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        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457795  12 AEVHAKLLTGPWQVSILTtpqlrRYRNRGFQHGWRlvIPHGEGTLDFDVLVTEHFPHQPPRISLATLQRFLVWPHVEEDG 91
Cdd:pfam14461   2 AFRWLADLAQPCAIDELK-----RDSGKKVTMELS--VPEGGGPVDLTLVLPDSFPLLPPKVFLVDLGQYKLLPHINTDG 74

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1830457795  92 VLCLL-SSEATINSARPGEVTLSLLQDALQLVLESEIGNNQQDFRNEFTTYWGRKCP 147
Cdd:pfam14461  75 ELCYApQMGTPLDFWDPNGSAQQLLDQAPLALKAGMSGDEDKEFAEEFGAYWNSYEN 131

Bacterial trigger factor protein (TF); In the E. coli cytosol, a fraction of the newly synthesized proteins requires the activity of molecular chaperones for folding to the native state. The major chaperones implicated in this folding process are the ribosome-associated Trigger Factor (TF), and the DnaK and GroEL chaperones with their respective co-chaperones. Trigger Factor is an ATP-independent chaperone and displays chaperone and peptidyl-prolyl-cis-trans-isomerase (PPIase) activities in vitro. It is composed of at least three domains, an N-terminal domain which mediates association with the large ribosomal subunit, a central substrate binding and PPIase domain with homology to FKBP proteins, and a C-terminal domain of unknown function. The positioning of TF at the peptide exit channel, together with its ability to interact with nascent chains as short as 57 residues renders TF a prime candidate for being the first chaperone that binds to the nascent polypeptide chains. This family represents the N-terminal region of the protein.

                          10        20
                  ....*....|....*....|..
gi 1830457795 287 IDGFRPGKAPKEVVQSQIKSSL 308
Cdd:pfam05697  41 IPGFRKGKVPRSVIEKRYGKEV 62

Prokaryotic E2 family B; A member of the E2/UBC superfamily of proteins found in several bacteria. The active site residues are similar to the eukaryotic E2 proteins but lack the conserved asparagine. Members of this family are usually fused to an E1 domain at the C-terminus. The protein is usually in the gene neighborhood of a gene encoding a member of the pol-beta nucleotidyltransferase superfamily. Many of the operons in this family are in ICE-like mobile elements and plasmids.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457795  12 AEVHAKLLTGPWQVSILTtpqlrRYRNRGFQHGWRlvIPHGEGTLDFDVLVTEHFPHQPPRISLATLQRFLVWPHVEEDG 91
Cdd:pfam14461   2 AFRWLADLAQPCAIDELK-----RDSGKKVTMELS--VPEGGGPVDLTLVLPDSFPLLPPKVFLVDLGQYKLLPHINTDG 74

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1830457795  92 VLCLL-SSEATINSARPGEVTLSLLQDALQLVLESEIGNNQQDFRNEFTTYWGRKCP 147
Cdd:pfam14461  75 ELCYApQMGTPLDFWDPNGSAQQLLDQAPLALKAGMSGDEDKEFAEEFGAYWNSYEN 131

Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457795 339 TIAILGCGSIGSHLAFLLAEAGVGKLVLCDPEPLKWANVGRHALASDS-VGTSKAKSLATTLKNSYPS---SVGFDGYck 414
Cdd:cd01483     1 RVLLVGLGGLGSEIALNLARSGVGKITLIDFDTVELSNLNRQFLARQAdIGKPKAEVAARRLNELNPGvnvTAVPEGI-- 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1830457795 415 twegLASSMPEKLLTCDLLIAATGNWTTEASLNAWRKtaDFRQPLL 460
Cdd:cd01483    79 ----SEDNLDDFLDGVDLVIDAIDNIAVRRALNRACK--ELGIPVI 118

thiazole biosynthesis adenylyltransferase ThiF, E. coli subfamily; Members of the HesA/MoeB/ThiF family of proteins (pfam00899) include a number of members encoded in the midst of thiamine biosynthetic operons. This mix of known and putative ThiF proteins shows a deep split in phylogenetic trees, with the Escherichia. coli ThiF and the E. coli MoeB proteins seemingly more closely related than E. coli ThiF and Campylobacter (for example) ThiF. This model represents the more widely distributed clade of ThiF proteins such found in E. coli. [Biosynthesis of cofactors, prosthetic groups, and carriers, Thiamine]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457795 333 KTLQSSTIAILGCGSIGSHLAFLLAEAGVGKLVLCDPEPLKWANVGRHAL-ASDSVGTSKAKSLATTLKNsYPSSVGFDG 411
Cdd:TIGR02356  17 QRLLNSHVLIIGAGGLGSPAALYLAGAGVGTIVIVDDDHVDLSNLQRQILfTEEDVGRPKVEVAAQRLRE-LNSDIQVTA 95

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1830457795 412 YCKtwEGLASSMPEKLLTCDLLIAATGNWTTEASLNA 448
Cdd:TIGR02356  96 LKE--RVTAENLELLINNVDLVLDCTDNFATRYLIND 130

Bacterial trigger factor protein (TF); In the E. coli cytosol, a fraction of the newly synthesized proteins requires the activity of molecular chaperones for folding to the native state. The major chaperones implicated in this folding process are the ribosome-associated Trigger Factor (TF), and the DnaK and GroEL chaperones with their respective co-chaperones. Trigger Factor is an ATP-independent chaperone and displays chaperone and peptidyl-prolyl-cis-trans-isomerase (PPIase) activities in vitro. It is composed of at least three domains, an N-terminal domain which mediates association with the large ribosomal subunit, a central substrate binding and PPIase domain with homology to FKBP proteins, and a C-terminal domain of unknown function. The positioning of TF at the peptide exit channel, together with its ability to interact with nascent chains as short as 57 residues renders TF a prime candidate for being the first chaperone that binds to the nascent polypeptide chains. This family represents the N-terminal region of the protein.

                          10        20
                  ....*....|....*....|..
gi 1830457795 287 IDGFRPGKAPKEVVQSQIKSSL 308
Cdd:pfam05697  41 IPGFRKGKVPRSVIEKRYGKEV 62

Prokaryotic E2 family B; A member of the E2/UBC superfamily of proteins found in several bacteria. The active site residues are similar to the eukaryotic E2 proteins but lack the conserved asparagine. Members of this family are usually fused to an E1 domain at the C-terminus. The protein is usually in the gene neighborhood of a gene encoding a member of the pol-beta nucleotidyltransferase superfamily. Many of the operons in this family are in ICE-like mobile elements and plasmids.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457795  12 AEVHAKLLTGPWQVSILTtpqlrRYRNRGFQHGWRlvIPHGEGTLDFDVLVTEHFPHQPPRISLATLQRFLVWPHVEEDG 91
Cdd:pfam14461   2 AFRWLADLAQPCAIDELK-----RDSGKKVTMELS--VPEGGGPVDLTLVLPDSFPLLPPKVFLVDLGQYKLLPHINTDG 74

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1830457795  92 VLCLL-SSEATINSARPGEVTLSLLQDALQLVLESEIGNNQQDFRNEFTTYWGRKCP 147
Cdd:pfam14461  75 ELCYApQMGTPLDFWDPNGSAQQLLDQAPLALKAGMSGDEDKEFAEEFGAYWNSYEN 131

Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457795 339 TIAILGCGSIGSHLAFLLAEAGVGKLVLCDPEPLKWANVGRHALASDS-VGTSKAKSLATTLKNSYPS---SVGFDGYck 414
Cdd:cd01483     1 RVLLVGLGGLGSEIALNLARSGVGKITLIDFDTVELSNLNRQFLARQAdIGKPKAEVAARRLNELNPGvnvTAVPEGI-- 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1830457795 415 twegLASSMPEKLLTCDLLIAATGNWTTEASLNAWRKtaDFRQPLL 460
Cdd:cd01483    79 ----SEDNLDDFLDGVDLVIDAIDNIAVRRALNRACK--ELGIPVI 118

ThiF_MoeB_HesA. Family of E1-like enzymes involved in molybdopterin and thiamine biosynthesis family. The common reaction mechanism catalyzed by MoeB and ThiF, like other E1 enzymes, begins with a nucleophilic attack of the C-terminal carboxylate of MoaD and ThiS, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS. MoeB, as the MPT synthase (MoaE/MoaD complex) sulfurase, is involved in the biosynthesis of the molybdenum cofactor, a derivative of the tricyclic pterin, molybdopterin (MPT). ThiF catalyzes the adenylation of ThiS, as part of the biosynthesis pathway of thiamin pyrophosphate (vitamin B1).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457795 335 LQSSTIAILGCGSIGSHLAFLLAEAGVGKLVLCDPEPLKWANVGRHALASDS-VGTSKAKSLATTLK--NsypSSVGFDG 411
Cdd:cd00757    19 LKNARVLVVGAGGLGSPAAEYLAAAGVGKLGLVDDDVVELSNLQRQILHTEAdVGQPKAEAAAERLRaiN---PDVEIEA 95

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1830457795 412 YCktwEGLASSMPEKLL-TCDLLIAATGNWTT 442
Cdd:cd00757    96 YN---ERLDAENAEELIaGYDLVLDCTDNFAT 124

Family of activating enzymes (E1) of ubiquitin-like proteins related to the E.coli hypothetical protein ygdL. The common reaction mechanism catalyzed by E1-like enzymes begins with a nucleophilic attack of the C-terminal carboxylate of the ubiquitin-like substrate, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of the substrate. The exact function of this family is unknown.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457795 329 DPKVKTLQSSTIAILGCGSIGSHLAFLLAEAGVGKLVLCDPEPLKWANVGR--HALASDsVGTSKAKSLA 396
Cdd:cd00755     3 EEGLEKLRNAHVAVVGLGGVGSWAAEALARSGVGKLTLIDFDVVCVSNLNRqiHALLST-VGKPKVEVMA 71

molybdopterin-synthase adenylyltransferase MoeB;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1830457795 335 LQSSTIAILGCGSIGSHLAFLLAEAGVGKLVLCDPEPLKWANVGRHAL-ASDSVGTSKAKSLATTL 399
Cdd:PRK08762  133 LLEARVLLIGAGGLGSPAALYLAAAGVGTLGIVDHDVVDRSNLQRQILhTEDRVGQPKVDSAAQRL 198

thiamine/molybdopterin biosynthesis MoeB-like protein; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457795 333 KTLQSSTIAILGCGSIGSHLAFLLAEAGVGKLVLCDPEPLKWANVGRHALASDSVGTS---KAKSLATTLKnSYPSSVGF 409
Cdd:PRK12475   20 RKIREKHVLIVGAGALGAANAEALVRAGIGKLTIADRDYVEWSNLQRQQLYTEEDAKQkkpKAIAAKEHLR-KINSEVEI 98

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1830457795 410 DGYCKtwEGLASSMPEKLLTCDLLIAATGNWTTEASLN 447
Cdd:PRK12475   99 VPVVT--DVTVEELEELVKEVDLIIDATDNFDTRLLIN 134

hypothetical protein; Validated

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1830457795 333 KTLQSSTIAILGCGSI-GSHLaFLLAEAGVGKLVLCDPEPLKWANVGRHALAS-DSVGTSKAKSLATTLKNSYP 404
Cdd:PRK08223   23 QRLRNSRVAIAGLGGVgGIHL-LTLARLGIGKFTIADFDVFELRNFNRQAGAMmSTLGRPKAEVLAEMVRDINP 95

Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]; Glutamate dehydrogenase/leucine dehydrogenase is part of the Pathway/BioSystem: Glutamine biosynthesis

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457795 333 KTLQSSTIAILGCGSIGSHLAFLLAEAGvGKLVLC--------DPEPLKWANVGRHALASDSV-GTSKAKSLAttlknsy 403
Cdd:COG0334   204 LSLEGKTVAVQGFGNVGSYAAELLHELG-AKVVAVsdssggiyDPDGIDLDALKEHKEERGSVaGYPGAEFIT------- 275

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1830457795 404 pssvgfdgycktweglassmPEKLLT--CDLLI-AATGN 439
Cdd:COG0334   276 --------------------NEELLEldCDILIpAALEN 294

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        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457795  32 QLRRYRNRGFQHG--------WRLVIPHGEGTL------DFDVLVTEHFPHQPPRIslatlqRFL--VW-PHVEEDGVLC 94
Cdd:pfam00179   8 ELLKDPPPGISAGpvddnlfeWKVTIIGPDGTPyeggvfKLSVEFPEDYPFKPPKV------KFTtkIYhPNVDSSGEVC 81

                  .
gi 1830457795  95 L 95
Cdd:pfam00179  82 L 82

Bacterial trigger factor protein (TF); In the E. coli cytosol, a fraction of the newly synthesized proteins requires the activity of molecular chaperones for folding to the native state. The major chaperones implicated in this folding process are the ribosome-associated Trigger Factor (TF), and the DnaK and GroEL chaperones with their respective co-chaperones. Trigger Factor is an ATP-independent chaperone and displays chaperone and peptidyl-prolyl-cis-trans-isomerase (PPIase) activities in vitro. It is composed of at least three domains, an N-terminal domain which mediates association with the large ribosomal subunit, a central substrate binding and PPIase domain with homology to FKBP proteins, and a C-terminal domain of unknown function. The positioning of TF at the peptide exit channel, together with its ability to interact with nascent chains as short as 57 residues renders TF a prime candidate for being the first chaperone that binds to the nascent polypeptide chains. This family represents the N-terminal region of the protein.

                          10        20
                  ....*....|....*....|..
gi 1830457795 287 IDGFRPGKAPKEVVQSQIKSSL 308
Cdd:pfam05697  41 IPGFRKGKVPRSVIEKRYGKEV 62