETRVPLRQQQIHFNGKEMQNTEKLSAAGVQDGDLVMMFSTSE 74
Cdd:cd16104     3 KVNVKWGKEKFDDVELDTDEPPLVFKAQLFALTGVPPERQKIMVKGGVLKDDDDLSKLKLKDGQTLMLMGSAE 75

UBA domain found in proteins involved in ubiquitin-mediated proteolysis; The ubiquitin-associated (UBA) domains are commonly occurring sequence motifs found in proteins involved in ubiquitin-mediated proteolysis. They contribute to ubiquitin (Ub) binding or ubiquitin-like (UbL) domain binding. However, some kinds of UBA domains can only the bind UbL domain, but not the Ub domain. UBA domains are normally comprised of compact three-helix bundles which contain a conserved GF/Y-loop. They can bind polyubiquitin with high affinity. They also bind monoubiquitin and other proteins. Most UBA domain-containing proteins have one UBA domain, but some harbor two or three UBA domains.

                          10        20
                  ....*....|....*....|....*....
gi 1142696096 374 VTKLVELGFDRASVTQALKLFNGNEEQAA 402
Cdd:cd14270     1 LAQLVEMGFSREQARRALRATNGDVEAAV 29

UBA domain found in plant ubiquitin-conjugating enzyme E2 27 and similar proteins; UBC27, also called ubiquitin carrier protein 27, functions as a class II ubiquitin-conjugating (UBC) enzyme (E2). E2, together with E1 (ubiquitin-activating enzyme UBA) and E3 (ubiquitin ligase), is required in the multi-step reaction of ubiquitin conjugation. Unlike other Arabidopsis UBCs, in addition to an N-terminal ubiquitin-conjugating enzyme E2 catalytic domain (UBCc), UBC27 has an additional C-terminal ubiquitin-associated domain (UBA).

                          10        20        30
                  ....*....|....*....|....*....|.
gi 1142696096 371 EAKVTKLVELGFDRASVTQALKLFNGNEEQA 401
Cdd:cd14312     1 EEKVQRLVEMGFPRDQAVVALESAGGDENAA 31

ubiquitin-like (Ubl) domain found in IQ and ubiquitin-like domain-containing protein (IQUB) and similar proteins; IQUB is an IQ motif and ubiquitin domain-containing protein that may play roles in cilia formation and/or maintenance. It contains a conserved ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1142696096   9 DEQIVTLDVDRDESVENLKALLEVETRVPLRQQQIHFNGKEMQNTEKLSAAGVQ 62
Cdd:cd17061    12 SGQVITLAFTLGQTIGELKEHFSSELKIPPDVLQIMFDGKLVEDNTTLVDLGVR 65

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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1142696096   1 MKVTVMTGDEqiVTLDVDRDESVENLKALLEVETRVPLRQQQ--IHFNGKEMQNTEKLSAAGVQDGDLVMM 69
Cdd:cd01792     3 LTVKMLTGNE--FQVSVSPSMTVSELKAQITQKIGVPAFQQRlaVQPSGVELQDGVRLASQGLGPSSTVLL 71

UBA2 domain of Rad23 proteins found in eukaryotes; 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 a ubiquitin-like (UBL) and two ubiquitin-associated (UBA) domains, as well as a xeroderma pigmentosum group C (XPC) protein-binding domain. UBL domain is responsible for the binding to proteasome. UBA domains are important for binding of ubiquitin (Ub) or multi-ubiquitinated substrates which suggests Rad23 proteins might be involved in certain pathways of ubiquitin metabolism. Both UBL domain and XPC-binding domain are necessary for efficient NER function of Rad23 proteins. This model corresponds to the UBA2 domain.

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1142696096 371 EAKVTKLVELGFDRASVTQALKLFNGNEEQAAAFLF 406
Cdd:cd14281     3 REAIERLVALGFSRDQAIEAYLACDKNEELAANYLF 38

UBA1 domain found in NEDD8 ultimate buster 1 (NUB1) and similar proteins; NUB1, also called negative regulator of ubiquitin-like proteins 1, renal carcinoma antigen NY-REN-18, or protein BS4, is a NEDD8-interacting protein that can be induced by interferon. It functions as a strong post-transcriptional down-regulator of the NEDD8 expression and plays critical roles in regulating many biological events, such as cell growth, NF-kappaB signaling, and biological responses to hypoxia. NUB1 can also interact with aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1) which may function in the regulation of cell cycle progression. NUB1 contains three ubiquitin-associated domains (UBA), a bipartite nuclear localization signal (NLS) and a PEST motif. This model corresponds to UBA1 domain.

                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1142696096 371 EAKVTKLVELGFDRASVTQALKLFNGNEEQAAAFL 405
Cdd:cd14291     2 EDKLQQLMEMGFSEAEARLALRACNGNVERAVDYI 36

clan AA aspartic protease, TIGR02281 family; This family consists of predicted aspartic proteases, typically from 180 to 230 amino acids in length, in MEROPS clan AA. This model describes the well-conserved 121-residue C-terminal region. The poorly conserved, variable length N-terminal region usually contains a predicted transmembrane helix. Sequences in the seed alignment and those scoring above the trusted cutoff are Proteobacterial; homologs scroing between trusted and noise are found in Pyrobaculum aerophilum str. IM2 (archaeal), Pirellula sp. (Planctomycetes), and Nostoc sp. PCC 7120 (Cyanobacteria). [Protein fate, Degradation of proteins, peptides, and glycopeptides]

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1142696096 197 YVDMEVNGVPLKAFVDSGAQSTIISKSCAERCGLLRLLDQRFRGIAVGVGQSEIlGRIHVAPIKIGNIF 265
Cdd:TIGR02281  13 YATGRVNGRNVRFLVDTGATSVALNEEDAQRLGLDLNRLGYTVTVSTANGQIKA-ARVTLDRVAIGGIV 80

UBA1 domain of Rad23 proteins found in eukaryotes; 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 a ubiquitin-like (UBL) and two ubiquitin-associated (UBA) domains, as well as a xeroderma pigmentosum group C (XPC) protein-binding domain. UBL domain is responsible for the binding to proteasome. UBA domains are important for binding of ubiquitin (Ub) or multi-ubiquitinated substrates which suggests Rad23 proteins might be involved in certain pathways of ubiquitin metabolism. Both UBL domain and XPC-binding domain are necessary for efficient NER function of Rad23 proteins. This model corresponds to the UBA1 domain.

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gi 1142696096 369 DFEAKVTKLVELGFDRASVTQALKL-FNgNEEQAAAFLF 406
Cdd:cd14280     1 ELEATINNIMSMGFEREQVVRALRAaFN-NPDRAVEYLL 38