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]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966991321    2 VKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALKEYKIDEKNFVVVMVTKPKAVSTPApattqqsapasttaitss 81
Cdd:TIGR00601  23 VKELKEKIEAEQGKDAYPVAQQKLIYSGKILSDDKTVKEYKIKEKDFVVVMVSKPKTGTGKV------------------ 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966991321   82 tattvaQAPTPVPALAPTSTPAsiTPASATASSEPAPASATKQEKPAEKPAETPVATSPTATDSTSGDssrsnlfeDATS 161
Cdd:TIGR00601  85 ------APPAATPTSAPTPTPS--PPASPASGMSAAPASAVEEKSPSEESATATAPESPSTSVPSSGS--------DAAS 148

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966991321  162 ALVTGQSYENMVTEIMSMGYEREQVIAALRASFNNPDRAVEYLLMGIPGDRESQAVVDPPQA------ASTGAPQSSAVA 235
Cdd:TIGR00601 149 TLVVGSERETTIEEIMEMGYEREEVERALRAAFNNPDRAVEYLLTGIPEDPEQPEPVQQTAAstaaatTETPQHGSVFEQ 228

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966991321  236 AAAATTTATTTTTSSGGHPLEFLRNQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNEPVQEAg 315
Cdd:TIGR00601 229 AAQGGTEQPATEAAQGGNPLEFLRNQPQFQQLRQVVQQNPQLLPPLLQQIGQENPQLLQQISQHPEQFLQMLNEPVGEL- 307

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 966991321  316 GQGGGGGGGSGGIAEAGSGHMNYIQVTPQEKEAIERLKALGFPEGLVIQAYFACEKNENLAANFLLQQNFD 386
Cdd:TIGR00601 308 ASESDMEGGVGAIAEAGLPQMNQIQVTPEEKEAIERLCALGFDRGLVIQAYFACDKNEELAANYLLSQNFD 378

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]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966991321    2 VKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALKEYKIDEKNFVVVMVTKPKAVSTPApattqqsapasttaitss 81
Cdd:TIGR00601  23 VKELKEKIEAEQGKDAYPVAQQKLIYSGKILSDDKTVKEYKIKEKDFVVVMVSKPKTGTGKV------------------ 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966991321   82 tattvaQAPTPVPALAPTSTPAsiTPASATASSEPAPASATKQEKPAEKPAETPVATSPTATDSTSGDssrsnlfeDATS 161
Cdd:TIGR00601  85 ------APPAATPTSAPTPTPS--PPASPASGMSAAPASAVEEKSPSEESATATAPESPSTSVPSSGS--------DAAS 148

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966991321  162 ALVTGQSYENMVTEIMSMGYEREQVIAALRASFNNPDRAVEYLLMGIPGDRESQAVVDPPQA------ASTGAPQSSAVA 235
Cdd:TIGR00601 149 TLVVGSERETTIEEIMEMGYEREEVERALRAAFNNPDRAVEYLLTGIPEDPEQPEPVQQTAAstaaatTETPQHGSVFEQ 228

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966991321  236 AAAATTTATTTTTSSGGHPLEFLRNQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNEPVQEAg 315
Cdd:TIGR00601 229 AAQGGTEQPATEAAQGGNPLEFLRNQPQFQQLRQVVQQNPQLLPPLLQQIGQENPQLLQQISQHPEQFLQMLNEPVGEL- 307

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 966991321  316 GQGGGGGGGSGGIAEAGSGHMNYIQVTPQEKEAIERLKALGFPEGLVIQAYFACEKNENLAANFLLQQNFD 386
Cdd:TIGR00601 308 ASESDMEGGVGAIAEAGLPQMNQIQVTPEEKEAIERLCALGFDRGLVIQAYFACDKNEELAANYLLSQNFD 378

XPC-binding domain; Members of this family adopt a structure consisting of four alpha helices, arranged in an array. They bind specifically and directly to the xeroderma pigmentosum group C protein (XPC) to initiate nucleotide excision repair.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 966991321  255 LEFLRNQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNEPV 311
Cdd:pfam09280   1 LDFLRNNPQFQQLRQLVQQNPQLLQPLLQQLAQSNPQLAQLIQQNQEEFLQLLNEPG 57

envelope glycoprotein C; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966991321  60 STPAPATTQQSA----PASTTAITSSTATTVAQAPTPVPALAPTSTPASITPASATASSEPAPAS-ATKQEKPAEKPAET 134
Cdd:PHA03269  40 PDPAPAPHQAASrapdPAVAPTSAASRKPDLAQAPTPAASEKFDPAPAPHQAASRAPDPAVAPQLaAAPKPDAAEAFTSA 119

                         90       100
                 ....*....|....*....|
gi 966991321 135 PVATSPTATDSTSGDSSRSN 154
Cdd:PHA03269 120 AQAHEAPADAGTSAASKKPD 139

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]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966991321    2 VKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALKEYKIDEKNFVVVMVTKPKAVSTPApattqqsapasttaitss 81
Cdd:TIGR00601  23 VKELKEKIEAEQGKDAYPVAQQKLIYSGKILSDDKTVKEYKIKEKDFVVVMVSKPKTGTGKV------------------ 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966991321   82 tattvaQAPTPVPALAPTSTPAsiTPASATASSEPAPASATKQEKPAEKPAETPVATSPTATDSTSGDssrsnlfeDATS 161
Cdd:TIGR00601  85 ------APPAATPTSAPTPTPS--PPASPASGMSAAPASAVEEKSPSEESATATAPESPSTSVPSSGS--------DAAS 148

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966991321  162 ALVTGQSYENMVTEIMSMGYEREQVIAALRASFNNPDRAVEYLLMGIPGDRESQAVVDPPQA------ASTGAPQSSAVA 235
Cdd:TIGR00601 149 TLVVGSERETTIEEIMEMGYEREEVERALRAAFNNPDRAVEYLLTGIPEDPEQPEPVQQTAAstaaatTETPQHGSVFEQ 228

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966991321  236 AAAATTTATTTTTSSGGHPLEFLRNQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNEPVQEAg 315
Cdd:TIGR00601 229 AAQGGTEQPATEAAQGGNPLEFLRNQPQFQQLRQVVQQNPQLLPPLLQQIGQENPQLLQQISQHPEQFLQMLNEPVGEL- 307

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 966991321  316 GQGGGGGGGSGGIAEAGSGHMNYIQVTPQEKEAIERLKALGFPEGLVIQAYFACEKNENLAANFLLQQNFD 386
Cdd:TIGR00601 308 ASESDMEGGVGAIAEAGLPQMNQIQVTPEEKEAIERLCALGFDRGLVIQAYFACDKNEELAANYLLSQNFD 378

XPC-binding domain; Members of this family adopt a structure consisting of four alpha helices, arranged in an array. They bind specifically and directly to the xeroderma pigmentosum group C protein (XPC) to initiate nucleotide excision repair.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 966991321  255 LEFLRNQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNEPV 311
Cdd:pfam09280   1 LDFLRNNPQFQQLRQLVQQNPQLLQPLLQQLAQSNPQLAQLIQQNQEEFLQLLNEPG 57

UBA2 domain of UV excision repair protein RAD23 homolog B (HR23B) found in vertebrates; HR23B, also called xeroderma pigmentosum group C (XPC) repair-complementing complex 58 kDa protein (p58), is tightly complexed with XPC protein to form the XPC-HR23B complex. Although it displays a high affinity for both single- and double-stranded DNA, the XPC-HR23B complex functions as a global genome repair (GGR)-specific repair factor that is specifically involved in global genome but not transcription-coupled nucleotide excision repair (NER). HR23B also interacts specifically with S5a subunit of the human 26 S proteasome, and plays an important role in shuttling ubiquitinated cargo proteins to the proteasome. HR23B contains an N-terminal ubiquitin-like (UBL) domain that binds proteasomes and two C-terminal ubiquitin-associated (UBA) domains that bind ubiquitin or multi-ubiquitinated substrates. In addition, it has a XPC protein-binding domain that might be necessary for its efficient NER function. This model corresponds to the UBA2 domain.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 966991321 344 QEKEAIERLKALGFPEGLVIQAYFACEKNENLAANFLLQQNFDED 388
Cdd:cd14428    1 QEKEAIERLKALGFPEGLVIQAYFACEKNENLAANFLLQQNFDDD 45

UBA1 domain of UV excision repair protein RAD23 homolog B (HR23B) found in vertebrates; HR23B, also called xeroderma pigmentosum group C (XPC) repair-complementing complex 58 kDa protein (p58), is tightly complexed with XPC protein to form the XPC-HR23B complex. Although it displays a high affinity for both single- and double-stranded DNA, the XPC-HR23B complex functions as a global genome repair (GGR)-specific repair factor that is specifically involved in global genome but not transcription-coupled nucleotide excision repair (NER). HR23B also interacts specifically with S5a subunit of the human 26 S proteasome, and plays an important role in shuttling ubiquitinated cargo proteins to the proteasome. HR23B contains an N-terminal ubiquitin-like (UBL) domain that binds proteasomes and two C-terminal ubiquitin-associated (UBA) domains that bind ubiquitin or multi-ubiquitinated substrates. In addition, it has a XPC protein-binding domain that might be necessary for its efficient NER function. This model corresponds to the UBA1 domain.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 966991321 164 VTGQSYENMVTEIMSMGYEREQVIAALRASFNNPDRAVEYLLMGIP 209
Cdd:cd14426    1 VTGQSYENMVTEIMSMGYEREQVIAALRASFNNPDRAVEYLLMGIP 46

UBA2 domain of Rad23 proteins found in metazoa; The family includes mammalian orthologs of yeast nucleotide excision repair (NER) proteins, Rad23p (in Saccharomyces cerevisiae) and Rhp23p (in Schizosaccharomyces pombe). 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 966991321 344 QEKEAIERLKALGFPEGLVIQAYFACEKNENLAANFLLQ 382
Cdd:cd14380    1 EEREAIERLKALGFPEGLVIQAYFACDKNENLAANFLLS 39

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.

                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 966991321 169 YENMVTEIMSMGYEREQVIAALRASFNNPDRAVEYLL 205
Cdd:cd14280    2 LEATINNIMSMGFEREQVVRALRAAFNNPDRAVEYLL 38

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 966991321 344 QEKEAIERLKALGFPEGLVIQAYFACEKNENLAANFLL 381
Cdd:cd14281    1 EEREAIERLVALGFSRDQAIEAYLACDKNEELAANYLF 38

UBA1 domain of putative DNA repair proteins Rad23 found in plant; The radiation sensitive 23 (Rad23) subfamily consists of four isoforms of putative DNA repair proteins from Arabidopsis thaliana and similar proteins from other plants. The nuclear-enriched Rad23 proteins function in the cell cycle, morphology, and fertility of plants through their delivery of ubiquitin (Ub)/26S proteasome system (UPS) substrates to the 26S proteasome. Rad23 proteins contain an N-terminal ubiquitin-like (UBL) domain that associates with the 26S proteasome Ub receptor RPN10, and two C-terminal ubiquitin-associated (UBA) domains that bind Ub conjugates. This model corresponds to the UBA1 domain.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 966991321 163 LVTGQSYENMVTEIMSMG---YEREQVIAALRASFNNPDRAVEYLLMGIP 209
Cdd:cd14379    1 LVAGSSLEQTVQQIMDMGggsWDRDTVVRALRAAYNNPERAVEYLYSGIP 50

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
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 966991321    2 VKALKEKIESEKGkdaFPVAGQKLIYAGKILNDDTALKEYKIDEKNFVVVMVTKP 56
Cdd:pfam00240  21 VLELKEKIAEKEG---VPPEQQRLIYSGKVLEDDQTLGEYGIEDGSTIHLVLRQR 72

UBA2 domain of Schizosaccharomyces pombe UV excision repair protein Rhp23p and its fungal homologs; The subfamily contains several fungal multiubiquitin receptors, including Schizosaccharomyces pombe Rhp23p and Saccharomyces cerevisiae Rad23p, both of which are orthologs of human HR23A. They play roles in nucleotide excision repair (NER) and in cell cycle regulation. They also function as shuttle proteins transporting ubiquitinated substrates destined for degradation from the E3 ligase to the 26S proteasome. For instance, S. pombe Rhp23p forms a complex with Rhp41p to recognize photolesions and help initiate DNA repair, and it also protects ubiquitin chains against disassembly by deubiquitinating enzymes. Like human HR23A, members in this subfamily interact with the proteasome through their N-terminal ubiquitin-like domain (UBL), and with ubiquitin (Ub), or multi-ubiquitinated substrates, through their two ubiquitin-associated domains (UBA), termed internal UBA1 and C-terminal UBA2. In addition, they contain a xeroderma pigmentosum group C (XPC) protein-binding domain that might be necessary for its efficient NER function. This model corresponds to the UBA2 domain.

                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 966991321 344 QEKEAIERLKALGFPEGLVIQAYFACEKNENLAANFLLQ 382
Cdd:cd14381    1 EEDQAIDRLCELGFDRDLVIQAYLACDKNEEMAANFLFE 39

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
                 ....*....|....*....|....*....|....*....|....*....|.
gi 966991321   2 VKALKEKIESEKGkdaFPVAGQKLIYAGKILNDDTALKEYKIDEKNFVVVM 52
Cdd:cd17039   21 VADLKEKIEEKTG---IPVEQQRLIYNGKELKDDKTLSDYGIKDGSTIHLV 68

UBA2 domain found in ubiquitin carboxyl-terminal hydrolase 13 (UBP13); UBP13, also called deubiquitinating enzyme 13, Isopeptidase T-3 (isoT3), ubiquitin thioesterase 13, or ubiquitin-specific-processing protease 13 is an ortholog of UBP5 implicated in catalyzing hydrolysis of various ubiquitin (Ub)-chains. It contains a zinc finger (ZnF) domain, a catalytic ubiquitin-specific processing protease (UBP) domain (catalytic C-box and H-box), and two ubiquitin-associated (UBA) domains. Due to the non-activating catalysis for K63-polyubiquitin chains, UBP13 may function differently from USP5 in cellular deubiquitination processes. Moreover, the zinc finger (ZnF) domain of USP13 cannot bind to Ub. Its tandem UBA domains can bind with different types of diUb but preferentially with K63-linked.USP13 can also regulate the protein level of CD3delta in cells via its UBA domains. This model corresponds to the UBA2 domain.

                         10        20        30
                 ....*....|....*....|....*....|....*
gi 966991321 170 ENMVTEIMSMGYEREQVIAALRASFNNPDRAVEYL 204
Cdd:cd14387    1 EESIAILMSMGFPRNRAIEALKRTNNNLDRALDWL 35

Heat shock chaperonin-binding motif;

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 966991321   254 PLEFLRNQ-PQFQQMRQIIQQNPSLLPALLQQigreNPQLLQQI 296
Cdd:smart00727   2 PEMALRLQnPQVQSLLQDMQQNPDMLAQMLQE----NPQLLQLI 41

UBA2 domain found in ubiquitin carboxyl-terminal hydrolase 5 (UBP5); UBP5, also called deubiquitinating enzyme 5, Isopeptidase T (IsoT), ubiquitin thioesterase 5, or ubiquitin-specific-processing protease 5, is a deubiquitinating enzyme largely responsible for the disassembly of the majority of unanchored polyubiquitin in the cell. Zinc is required for its catalytic activity. UBP5 contains four ubiquitin (Ub)-binding sites including an N-terminal zinc finger (ZnF) domain, a catalytic ubiquitin-specific processing protease (UBP) domain (catalytic C-box and H-box), and two ubiquitin-associated (UBA) domains. ZnF domain binds the proximal ubiquitin. UBP domain forms the active site. UBA domains are involved in binding linear or K48-linked polyubiquitin. This model corresponds to the UBA2 domain.

                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 966991321 170 ENMVTEIMSMGYEREQVIAALRASFNNPDRAVEYLLMGI 208
Cdd:cd14386    3 EEAVAMLVSMGFTRDQAIKALKATDNNVERAADWIFSHP 41

ubiquitin-like (Ubl) domain found in BCL2-associated athanogene 6 (BAG6) and similar proteins; BAG6, also termed large proline-rich protein BAG6, or BAG family molecular chaperone regulator 6, or HLA-B-associated transcript 3 (Bat3), or protein Scythe, or protein G3, is a nucleo-cytoplasmic shuttling chaperone protein that is highly conserved in eukaryotes. It functions in two distinct biological pathways, ubiquitin-mediated protein degradation of defective polypeptides and tail-anchored transmembrane protein biogenesis in mammals. BAG6 is a component of the heterotrimeric BAG6 sortase complex composed of BAG6, transmembrane recognition complex 35 (TRC35) and ubiquitin-like protein 4A (UBL4A). The BAG6 complex together with the cochaperone small, glutamine-rich, tetratricopeptide repeat-containing, protein alpha (SGTA) plays a role in the biogenesis of tail-anchored membrane proteins and subsequently shown to regulate the ubiquitination and proteasomal degradation of mislocalized proteins. Moreover, BAG6 acts as an apoptotic regulator that binds reaper, a potent apoptotic inducer. BAG6/reaper is thought to signal apoptosis, in part through regulating the folding and activity of apoptotic signaling molecules. It is also likely a key regulator of the molecular chaperone Heat Shock Protein A2 (HSPA2) stability/function in human germ cells. Furthermore, aspartyl protease-mediated cleavage of BAG6 is necessary for autophagy and fungal resistance in plants. BAG6 contains a ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, which provides a platform for discriminating substrates with shorter hydrophobicity stretches as a signal for defective proteins.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 966991321   2 VKALKEKIESEKGkdaFPVAGQKLIYAGKILNDDTALKEYKIDEK 46
Cdd:cd01809   23 VKEFKEHIASSVN---IPAEKQRLIFQGRVLQDDKKLKEYDVDGK 64

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.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 966991321   2 VKALKEKIESEKGkdaFPVAGQKLIYAGKILNDDTALKEYKIdEKNFVVVMV 53
Cdd:cd16106   23 VLELKELIAEKSD---IPAEQQRLIYKGKILKDEETLSSYKI-QDGHTVHLV 70

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.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 966991321   2 VKALKEKIESEKGkdaFPVAGQKLIYAGKILNDDTALKEYKIDE 45
Cdd:cd01806   21 VERIKERVEEKEG---IPPQQQRLIFSGKQMNDEKTAADYKIEG 61

UBA2 domain found in Schizosaccharomyces pombe ubiquitin carboxyl-terminal hydrolase 14 (spUBP14) and similar proteins; spUBP14, also called deubiquitinating enzyme 14, UBA domain-containing protein 2, ubiquitin thioesterase 14, or ubiquitin-specific-processing protease 14, functions as a deubiquitinating enzyme that is involved in protein degradation in fission yeast. Members in this family contain two tandem ubiquitin-association (UBA) domains. This model corresponds to the UBA2 domain.

                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 966991321 170 ENMVTEIMSMGYEREQVIAALRASFNNPDRAVEYLL 205
Cdd:cd14297    1 EDLVKQLVDMGFTEAQARKALRKTNNNVERAVDWLF 36

UBA domain found in Arabidopsis thaliana E3 ubiquitin-protein ligase UPL1 (atUPL1), UPL2 (atUPL2) and similar proteins; The family includes two highly similar 405-kDa HECT E3 ubiquitin-protein ligases (UPLs), UPL1 and UPL2, from Arabidopsis thaliana. The HECT E3 UPL family plays a prominent role in the ubiquitination of plant proteins. The biological functions of UPL1 and UPL2 remain unclear. Both of them contain a ubiquitin-associated (UBA) domain and a C-terminal HECT domain. UBA domain may be involved in ubiquitin metabolism. HECT domain is necessary and sufficient for their E3 catalytic activity, but requires ATP, E1 and an E2 of the Arabidopsis UBC8 family to ubiquitinate proteins.

                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 966991321 171 NMVTEIMSMGYEREQVIAALRA-SFNNPDRAVEYLL 205
Cdd:cd14327    1 EAVAQLVEMGFSRERAEEALRAvGTNSVELAMEWLF 36

envelope glycoprotein C; Provisional

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 966991321  62 PAPATTQQSApastTAITSSTATTVAQAPTPVPALAPTST----PASITPASATASSEPAPASATKQEKPA 128
Cdd:PHA03269  84 PAPAPHQAAS----RAPDPAVAPQLAAAPKPDAAEAFTSAaqahEAPADAGTSAASKKPDPAAHTQHSPPP 150

DNA polymerase III subunits gamma and tau; Validated

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966991321  56 PKAVSTPAPATTQQSAPA---STTAITSSTATTVAQAPTPVPALAPTSTPASITPASATASSEPAPASATKQEKPAEKPA 132
Cdd:PRK07764 417 PAAAAAPAPAAAPQPAPApapAPAPPSPAGNAPAGGAPSPPPAAAPSAQPAPAPAAAPEPTAAPAPAPPAAPAPAAAPAA 496

                         90
                 ....*....|..
gi 966991321 133 ETPVATSPTATD 144
Cdd:PRK07764 497 PAAPAAPAGADD 508

DNA polymerase III subunits gamma and tau; Validated

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966991321  55 KPKAVSTPAPATTQQSAPASTTAITSSTATTVAQAPTPVPALAPTSTPASItPASATASSEPAPASATKQEKPAEKPAET 134
Cdd:PRK07994 360 HPAAPLPEPEVPPQSAAPAASAQATAAPTAAVAPPQAPAVPPPPASAPQQA-PAVPLPETTSQLLAARQQLQRAQGATKA 438

                         90       100
                 ....*....|....*....|....*...
gi 966991321 135 PVATSPTATDSTSGDSSRSNLFEDATSA 162
Cdd:PRK07994 439 KKSEPAAASRARPVNSALERLASVRPAP 466

ubiquitin-like (Ubl) domain found in plant membrane-anchored ubiquitin-fold proteins (MUBs); The plant MUBs belong to a family of ubiquitin-fold proteins that are plasma membrane-anchored by prenylation. They may serve as docking site to facilitate the association of specific E2s to the plasma membrane. MUBs contain a ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 966991321   2 VKALKEKIESE--KGKDAFP--VAGQKLIYAGKILNDDTALKEYKI---DEKNFVVVM 52
Cdd:cd01814   25 VATLKEKVIAEwpKDKENGPksINDVKLIYAGKVLENGKTLADSRTpgkVPPGGVITM 82

DNA polymerase III subunit gamma/tau;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966991321  55 KPKAVSTPAPAT----TQQSAPASTTAITSSTATTVAQAPTPVPALAPTSTPASITPASATASSEPAPASATKQEKPAEK 130
Cdd:PRK07003 405 AAGAALAPKAAAaaaaTRAEAPPAAPAPPATADRGDDAADGDAPVPAKANARASADSRCDERDAQPPADSGSASAPASDA 484

                         90       100       110
                 ....*....|....*....|....*....|..
gi 966991321 131 PAETPVATSPTATDSTSGDSSRSNLFEDATSA 162
Cdd:PRK07003 485 PPDAAFEPAPRAAAPSAATPAAVPDARAPAAA 516

UBA domain found in vacuolar protein sorting-associated protein 13D (VP13D) and similar proteins; VP13D is a chorea-acanthocytosis (CHAC)-similar protein encoded by gene VPS13D. it contains two putative domains, ubiquitin-associated (UBA) domain and lectin domain of ricin B chain profile (ricin-B-lectin), suggesting it may interact with, and be involved in the trafficking of, proteins modified with ubiquitin and/or carbohydrate molecules. Further investigation is required.

                         10        20        30
                 ....*....|....*....|....*....|...
gi 966991321 173 VTEIMSMGYEREQVIAALRASFNNPDRAVEYLL 205
Cdd:cd14306    1 VAKLMELGFPEEDCIRALRACGGNVEEAANWLL 33

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 966991321 347 EAIERLKALGFPEGLVIQAYFACEKNENLAANFLL 381
Cdd:cd14309    2 EKIAQLMDLGFSREEAIQALEATNGNVELAASLLF 36

multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine pyrophosphate-binding subunit/dihydrolipoyllysine-residue succinyltransferase subunit;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966991321   54 TKPKAVSTPAPATTQQSAPASTTAITSSTATTVAQAPTPVPALAPTSTPASITPASATASSEPAPASATKQEKPAEKPAE 133
Cdd:PRK12270   42 AAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAAAAAAAAAPAAPPAAAAAAAPAAAAVEDEVTPLR 121

                          90       100
                  ....*....|....*....|
gi 966991321  134 TPVA----------TSPTAT 143
Cdd:PRK12270  122 GAAAavaknmdaslEVPTAT 141

ubiquitin-like (Ubl) domain found in NEDD8 ultimate buster 1 (NUB1) and similar proteins; NUB1, also termed negative regulator of ubiquitin-like proteins 1, or 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 a conserved ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, three ubiquitin-associated domains (UBA), a bipartite nuclear localization signal (NLS) and a PEST motif.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 966991321   1 MVKALKEKIESEKGKDAFPVagqKLIYAGKILNDDTALKEYKIdeKNFVVVMVTK 55
Cdd:cd17062   28 TGSELREKIAEELGVPEDRI---KLISNGKVLKDEKTLAEQGV--KNNSQVMVLV 77

ubiquitin-like (Ubl) domain found in AN1-type zinc finger protein 4 (ZFAND4) and similar proteins; ZFAND4, also termed AN1-type zinc finger and ubiquitin domain-containing protein-like 1 (ANUBL1), may function as an oncogene that promotes proliferation and regulates relevant tumor suppressor genes in gastric cancer, suggesting a role in gastric cancer initiation and progression. ZFAND4contains an N-terminal ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions, as well as a C-terminal AN1-type zinc finger. Unlike ubiquitin polyproteins and most ubiquitin fusion proteins, the N-terminal Ubl domain of ZFAND4 does not undergo proteolytic processing.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 966991321   2 VKALKEKIESEKGkdaFPVAGQKLIYAGKILNDDTALKEYKIDE 45
Cdd:cd01802   23 VASVKAKIQRLEG---IPVSQQHLIWSGRELEDDYCLHDYNITD 63

large tegument protein UL36; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966991321   60 STPAPATTQQSAPASTTAITSSTATTVAQAP-TPVPALAPTSTPASITPASATASSEPAPAS-ATKQEKPAEKPAETPVA 137
Cdd:PHA03247  377 RASLPTRKRRSARHAATPFARGPGGDDQTRPaAPVPASVPTPAPTPVPASAPPPPATPLPSAePGSDDGPAPPPERQPPA 456

                          90
                  ....*....|....*...
gi 966991321  138 TSPTATDSTSGDSSRSNL 155
Cdd:PHA03247  457 PATEPAPDDPDDATRKAL 474

ubiquitin-like (Ubl) domain found in homocysteine-inducible endoplasmic reticulum stress protein HERP; HERP is an endoplasmic reticulum (ER) integral membrane protein containing an N-terminal ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold. The Ubl domain is required for the degradation of HERP itself as well as for HERP-mediated anti-apoptotic effects. HERP is induced by the ER stress response pathway and is involved in improving the balance of folding capacity and protein loads in the ER. There are two types of HERP, HERP1 and HERP2, which are encoded by the HERPUD1 and HERPUD2 genes, respectively.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 966991321   2 VKALKEKIEsekgkDAFP----VAGQKLIYAGKILNDDTALKEYKIDEKNFVVVMV 53
Cdd:cd01790   25 VLKLKEHLS-----EVYPskplPEDQKLIYSGKLLEDHQTLKDVLREDDPEQVHTV 75

Uncharacterized membrane protein [Function unknown];

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 966991321  57 KAVSTPAPATTQQSAPASttaitsstattvAQAPTPVPALAPTSTPASITPASATAsSEPAPASATKQEKPAEKPA 132
Cdd:COG5373   40 AAEAASAPAEPEPEAAAA------------ATAAAPEAAPAPVPEAPAAPPAAAEA-PAPAAAAPPAEAEPAAAPA 102

cytoskeleton protein RodZ;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966991321  60 STPAPATTQQSAPAsttaitsstattVAQAPTPVPALAPTSTPASITPASATASSEPAPASATkqekPAEKPAETPVATS 139
Cdd:PRK10856 168 TTTDPATTPAPAAP------------VDTTPTNSQTPAVATAPAPAVDPQQNAVVAPSQANVD----TAATPAPAAPATP 231

                         90       100
                 ....*....|....*....|....*
gi 966991321 140 PTATDSTSGDSSRSNLFEDAtSALV 164
Cdd:PRK10856 232 DGAAPLPTDQAGVSTPAADP-NALV 255

dihydrolipoamide succinyltransferase; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966991321  50 VVMVTKPKAV--STPAPATTQQSAPASTTAITSSTATTVAQAPTPVPALAPTSTPASITPASATASSEPAPASATKQEKP 127
Cdd:PTZ00144 108 TVEVGAPLSEidTGGAPPAAAPAAAAAAKAEKTTPEKPKAAAPTPEPPAASKPTPPAAAKPPEPAPAAKPPPTPVARADP 187

                 ...
gi 966991321 128 AEK 130
Cdd:PTZ00144 188 RET 190

UBA domain found in ubiquitin-associated domain-containing protein 2 (UBAC2) and similar proteins; UBAC2, also called phosphoglycerate dehydrogenase-like protein 1, is a ubiquitin-associated domain (UBA)-domain containing protein encoded by gene UBAC2 (or PHGDHL1), a risk gene for Behcet's disease (BD). It may play an important role in the development of BD through its transcriptional modulation. Members in this family contain an N-terminal rhomboid-like domain and a C-terminal UBA domain.

                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 966991321 170 ENMVTEIMSMGYEREQVIAALRASFNNPDRAVEYLL 205
Cdd:cd14305    3 EEQVQQLVDMGFSREDVLEALRQSNNDVNAATNLLL 38

DNA polymerase III subunits gamma and tau; Validated

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966991321  49 VVVMVTKPKAVSTPAPATTQQSAPASTTAITSSTATTVAQAPTPVP------ALAPTSTPASITPASATASSEPAPASAT 122
Cdd:PRK07994 370 VPPQSAAPAASAQATAAPTAAVAPPQAPAVPPPPASAPQQAPAVPLpettsqLLAARQQLQRAQGATKAKKSEPAAASRA 449

                         90       100       110
                 ....*....|....*....|....*....|.
gi 966991321 123 KQEKPA-EKPAETPVATSPTATDSTSGDSSR 152
Cdd:PRK07994 450 RPVNSAlERLASVRPAPSALEKAPAKKEAYR 480

Ribosome receptor lysine/proline rich region; This highly conserved region is found towards the C-terminus of the transmembrane domain. The function is unclear.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 966991321   86 VAQAPTPVPALAPTSTPASITPASATASSEPAPASATKQEKPAE----KPAETPVATSPTAT 143
Cdd:pfam05104  71 EAPSAALEPEPVPTPVPAPVEPEPAPPSESPAPSPKEKKKKEKKsakvEPAETPEAVQPKPA 132