UBA domain-like superfamily; The ubiquitin-associated (UBA) domain-like superfamily contains alpha-helical structural homology ubiquitin-binding domains, including UBA domains and coupling of ubiquitin conjugation to endoplasmic reticulum degradation (CUE) domains which share a common three-helical bundle architecture. 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 bind the 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. CUE domain containing proteins are characterized by an FP and a di-leucine-like sequence and bind to monoubiquitin with varying affinities. Some higher eukaryotic CUE domain proteins do not bind monoubiquitin efficiently, since they carry LP, rather than FP among CUE domains. This superfamily also includes many UBA-like domains found in AMP-activated protein kinase (AMPK) related kinases, the NXF family of mRNA nuclear export factors, elongation factor Ts (EF-Ts), nascent polypeptide-associated complex subunit alpha (NACA) and similar proteins. Although many UBA-like domains may have a conserved TG but not GF/Y-loop, they still show a high level of structural and sequence similarity with three-helical ubiquitin binding domains.

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1387271694 112 TKKIENLCAMGFDRNAVIVALSSKSWDVETATELLLSN 149
Cdd:cd14390     1 TKKIENLCAMGFDRNAVIVALSSKSWDVETATELLLSN 38

Ubiquitin-conjugating enzyme E2, catalytic domain homologues; Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. This pathway functions in regulating many fundamental processes required for cell viability.TSG101 is one of several UBC homologues that lacks this active site cysteine.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387271694   22 VRFITKIWHPNISSvTGAICLDILK-DQWAAAMTLRTVLLSLQALLAAAEPDDPQDAVVANQYKQNPEMFKQTARLWAHV 100
Cdd:smart00212  64 VKFITKIYHPNVDS-SGEICLDILKqEKWSPALTLETVLLSLQSLLSEPNPDSPLNADAAELYKKNREEFKKKAREWTKK 142

                   ...
gi 1387271694  101 YAG 103
Cdd:smart00212 143 YAE 145

Ubiquitin-conjugating enzyme; Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologs. TSG101 is one of several UBC homologs that lacks this active site cysteine.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1387271694  22 VRFITKIWHPNISSvTGAICLDILKDQ-WAAAMTLRTVLLSLQALLAAAEPDDPQDAVVANQYKQNPEMFKQTARLWA 98
Cdd:pfam00179  63 VKFTTKIYHPNVDS-SGEVCLDILKDErWSPALTLEQVLLSIQSLLSEPNPEDPLNAEAAKLYRKNREEFEKKVREYV 139

UBA/TS-N domain; This small domain is composed of three alpha helices. This family includes the previously defined UBA and TS-N domains. The UBA-domain (ubiquitin associated domain) is a novel sequence motif found in several proteins having connections to ubiquitin and the ubiquitination pathway. The structure of the UBA domain consists of a compact three helix bundle. This domain is found at the N terminus of EF-TS hence the name TS-N. The structure of EF-TS is known and this domain is implicated in its interaction with EF-TU. The domain has been found in non EF-TS proteins such as alpha-NAC and MJ0280.

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1387271694 110 EYTKKIENLCAMGFDRNAVIVALSSKSWDVETATELL 146
Cdd:pfam00627   1 EDEEAIQRLVEMGFDREQVREALRATGNNVERAAEYL 37

Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones];

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1387271694  21 EVRFITKIWHPNISSVTGAICLDILkDQWAAAMTLRTVLLSLQA--LLAAAEPDDPQDAVVANQYKQNPEMF 90
Cdd:COG5078    76 QVRWLTPIFHPNIYEAGGSVCIGRA-DHWTPSLTLDDLIISLARllQYENYAPHSPVNLEAARWYRSNKDLF 146

Ubiquitin-conjugating enzyme E2, catalytic domain homologues; Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. This pathway functions in regulating many fundamental processes required for cell viability.TSG101 is one of several UBC homologues that lacks this active site cysteine.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387271694   22 VRFITKIWHPNISSvTGAICLDILK-DQWAAAMTLRTVLLSLQALLAAAEPDDPQDAVVANQYKQNPEMFKQTARLWAHV 100
Cdd:smart00212  64 VKFITKIYHPNVDS-SGEICLDILKqEKWSPALTLETVLLSLQSLLSEPNPDSPLNADAAELYKKNREEFKKKAREWTKK 142

                   ...
gi 1387271694  101 YAG 103
Cdd:smart00212 143 YAE 145

Ubiquitin-conjugating enzyme; Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologs. TSG101 is one of several UBC homologs that lacks this active site cysteine.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1387271694  22 VRFITKIWHPNISSvTGAICLDILKDQ-WAAAMTLRTVLLSLQALLAAAEPDDPQDAVVANQYKQNPEMFKQTARLWA 98
Cdd:pfam00179  63 VKFTTKIYHPNVDS-SGEVCLDILKDErWSPALTLEQVLLSIQSLLSEPNPEDPLNAEAAKLYRKNREEFEKKVREYV 139

Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain of ubiquitin-conjugating enzyme E2 N and related proteins; The E2N subfamily includes mammalian ubiquitin-conjugating enzymes E2 N (UBE2N/UBCH13/UBC13/BLU), yeast ubiquitin-conjugating enzyme E2 13 (UBC13), and plant ubiquitin-conjugating enzyme E2 35-36 (UBC35/UBC13A/UBG13A, UBC36/UBC13B/UBG13B), which function as ubiquitin-conjugating enzymes (EC 2.3.2.23). UBE2N, also called Bendless-like ubiquitin-conjugating enzyme, forms heterodimers with UBE2V1 and UBE2V2, respectively. The UBE2V1/UBE2N and UBE2V2/UBE2N heterodimers catalyze the synthesis of non-canonical 'Lys-63'-linked polyubiquitin chains. This type of polyubiquitination does not lead to protein degradation by the proteasome. UBE2N also plays a role in the control of progress through the cell cycle and differentiation, as well as in the error-free DNA repair pathway, and contributes to the survival of cells after DNA damage. Saccharomyces cerevisiae UBC13 has a role in the DNA error-free post-replication repair (PRR) pathway. The UBC13/MMS2 heterodimer catalyzes the synthesis of non-canonical poly-ubiquitin chains that are linked through 'Lys-63'. Arabidopsis thaliana UBC35 and UBC36 catalyze the synthesis of non-canonical poly-ubiquitin chains that are linked through 'Lys-63'. They mediate transcriptional activation of target genes. They are required for post-replication repair of UV-damaged DNA and for adapting root developmental programs to suboptimal availability of iron.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387271694  22 VRFITKIWHPNISSVtGAICLDILKDQWAAAMTLRTVLLSLQALLAAAEPDDPQDAVVANQYKQNPEMFKQTARLWAHVY 101
Cdd:cd23813    66 VRFLTKIYHPNIDKL-GRICLDILKDKWSPALQIRTVLLSIQALLSAPNPDDPLANDVAEHWKTNEAGAIATAREWTRLY 144

Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain of ubiquitin conjugating enzyme E2 T and related enzymes; The E2T subfamily includes mammalian ubiquitin-conjugating enzymes E2 T (UBE2T/HSPC150/PIG50), plant ubiquitin-conjugating enzyme E2 37 (UBC37), and similar proteins. They are ubiquitin-conjugating enzymes (EC 2.3.2.23) that accept ubiquitin from the E1 complex and catalyze the covalent attachment to other proteins. UBE2T, also called cell proliferation-inducing gene 50 protein, catalyzes monoubiquitination. It is involved in mitomycin-C (MMC)-induced DNA repair. It acts as a specific E2 ubiquitin-conjugating enzyme for the Fanconi anemia complex by associating with E3 ubiquitin-protein ligase FANCL and catalyzing monoubiquitination of FANCD2, a key step in the DNA damage pathway. UBE2T also mediates monoubiquitination of FANCL and FANCI. It may contribute to ubiquitination and degradation of BRCA1. In vitro, UBE2T can promote polyubiquitination using all 7 ubiquitin Lys residues, but may prefer 'Lys-11'-, 'Lys-27'-, 'Lys-48'- and 'Lys-63'-linked polyubiquitination.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387271694  22 VRFITKIWHPNISSvTGAICLDILK----DQWAAAMTLRTVLLSLQALLAAAEPDDPQDAVVANQYKQNPEMFKQTARLW 97
Cdd:cd23805    64 VRFLTPIYHPNIDS-AGRICLDILKmppkGSWKPSLNISTVLTSIRLLLAEPNPDDPLMADIAAEYKYNRALFDAKAKEW 142

ubiquitin conjugating enzyme; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387271694  17 LKSEEVRFITKIWHPNISSvTGAICLDILKDQWAAAMTLRTVLLSLQALLAAAEPDDPQDAVVANQYKQNPEMFKQTARL 96
Cdd:PLN00172   62 FKPPKVQFTTKIYHPNINS-NGSICLDILRDQWSPALTVSKVLLSISSLLTDPNPDDPLVPEIARVFKENRSRYEATARE 140

                  ....*.
gi 1387271694  97 WAHVYA 102
Cdd:PLN00172  141 WTQRYA 146

Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain of ubiquitin conjugating enzyme E2 E1-E3 and related proteins; The E2E subfamily includes mammalian ubiquitin-conjugating enzyme E2 E1-3 (UBE2E1/UBCH6, UBE2E2/UBCH8, UBE2E3/UBCH9) and similar proteins. UBE2E, also known as (E3-independent) E2 ubiquitin-conjugating enzyme E, or E2 ubiquitin-conjugating enzyme E, accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. UBE2E1 (EC 2.3.2.23 and EC 2.3.2.24) catalyzes the covalent attachment of ISG15 to other proteins. It mediates the selective degradation of short-lived and abnormal proteins. In vitro, it also catalyzes 'Lys-48'-linked polyubiquitination. In vitro, both UBE2E2 (EC 2.3.2.23) and UBE2E3 (EC 2.3.2.23) catalyze 'Lys-11'- and 'Lys-48'-, as well as 'Lys-63'-linked polyubiquitination. UBE2E2 catalyzes the ISGylation of influenza A virus NS1 protein. UBE2E3 participates in the regulation of trans-epithelial sodium transport in renal cells. It may be involved in cell growth arrest.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387271694  18 KSEEVRFITKIWHPNISSvTGAICLDILKDQWAAAMTLRTVLLSLQALLAAAEPDDPQDAVVANQYKQNPEMFKQTARLW 97
Cdd:cd23793    60 KPPKVTFRTRIYHCNINS-QGVICLDILKDNWSPALTISKVLLSICSLLTDCNPADPLVGSIATQYLTDREEHDRIAREW 138

Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain of ubiquitin conjugating enzymes E2 F, E2 M and related proteins; The E2F/E2M subfamily includes mammalian ubiquitin-conjugating enzymes E2 F (UBE2F/NCE2, EC 2.3.2.32) and E2 M (UBE2M/UBC12, EC 2.3.2.34), yeast NEDD8-conjugating enzyme UBC12 (EC 2.3.2.24), plant RUB1-conjugating enzyme 1-2 (RCE1/UBC12 and RCE2/UBC12L, EC 2.3.2.-), and similar proteins. UBE2F (also called EDD8-conjugating enzyme UBE2F, NEDD8 carrier protein UBE2F, NEDD8 protein ligase UBE2F, NEDD8-conjugating enzyme 2, or RING-type E3 NEDD8 transferase UBE2F) and UBE2M (also called NEDD8-conjugating enzyme UBC12, or NEDD8 carrier protein) accept the ubiquitin-like protein NEDD8 from the UBA3-NAE1 E1 complex and catalyzes its covalent attachment to other proteins. The RBX2-UBE2F complex neddylates specific target proteins, such as CUL5. The RBX1-UBE2M complex neddylates specific target proteins, such as CUL1, CUL2, CUL3 and CUL4. UBE2M is involved in cell proliferation. Saccharomyces cerevisiae UBC12 and Arabidopsis thaliana RCE1/RCE2 accept the ubiquitin-like protein NEDD8/RUB1 from the UBA3-ULA1 E1 complex and the ECR1-AXR1 E1 complex, respectively.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1387271694  21 EVRFITKIWHPNISSvTGAICLDILKDQWAAAMTLRTVLLSLQALLAAAEPDDPQDAVVANQYKQNPEMFKQTAR 95
Cdd:cd23794    64 KVKCLTKIYHPNIDE-EGNVCLNILREDWKPVLSLKDVILGLLFLFLEPNPDDPLNKEAAELLLRDPEEFERNVR 137

Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain/ubiquitin E2 variant (UEV) domain; The family includes ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain and ubiquitin (Ub) E2 variant (UEV) domain. They belong to the ubiquitin-conjugating (UBC) superfamily that represents a structural domain with an alpha-beta(4)-alpha(3) core fold. E2 is part of the ubiquitin-mediated protein degradation pathway in which a thioester linkage forms between a conserved cysteine and the C-terminus of ubiquitin, and complexes with ubiquitin protein ligase enzymes, E3. This pathway regulates many fundamental cellular processes. There are also other E2s which form thioester linkages without the use of E3s. Several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) contains the UEV domain, which lacks the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways.

                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1387271694  21 EVRFITKIWHPNISSvTGAICLDILK-DQWAAAMTLRTV 58
Cdd:cd00195    63 KVRFLTPIYHPNVDP-DGEICLDILKsEGWSPALTLRSV 100

Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain of Acanthamoeba polyphaga mimivirus bifunctional E2/E3 enzyme R795 and related proteins; R795 (EC 2.3.2.23/EC 2.3.2.27) is a bifunctional enzyme which acts as an E2 ubiquitin-conjugating enzyme that catalyzes the covalent attachment of ubiquitin to other proteins. It also acts as a RING-type E3 ubiquitin-protein transferase.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1387271694  21 EVRFITKIWHPNISSVtGAICLDILKDQWAAAMTLRTVLLSLQALLAAAEPDDPQD 76
Cdd:cd23833    63 EVRFITPIYHCNINSD-GRICHSILDRNYTPDTTMREILDAVYGLLLTPEPDDPLD 117

Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain of ubiquitin conjugating enzyme E2 S and related domains; The E2S subfamily includes mammalian ubiquitin-conjugating enzymes E2 S (UBE2S/E2EPF), plant ubiquitin-conjugating enzyme E2 22 (UBC22), and similar proteins. They are ubiquitin-conjugating enzymes (EC2.3.2.23) that accept ubiquitin from the E1 complex and catalyze the covalent attachment to other proteins. UBE2S catalyzes 'Lys-11'-linked polyubiquitination. It acts as an essential factor of the anaphase promoting complex/cyclosome (APC/C), a cell cycle-regulated ubiquitin ligase that controls progression through mitosis. UBE2S acts by specifically elongating 'Lys-11'-linked polyubiquitin chains initiated by the E2 enzyme UBE2C/UBCH10 on APC/C substrates, enhancing the degradation of APC/C substrates by the proteasome and promoting mitotic exit. It also acts by elongating ubiquitin chains initiated by the E2 enzyme UBE2D1/UBCH5 in vitro; it is however unclear whether UBE2D1/UBCH5 acts as an E2 enzyme for the APC/C in vivo. UBE2S is also involved in ubiquitination and subsequent degradation of VHL, resulting in an accumulation of HIF1A. In vitro, it can promote polyubiquitination using all 7 ubiquitin Lys residues, except 'Lys-48'-linked polyubiquitination.

                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1387271694  24 FITKIWHPNISSvTGAICLDILKDQWAAAMTLRTV 58
Cdd:cd23804    70 FLTKIFHPNVSP-TGEICVNTLKKDWKPELGLRHI 103

Ubiquitin associated domain; Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.

                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 1387271694  111 YTKKIENLCAMGFDRNAVIVALSSKSWDVETATELLL 147
Cdd:smart00165   1 DEEKIDQLLEMGFSREEALKALRAANGNVERAAEYLL 37

Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain of ubiquitin-conjugating enzyme E2 L3, L5, L6 and related proteins; The E2L3-like subfamily includes mammalian ubiquitin-conjugating enzymes E2 L3 (UBE2L3/UBCH7/UBCE7), L5 (UBE2L5), L6 (UBE2L6/UBCH8), and similar proteins. They are ubiquitin-conjugating enzymes (EC 2.3.2.23) that accept ubiquitin from the E1 complex and catalyze the covalent attachment to other proteins. UBE2L3 specifically acts with HECT-type and RBR family E3 ubiquitin-protein ligases. It does not function with most RING-containing E3 ubiquitin-protein ligases because it lacks intrinsic E3-independent reactivity with lysine: in contrast, it has activity with the RBR family E3 enzymes, such as PRKN and ARIH1, that function like RING-HECT hybrids. In vitro, UBE2L3 catalyzes 'Lys-11'-linked polyubiquitination. It is involved in the selective degradation of short-lived and abnormal proteins. In addition to ubiquitin, UBE2L6 also catalyzes the covalent attachment of ISG15 to other proteins. It functions in the E6/E6-AP-induced ubiquitination of p53/TP53. It promotes ubiquitination and subsequent proteasomal degradation of FLT3.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387271694  22 VRFITKIWHPNISSvTGAICLDIL-KDQWAAAMTLRTVLLSLQALLAAAEPDDPQDAVVANQYKQNPEMFKQTARLWAHV 100
Cdd:cd23801    66 ITFKTKIYHPNVDE-KGQVCLPIIsPENWKPATKIDQVLQALLALINDPEPEHPLRADLAEEYSKDKKKFLKNAEEFTKK 144

                  ..
gi 1387271694 101 YA 102
Cdd:cd23801   145 HA 146

UBA domain found in Drosophila melanogaster ubiquitin-conjugating enzyme E2-22 kDa (UbcD4) and similar proteins; UbcD4, also called ubiquitin carrier protein or ubiquitin-protein ligase, is a class II E2 ubiquitin-conjugating enzyme encoded by Drosophila E2 gene which is only expressed in pole cells in embryos. It is a putative E2 enzyme homologous to the Huntingtin interacting protein-2 (HIP2) of human. UbcD4 specifically interacts with the polyubiquitin-binding subunit of the proteasome. It contains a C-terminal ubiquitin-associated (UBA) domain in addition to an N-terminal catalytic ubiquitin-conjugating enzyme E2 (UBCc) domain.

                          10        20        30
                  ....*....|....*....|....*....|....
gi 1387271694 114 KIENLCAMGFDRNAVIVALSSKSWDVETATELLL 147
Cdd:cd14391     3 KIRQLMDMGFDEHKARVALSSHNWDLEKATESLF 36

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 1387271694 114 KIENLCAMGFDRNAVIVALSSKSWDVETATELLL 147
Cdd:cd14309     3 KIAQLMDLGFSREEAIQALEATNGNVELAASLLF 36

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        30
                  ....*....|....*....|....*....|
gi 1387271694 115 IENLCAMGFDRNAVIVALSSKSWDVETATE 144
Cdd:cd14270     1 LAQLVEMGFSREQARRALRATNGDVEAAVE 30

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 1387271694 114 KIENLCAMGFDRNAVIVALSSKSWDVETATELLL 147
Cdd:cd14305     5 QVQQLVDMGFSREDVLEALRQSNNDVNAATNLLL 38

Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain of ubiquitin-conjugating enzyme E2 G1 and related proteins; The subfamily includes mammalian ubiquitin-conjugating enzymes E2 G1 (UBE2G1/UBC7/E217K), fission yeast ubiquitin-conjugating enzyme E2 15 (UBC15), plant ubiquitin-conjugating enzymes E2 7 (UBC7), E2 13 (UBC13) and E2 14 (UBC14). They are ubiquitin-conjugating enzymes (EC 2.3.2.23) that accept ubiquitin from the E1 complex and catalyze the covalent attachment to other proteins. In vitro, UBE2G1 catalyzes 'Lys-48'-, as well as 'Lys-63'-linked polyubiquitination. It may be involved in the degradation of muscle-specific proteins and may mediate polyubiquitination of CYP3A4. Schizosaccharomyces pombe UBC15 has a role in the formation of chromatin structures that influence the localization of transcriptional silencing factors. Arabidopsis thaliana UBC7, UBC13 and UBC14 are involved in the formation of multiubiquitin chains. They signal the protein for selective degradation.

                          10        20
                  ....*....|....*....|....*
gi 1387271694  21 EVRFITKIWHPNISSvTGAICLDIL 45
Cdd:cd23795    67 KMKFITEMWHPNVYP-DGDVCISIL 90

UBA domain found in microtubule-associated protein (MAP)/microtubule affinity-regulating kinase (MARK)/ partitioning-defective 1 (Par-1) and similar proteins; The MARK/Par-1 subfamily contains serine/threonine-protein kinases including mammal MARKs, and polarity kinases Par-1 found in Caenorhabditis elegans and Drosophila melanogaster. Those proteins are frequently found associated with membrane structures and participate in diverse processes from control of the cell cycle and polarity to intracellular signaling and microtubule stability. They are involved in nematode embryogenesis, cell cycle control, epithelial cell polarization, cell signaling, and neuronal migration and differentiation. The mammals MARKs have been implicated in carcinomas, Alzheimer's disease (through tau hyperphosphorylation), and autism. Four MARK isoforms exist in humans. Members in this subfamily contain an N-terminal protein kinase catalytic domain, followed by an ubiquitin-associated (UBA) domain and a C-terminal regulatory domain of 5'-AMP-activated protein kinase (AMPK).

                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1387271694 113 KKIENLCAMGFDRNAVIVALSSKSWDVETATELLL 147
Cdd:cd14337     4 KRIEIMVSMGFNREEIEESLKNRKFDEVMATYLLL 38

Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain of ubiquitin conjugating enzyme E2 W and related enzymes; The E2W subfamily includes mammalian ubiquitin-conjugating enzymes E2 W (UBE2W/UBC16), plant ubiquitin-conjugating enzyme E2 15-18 (UBC15-18), and similar proteins. They are ubiquitin-conjugating enzymes (EC 2.3.2.23) that accept ubiquitin from the E1 complex and catalyze the covalent attachment to other proteins. UBE2W, also called FLJ11011, E2 ubiquitin-conjugating enzyme W, N-terminal E2 ubiquitin-conjugating enzyme (EC 2.3.2.25), N-terminus-conjugating E2, ubiquitin carrier protein W, ubiquitin-conjugating enzyme 16 (UBC-16), or ubiquitin-protein ligase W, specifically monoubiquitinates the N-terminus of various substrates, including ATXN3, MAPT/TAU, POLR2H/RPB8 and STUB1/CHIP, by recognizing backbone atoms of disordered N-termini. In vitro, UBE2W catalyzes 'Lys-11'-linked polyubiquitination. UBE2W is an important protein for early postnatal survival and for the normal functioning of multiple organ systems.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1387271694  17 LKSEEVRFI-TKI-WHPNISSvTGAICLDILKDQWAAAMTL 55
Cdd:cd23808    60 IESPEVVFVgPPIpVHPHVYS-NGHICLSILYDDWSPALTV 99

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
                  ....*....|....*....|....*....|....*....|..
gi 1387271694 108 SPEYTKKIENLCAMGFDRNAVIVALSSKSWDVETATELLLSN 149
Cdd:TIGR00601 334 TPEEKEAIERLCALGFDRGLVIQAYFACDKNEELAANYLLSQ 375

Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain of ubiquitin-conjugating enzyme E2 I and related proteins; The E2I subfamily includes mammalian ubiquitin-conjugating enzymes E2 I (UBE2I/UBC9/UBCE9, EC 2.3.2.-), yeast ubiquitin-conjugating enzyme E2-18 kDa (UBC9, EC2.3.2.-), and plant SUMO-conjugating enzyme 1 (SCE1/AHUS5, EC2.3.2.-). UBE2I, also called SUMO-conjugating enzyme UBC9, RING-type E3 SUMO transferase UBC9, SUMO-protein ligase, ubiquitin carrier protein 9, ubiquitin carrier protein I, or ubiquitin-protein ligase I, accepts the ubiquitin-like proteins SUMO1, SUMO2, SUMO3, SUMO4 and SUMO1P1/SUMO5 from the UBLE1A-UBLE1B E1 complex and catalyzes their covalent attachment to other proteins with the help of an E3 ligase such as RANBP2, CBX4 and ZNF451. It can catalyze the formation of poly-SUMO chains. It is necessary for sumoylation of FOXL2 and KAT5 and essential for nuclear architecture and chromosome segregation. UBE2I also sumoylates p53/TP53 at 'Lys-386' and mediates sumoylation of ERCC6 which is essential for its transcription-coupled nucleotide excision repair activity. Saccharomyces cerevisiae UBC9, also called SUMO-conjugating enzyme UBC9, RING-type E3 SUMO transferase UBC9, ubiquitin carrier protein 9, ubiquitin-conjugating enzyme E2-18 kDa, acts as an E2 ubiquitin-like--protein ligase that mediates SUMO/Smt3 attachment to septins and PCNA. It may be involved in degradation of S- (CLB5) and M-phase cyclins (CLB2). Arabidopsis thaliana SCE1, also called SUMO-conjugating enzyme SCE1, protein EMBRYO DEFECTIVE 1637, or protein hus5 homolog, is a SUMO-conjugating enzyme that accepts the SUMO proteins from the E1 SUMO-activating heterodimer SAE1/SAE2 and catalyzes its covalent attachment to other proteins with the E3 SUMO ligases SIZ1 and MMS21. It associates with SIZ1 for sumoylation of the transcription factor GTE3.

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gi 1387271694  21 EVRFITKIWHPNISSvTGAICLDILKD--QWAAAMTLRTVLLSLQALLAAAEPDDPQDAVVANQYKQNPEMFKQTARLWA 98
Cdd:cd23798    71 KCKFDPPLFHPNVYP-SGTVCLSILNEdkDWKPSITIKQILLGIQDLLDEPNLDDPAQAEAYTLYKNNREEYERRVRAQA 149

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gi 1387271694  99 HVY 101
Cdd:cd23798   150 KKY 152

UBA domain of AMPK related kinases; The AMPK-RK family comprises AMP-activated protein kinases (AMPKs), MAP/microtubule affinity-regulating kinases (MARKs), Brain-specific kinases (BRSKs), Salt inducible kinases (SIKs), maternal embryonic leucine zipper kinase (MELK), and SNF-related serine/threonine-protein kinase (SNRK). It is the only kinase family in the human genome containing an ubiquitin-associated (UBA) or UBA-like domain which is located immediately C-terminal to their N-terminal protein kinase catalytic domain. In addition, most of family members contain a C-terminal regulatory domain of 5'-AMP-activated protein kinase (AMPK), but some are lack of this region. AMPK-RKs play central roles in metabolic control, energy homeostasis and stress responses in eukaryotes. They require phosphorylation by liver kinase B1 (LKB1) for full activity. Normally, AMPK-RKs appear to exist as heterotrimeric complexes consisting of a catalytic alpha-subunit and regulatory beta- and gamma-subunits. This model corresponds to the catalytic subunit. The UBA domain, previously called SNF1 homology (SNH) domain, regulates the conformation, LKB1-mediated phosphorylation and activation, and localization of the AMPK-RKs, but does not interact with ubiquitin-like molecules. In AMPKalpha subunits, the UBA-like autoinhibitory domain (AID) is responsible for AMPKalpha subunit autoinhibition. Due to the lack of UBA domain, NUAK1 kinase, also called ARK5 (AMPK-related kinase 5), and NUAK2 kinase, also called SNARK (SNF1/AMPK-related kinase), are not included in this family.

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gi 1387271694 115 IENLCAMGFDRNAVIVALSSKSWDVETATELLL 147
Cdd:cd14272     5 LQEMVELGYDREEIVESLRNNRYNDLAATYYLL 37

UBA domain found in eukaryotic E3 ubiquitin-protein ligase HUWE1 and similar proteins; HUWE1, also called ARF-binding protein 1 (ARF-BP1), HECT, UBA and WWE domain-containing protein 1, homologous to E6AP carboxyl terminus homologs protein 9 (HectH9), large structure of UREB1 (LASU1), Mcl-1 ubiquitin ligase E3 (Mule), upstream regulatory element-binding protein 1 (URE-B1), or URE-binding protein 1, may function as a ubiquitin-protein ligase that involves in the ubiquitination cascade that targets specific substrate proteins in proteolysis. It can ubiquitylate DNA polymerase beta (Pol beta), the major BER DNA polymerase and modulates base excision repair (BER). HUWE1 also acts as a critical mediator of both the p53-independent and p53-dependent tumor suppressor functions of ARF tumor suppressor in p53 regulation. Moreover, HUWE1 is both required and sufficient for the polyubiquitination of Mcl-1, an anti-apoptotic Bcl-2 family member involving in DNA damage-induced apoptosis. Furthermore, HUWE1 plays an important role in the regulation of Cdc6 stability after DNA damage. In addition, HUWE1 works as a partner of N-Myc oncoprotein in neural cells. It ubiquitinates N-Myc and primes it for proteasomal-mediated degradation. HUWE1 contains a ubiquitin-associated (UBA) domain, a WWE domain, and a Bcl-2 homology region 3 (BH3) domain at the N-terminus and a HECT domain at the C-terminus. WWE domain plays a role in the regulation of specific protein-protein interactions in a ubiquitin conjugation system. BH3 domain is responsible for the specific binding to Mcl-1. HECT domain involves in the inhibition of the transcriptional activity of p53 via a ubiquitin-dependent degradation pathway. It also controls neural differentiation and proliferation by destabilizing the N-Myc oncoprotein.

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gi 1387271694 115 IENLCAMGFDRNAVIVALSSKSwDVETATELLLSN 149
Cdd:cd14288     6 LQQLMDMGFTREHALEALLHTS-TLEQATEYLLTH 39

UBA domain of 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 Dsk2 protein, PLIC-1 (also called ubiquilin-1), PLIC-2 (also called ubiquilin-2 or Chap1), PLIC-3 (also called ubiquilin-3) and PLIC-4 (also called ubiquilin-4, Ataxin-1 interacting ubiquitin-like protein, A1Up, Connexin43-interacting protein of 75 kDa, or CIP75), and mouse PLIC proteins. They are ubiquitin-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 ubiquitin-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 ubiquitin-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 UBQLN3, 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 a ubiquitin-like nuclear protein that interacts with ataxin-1 and further links ataxin-1 with the chaperone and ubiquitin-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 ubiquitin-like (UBL) domain that is responsible for the binding of ubiquitin-interacting motifs (UIMs) expressed by proteasomes and endocytic adaptors, and C-terminal ubiquitin-associated (UBA) domain that interacts with ubiquitin 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 1387271694 111 YTKKIENLCAMGF-DRNAVIVALSSKSWDVETATELLLS 148
Cdd:cd14399     2 YASQLEQLQAMGFvDRQANIQALIATGGNVNAAIERLLG 40