Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus; Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus. PfpI is an ATP-independent intracellular proteases which may hydrolyze small peptides to provide a nutritional source. Only Cys of the catalytic triad typical of GATase1 domains is conserved in this group. This Cys residue is found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727179145   7 IVFPIYQGVTQLDFTGPLQFLRRMP----GAEIVVASVDGADVESEGlHFTQL--RPLPEIARCDVLCVPGGSGCTQALQ 80
Cdd:cd03139    1 VGILLFPGVEVLDVIGPYEVFGRAPrlaaPFEVFLVSETGGPVSSRS-GLTVLpdTSFADPPDLDVLLVPGGGGTRALVN 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727179145  81 DEAFMQQIRRLGADARYLTSVCTGSLILAAAGLLQGKRAACHWSMRDSLKLFGAVP-SSARVERDGNVISGGGVTAGIDF 159
Cdd:cd03139   80 DPALLDFIRRQAARAKYVTSVCTGALLLAAAGLLDGRRATTHWAAIDWLKEFGAIVvVDARWVVDGNIWTSGGVSAGIDM 159

                        170       180
                 ....*....|....*....|....
gi 727179145 160 ALALIAELHGEETAQMIQLYLEYA 183
Cdd:cd03139  160 ALALVARLFGEELAQAVALLIEYD 183

Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus; Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus. PfpI is an ATP-independent intracellular proteases which may hydrolyze small peptides to provide a nutritional source. Only Cys of the catalytic triad typical of GATase1 domains is conserved in this group. This Cys residue is found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727179145   7 IVFPIYQGVTQLDFTGPLQFLRRMP----GAEIVVASVDGADVESEGlHFTQL--RPLPEIARCDVLCVPGGSGCTQALQ 80
Cdd:cd03139    1 VGILLFPGVEVLDVIGPYEVFGRAPrlaaPFEVFLVSETGGPVSSRS-GLTVLpdTSFADPPDLDVLLVPGGGGTRALVN 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727179145  81 DEAFMQQIRRLGADARYLTSVCTGSLILAAAGLLQGKRAACHWSMRDSLKLFGAVP-SSARVERDGNVISGGGVTAGIDF 159
Cdd:cd03139   80 DPALLDFIRRQAARAKYVTSVCTGALLLAAAGLLDGRRATTHWAAIDWLKEFGAIVvVDARWVVDGNIWTSGGVSAGIDM 159

                        170       180
                 ....*....|....*....|....
gi 727179145 160 ALALIAELHGEETAQMIQLYLEYA 183
Cdd:cd03139  160 ALALVARLFGEELAQAVALLIEYD 183

DJ-1/PfpI family; The family includes the protease PfpI. This domain is also found in transcriptional regulators.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727179145    7 IVFPIYQGVTQLDFTGPLQFLRRMpGAEIVVASVDGADV-ESEGLHFTQLRPLPEI--ARCDVLCVPGG-SGCTQALQDE 82
Cdd:pfam01965   3 VLVLLADGFEDIELIYPADVLRRA-GIKVTVVSVDGGEVkGSRGVKVTVDASLDDVkpDDYDALVLPGGrAGPERLRDNE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727179145   83 AFMQQIRRLGADARYLTSVCTGSLILAAAGLLQGKRAACHWSMRDSLKLFGAVPSSARVERDGNVISGGGVTAGIDFALA 162
Cdd:pfam01965  82 KLVEFVKDFYEKGKPVAAICHGPQVLAAAGVLKGRKVTSHPAVKDDLINAGATYVDKPVVVDGNLVTSRGPGDAPEFALE 161

                  ....
gi 727179145  163 LIAE 166
Cdd:pfam01965 162 ILEQ 165

transcriptional activator FtrA; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727179145  61 IARCDVLCVPGGSGcTQALQDEAFMQQIRRLGADARYLTSVCTGSLILAAAGLLQGKRAACHWSMRDSLKlfgAVPSSAR 140
Cdd:PRK09393  73 LDRADTIVIPGWRG-PDAPVPEPLLEALRAAHARGARLCSICSGVFVLAAAGLLDGRRATTHWRYAERLQ---ARYPAIR 148

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727179145 141 VERD------GNVISGGGVTAGIDFALALIAELHGEETAQMIQLYLEYAPAPpfEGGTPELAPPHIYARVQAQMAESLQR 214
Cdd:PRK09393 149 VDPDvlyvdeGQILTSAGSAAGIDLCLHLVRRDFGSEAANRVARRLVVPPHR--DGGQAQFVPRPVASRESDRLGPLIDW 226

                 ....*..
gi 727179145 215 RRALVAQ 221
Cdd:PRK09393 227 MRAHLAE 233

Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus; Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus. PfpI is an ATP-independent intracellular proteases which may hydrolyze small peptides to provide a nutritional source. Only Cys of the catalytic triad typical of GATase1 domains is conserved in this group. This Cys residue is found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727179145   7 IVFPIYQGVTQLDFTGPLQFLRRMP----GAEIVVASVDGADVESEGlHFTQL--RPLPEIARCDVLCVPGGSGCTQALQ 80
Cdd:cd03139    1 VGILLFPGVEVLDVIGPYEVFGRAPrlaaPFEVFLVSETGGPVSSRS-GLTVLpdTSFADPPDLDVLLVPGGGGTRALVN 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727179145  81 DEAFMQQIRRLGADARYLTSVCTGSLILAAAGLLQGKRAACHWSMRDSLKLFGAVP-SSARVERDGNVISGGGVTAGIDF 159
Cdd:cd03139   80 DPALLDFIRRQAARAKYVTSVCTGALLLAAAGLLDGRRATTHWAAIDWLKEFGAIVvVDARWVVDGNIWTSGGVSAGIDM 159

                        170       180
                 ....*....|....*....|....
gi 727179145 160 ALALIAELHGEETAQMIQLYLEYA 183
Cdd:cd03139  160 ALALVARLFGEELAQAVALLIEYD 183

AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; A subgroup of AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain. AraC regulators are defined by a AraC-type helix-turn-helix DNA binding domain at their C-terminal. AraC family transcriptional regulators are widespread among bacteria and are involved in regulating diverse and important biological functions, including carbon metabolism, stress responses and virulence in different microorganisms. The catalytic triad typical of GATase1 domains is not conserved in this GATase1-like domain. However, in common with typical GATase1domains a reactive cys residue is found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727179145   6 VIVFPiyqGVTQLDFTGPLQFLRR------MPGAEIVVASVDGADVE-SEGLHFTQLRPLPEIARCDVLCVPGGSGCTQA 78
Cdd:cd03137    3 VLVFP---GVSLLDLSGPAEVFGEanralgPPAYELRVCSPEGGPVRsSSGLSLVADAGLDALAAADTVIVPGGPDVDGR 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727179145  79 LQDEAFMQQIRRLGADARYLTSVCTGSLILAAAGLLQGKRAACHWSMRDSL-KLFGAVpssaRVE------RDGNVISGG 151
Cdd:cd03137   80 PPPPALLAALRRAAARGARVASVCTGAFVLAEAGLLDGRRATTHWAYAEDLaRRFPAV----RVDpdvlyvDDGNVWTSA 155

                        170       180
                 ....*....|....*....|..
gi 727179145 152 GVTAGIDFALALIAELHGEETA 173
Cdd:cd03137  156 GVTAGIDLCLHLVREDLGAAVA 177

AraC transcriptional regulators having an N-terminal Type 1 glutamine amidotransferase (GATase1)-like domain; A subgroup of AraC transcriptional regulators having an N-terminal Type 1 glutamine amidotransferase (GATase1)-like domain. This group contains proteins similar to the Pseudomonas aeruginosa ArgR regulator. ArgR functions in the control of expression of certain genes of arginine biosynthesis and catabolism. AraC regulators are defined by a AraC-type helix-turn-helix DNA binding domain at their C-terminal. AraC family transcriptional regulators are widespread among bacteria and are involved in regulating diverse and important biological functions, including carbon metabolism, stress responses and virulence in different microorganisms. The catalytic triad typical of GATase1 domains is not conserved in this GATase1-like domain. However, in common with typical GATase1domains a reactive cys residue is found in some sequences in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727179145  23 PLQFLRRMPGAEIV---VASVDGADVE-SEGLHFTQLRPLPEIARCDVLCVPGGSGcTQALQDEAFMQQIRRLGADARYL 98
Cdd:cd03136   20 PLRAANRLAGRELYrwrVLSLDGAPVTsSNGLRVAPDAALEDAPPLDYLFVVGGLG-ARRAVTPALLAWLRRAARRGVAL 98

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 727179145  99 TSVCTGSLILAAAGLLQGKRAACHWSMRDSLK-LF-GAVPSSARVERDGNVISGGGVTAGIDFALALIAELHGEETAQ 174
Cdd:cd03136   99 GGIDTGAFLLARAGLLDGRRATVHWEHLEAFAeAFpRVQVTRDLFEIDGDRLTCAGGTAALDLMLELIARDHGAALAA 176

AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; A subgroup of AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain. AraC regulators are defined by a AraC-type helix-turn-helix DNA binding domain at their C-terminal. AraC family transcriptional regulators are widespread among bacteria and are involved in regulating diverse and important biological functions, including carbon metabolism, stress responses and virulence in different microorganisms. The catalytic triad typical of GATase1 domains is not conserved in this GATase1-like domain. However, in common with typical GATase1domains a reactive cys residue is found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727179145  34 EIVVASVDGADVESE-GLHFTQLRPLPEIARCDVLCVPGGSGCTQAL---QDEAFMQQIRRLGADARYLTSVCTGSLILA 109
Cdd:cd03138   39 EVRLVSLDGGPVLLAgGILILPDATLADVPAPDLVIVPGLGGDPDELllaDNPALIAWLRRQHANGATVAAACTGVFLLA 118

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727179145 110 AAGLLQGKRAACHWSMRDSLK-LFGAV--PSSARVERDGNVISGGGVTAGIDFALALIAELHGEETAQMI 176
Cdd:cd03138  119 EAGLLDGRRATTHWWLAPQFRrRFPKVrlDPDRVVVTDGNLITAGGAMAWADLALHLIERLAGPELAQLV 188

DJ-1 family protein; This model represents the DJ-1 clade of the so-called ThiJ/PfpI family of proteins. PfpI, represented by a distinct model, is a putative intracellular cysteine protease. DJ-1 is described as an oncogene that acts cooperatively with H-Ras. Many members of the DJ-1 clade are annotated (apparently incorrectly) as ThiJ, a protein of thiamine biosynthesis. However, published reports of ThiJ activity and identification of a ThiJ/ThiD bifunctional protein describe an unrelated locus mapping near ThiM, rather than the DJ-1 homolog of E. coli. The ThiJ designation for this family may be spurious; the cited paper refers to a locus near thiD and thiM in E. coli, unlike the gene represented here. Current public annotation reflects ThiJ/ThiD bifunctional activity, apparently a property of ThiD and not of this locus. [Unknown function, General]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727179145    6 VIVFPIYQGVTQLDFTGPLQFLRRmPGAEIVVASVDGADVE----SEGLHFTQLRPLPEIA--RCDVLCVPGGSGCTQAL 79
Cdd:TIGR01383   1 KVLVPLAPGFEEMEAVITVDVLRR-AGIKVTVAIAGLNGKLavkgSRGVKILADASLEDVDleKFDVIVLPGGMPGAENL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727179145   80 QD-EAFMQQIRRLGADARYLTSVCTGSLILAAAGLLQGKRAACHWSMRDSLkLFGAVPSSARVERDGNVISGGGVTAGID 158
Cdd:TIGR01383  80 RNsKLLLNILKSQESKGKLVAAICAAPAVLLAHGVLLGKKATCYPGFKEKL-LNGNYSVNKTVVVDGNLITSRGPGTAIE 158

                         170
                  ....*....|....*.
gi 727179145  159 FALALIAELHGEETAQ 174
Cdd:TIGR01383 159 FALELVELLAGKEKAQ 174

A type 1 glutamine amidotransferase (GATase1)-like domain found in PfpI from Pyrococcus furiosus; A type 1 glutamine amidotransferase (GATase1)-like domain found in PfpI from Pyrococcus furiosus. This group includes proteins similar to PfpI from P. furiosus. and PH1704 from Pyrococcus horikoshii. These enzymes are ATP-independent intracellular proteases and may hydrolyze small peptides to provide a nutritional source. Only Cys of the catalytic triad typical of GATase1 domains is conserved in this group. This Cys residue is found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow. For PH1704, it is believed that this Cys together with a different His in one monomer and Glu (from an adjacent monomer) forms a different catalytic triad from the typical GATase1domain. PfpI is homooligomeric. Protease activity is only found for oligomeric forms of PH1704.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727179145  14 GVTQLDFTGPLQFLRRmPGAEIVVASVDGADVESEGLHFTQLRPLPEIARC-----DVLCVPGGSGCTQALQDEAFMQQI 88
Cdd:cd03134    9 GFEDVELTYPLYRLRE-AGAEVVVAGPEAGGEIQGKHGYDTVTVDLTIADVdaddyDALVIPGGTNPDKLRRDPDAVAFV 87

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 727179145  89 RRLGADARYLTSVCTGSLILAAAGLLQGKRAACHWSMRDSLKLFGAVPSSARVERDGNVIS 149
Cdd:cd03134   88 RAFAEAGKPVAAICHGPWVLISAGVVRGRKLTSYPSIKDDLINAGANWVDEEVVVDGNLIT 148

Type 1 glutamine amidotransferase (GATase1)-like domain; Type 1 glutamine amidotransferase (GATase1)-like domain. This group includes proteins similar to Class I glutamine amidotransferases, the intracellular PH1704 from Pyrococcus horikoshii, the C-terminal of the large catalase: Escherichia coli HP-II, Sinorhizobium meliloti Rm1021 ThuA. and, the A4 beta-galactosidase middle domain. The majority of proteins in this group have a reactive Cys found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow. For Class I glutamine amidotransferases proteins which transfer ammonia from the amide side chain of glutamine to an acceptor substrate, this Cys forms a Cys-His-Glu catalytic triad in the active site. Glutamine amidotransferases activity can be found in a range of biosynthetic enzymes included in this cd: glutamine amidotransferase, formylglycinamide ribonucleotide, GMP synthetase, anthranilate synthase component II, glutamine-dependent carbamoyl phosphate synthase, cytidine triphosphate synthetase, gamma-glutamyl hydrolase, imidazole glycerol phosphate synthase and, cobyric acid synthase. For Pyrococcus horikoshii PH1704, the Cys of the nucleophile elbow together with a different His and, a Glu from an adjacent monomer form a catalytic triad different from the typical GATase1 triad. The E. coli HP-II C-terminal domain, S. meliloti Rm1021 ThuA and the A4 beta-galactosidase middle domain lack the catalytic triad typical GATaseI domains. GATase1-like domains can occur either as single polypeptides, as in Class I glutamine amidotransferases, or as domains in a much larger multifunctional synthase protein, such as CPSase.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727179145   7 IVFPIYQGVTQLDFTGPLQFLRRMpGAEIVVASVDGADVESEglhftqlrplPEIARCDVLCVPGGSGCTQAL-QDEAFM 85
Cdd:cd01653    1 VAVLLFPGFEELELASPLDALREA-GAEVDVVSPDGGPVESD----------VDLDDYDGLILPGGPGTPDDLaRDEALL 69

                         90       100
                 ....*....|....*....|...
gi 727179145  86 QQIRRLGADARYLTSVCTGSLIL 108
Cdd:cd01653   70 ALLREAAAAGKPILGICLGAQLL 92

Type 1 glutamine amidotransferase (GATase1)-like domain; Type 1 glutamine amidotransferase (GATase1)-like domain. This group contains proteins similar to Class I glutamine amidotransferases, the intracellular PH1704 from Pyrococcus horikoshii, the C-terminal of the large catalase: Escherichia coli HP-II, Sinorhizobium meliloti Rm1021 ThuA, the A4 beta-galactosidase middle domain and peptidase E. The majority of proteins in this group have a reactive Cys found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow. For Class I glutamine amidotransferases proteins which transfer ammonia from the amide side chain of glutamine to an acceptor substrate, this Cys forms a Cys-His-Glu catalytic triad in the active site. Glutamine amidotransferases activity can be found in a range of biosynthetic enzymes included in this cd: glutamine amidotransferase, formylglycinamide ribonucleotide, GMP synthetase, anthranilate synthase component II, glutamine-dependent carbamoyl phosphate synthase (CPSase), cytidine triphosphate synthetase, gamma-glutamyl hydrolase, imidazole glycerol phosphate synthase and, cobyric acid synthase. For Pyrococcus horikoshii PH1704, the Cys of the nucleophile elbow together with a different His and, a Glu from an adjacent monomer form a catalytic triad different from the typical GATase1 triad. Peptidase E is believed to be a serine peptidase having a Ser-His-Glu catalytic triad which differs from the Cys-His-Glu catalytic triad of typical GATase1 domains, by having a Ser in place of the reactive Cys at the nucleophile elbow. The E. coli HP-II C-terminal domain, S. meliloti Rm1021 ThuA and the A4 beta-galactosidase middle domain lack the catalytic triad typical GATaseI domains. GATase1-like domains can occur either as single polypeptides, as in Class I glutamine amidotransferases, or as domains in a much larger multifunctional synthase protein, such as CPSase. Peptidase E has a circular permutation in the common core of a typical GTAse1 domain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727179145   7 IVFPIYQGVTQLDFTGPLQFLRRMpGAEIVVASVDGADVESEglhftqlrplPEIARCDVLCVPGGSGCTQAL-QDEAFM 85
Cdd:cd03128    1 VAVLLFGGSEELELASPLDALREA-GAEVDVVSPDGGPVESD----------VDLDDYDGLILPGGPGTPDDLaWDEALL 69

                         90       100
                 ....*....|....*....|...
gi 727179145  86 QQIRRLGADARYLTSVCTGSLIL 108
Cdd:cd03128   70 ALLREAAAAGKPVLGICLGAQLL 92