intracellular protease, PfpI family; The member of this family from Pyrococcus horikoshii has been solved to 2 Angstrom resolution. It is an ATP-independent intracellular protease that crystallizes as a hexameric ring. Cys-101 is proposed as the active site residue in a catalytic triad with the adjacent His-102 and a Glu residue from an adjacent monomer. A member of this family from Bacillus subtilis, GSP18, has been shown to be expressed in response to several forms of stress. A role in the degradation of small peptides has been suggested. A closely related family consists of the thiamine biosynthesis protein ThiJ and its homologs. [Protein fate, Degradation of proteins, peptides, and glycopeptides]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498314432    6 LLLLCGDFAEDYETMVPFQALQAVGHRVDAVCpdKRAGesiataihdfegdqTYSEKPGHRFTLNADFAAVDPADYDGLV 85
Cdd:TIGR01382   2 LLVLTTDEFEDSELLYPLDRLREAGHEVDTVS--KEAG--------------TTVGKHGYSVTVDATIDEVNPEEYDALV 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498314432   86 VAGGRAPEYLRLNERVIEVVRHFFTEDKPVAAICHGAQLLAAARVLEGRTCSAYPACRPEVELAGGRYADIAVddAVTDG 165
Cdd:TIGR01382  66 IPGGRAPEYLRLNNKAVRLVREFVEKGKPVAAICHGPQLLISAGVLRGKKLTSYPAIIDDVKNAGAEYVDIEV--VVVDG 143

                         170       180
                  ....*....|....*....|...
gi 498314432  166 KLVTAPAWPAHPAWLAQFLAVLG 188
Cdd:TIGR01382 144 NLVTSRVPDDLPAFNREFLKLLG 166

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 498314432    4 KRLLLLCGDFAEDYETMVPFQALQAVGHRVDAVCPDKRagesiataihdfegdqTYSEKPGHRFTLNADFAAVDPADYDG 83
Cdd:pfam01965   1 KKVLVLLADGFEDIELIYPADVLRRAGIKVTVVSVDGG----------------EVKGSRGVKVTVDASLDDVKPDDYDA 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498314432   84 LVVAGGRA-PEYLRLNERVIEVVRHFFTEDKPVAAICHGAQLLAAARVLEGRTCSAYPACRPEVELAGGRYADiavDDAV 162
Cdd:pfam01965  65 LVLPGGRAgPERLRDNEKLVEFVKDFYEKGKPVAAICHGPQVLAAAGVLKGRKVTSHPAVKDDLINAGATYVD---KPVV 141

                         170       180
                  ....*....|....*....|...
gi 498314432  163 TDGKLVTAPAWPAHPAWLAQFLA 185
Cdd:pfam01965 142 VDGNLVTSRGPGDAPEFALEILE 164

intracellular protease, PfpI family; The member of this family from Pyrococcus horikoshii has been solved to 2 Angstrom resolution. It is an ATP-independent intracellular protease that crystallizes as a hexameric ring. Cys-101 is proposed as the active site residue in a catalytic triad with the adjacent His-102 and a Glu residue from an adjacent monomer. A member of this family from Bacillus subtilis, GSP18, has been shown to be expressed in response to several forms of stress. A role in the degradation of small peptides has been suggested. A closely related family consists of the thiamine biosynthesis protein ThiJ and its homologs. [Protein fate, Degradation of proteins, peptides, and glycopeptides]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498314432    6 LLLLCGDFAEDYETMVPFQALQAVGHRVDAVCpdKRAGesiataihdfegdqTYSEKPGHRFTLNADFAAVDPADYDGLV 85
Cdd:TIGR01382   2 LLVLTTDEFEDSELLYPLDRLREAGHEVDTVS--KEAG--------------TTVGKHGYSVTVDATIDEVNPEEYDALV 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498314432   86 VAGGRAPEYLRLNERVIEVVRHFFTEDKPVAAICHGAQLLAAARVLEGRTCSAYPACRPEVELAGGRYADIAVddAVTDG 165
Cdd:TIGR01382  66 IPGGRAPEYLRLNNKAVRLVREFVEKGKPVAAICHGPQLLISAGVLRGKKLTSYPAIIDDVKNAGAEYVDIEV--VVVDG 143

                         170       180
                  ....*....|....*....|...
gi 498314432  166 KLVTAPAWPAHPAWLAQFLAVLG 188
Cdd:TIGR01382 144 NLVTSRVPDDLPAFNREFLKLLG 166

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 498314432    4 KRLLLLCGDFAEDYETMVPFQALQAVGHRVDAVCPDKRagesiataihdfegdqTYSEKPGHRFTLNADFAAVDPADYDG 83
Cdd:pfam01965   1 KKVLVLLADGFEDIELIYPADVLRRAGIKVTVVSVDGG----------------EVKGSRGVKVTVDASLDDVKPDDYDA 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498314432   84 LVVAGGRA-PEYLRLNERVIEVVRHFFTEDKPVAAICHGAQLLAAARVLEGRTCSAYPACRPEVELAGGRYADiavDDAV 162
Cdd:pfam01965  65 LVLPGGRAgPERLRDNEKLVEFVKDFYEKGKPVAAICHGPQVLAAAGVLKGRKVTSHPAVKDDLINAGATYVD---KPVV 141

                         170       180
                  ....*....|....*....|...
gi 498314432  163 TDGKLVTAPAWPAHPAWLAQFLA 185
Cdd:pfam01965 142 VDGNLVTSRGPGDAPEFALEILE 164

Type 1 glutamine amidotransferase (GATase1)-like domain found in Human DJ-1; Type 1 glutamine amidotransferase (GATase1)-like domain found in Human DJ-1. DJ-1 is involved in multiple physiological processes including cancer, Parkinson's disease and male fertility. It is unclear how DJ-1 functions in these. DJ-1 has been shown to possess chaperone activity. DJ-1 is preferentially expressed in the testis and moderately in other tissues; it is induced together with genes involved in oxidative stress response. The Drosophila homologue (DJ-1A) plays an essential role in oxidative stress response and neuronal maintenance. Inhibition of DJ-1A function through RNAi, results in the cellular accumulation of reactive oxygen species, organismal hypersensitivity to oxidative stress, and dysfunction and degeneration of dopaminergic and photoreceptor neurons. DJ-1 has lacks enzymatic activity and the catalytic triad of typical GATase1 domains, however it does contain the highly conserved cysteine located at the nucelophile elbow region typical of these domains. This cysteine been proposed to be a site of regulation of DJ-1 activity by oxidation. DJ-1 is a dimeric enzyme.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498314432   6 LLLLCGDFAEDYETMVPFQALQAVGHRVDAVCPDKraGESIATAihdfegdqtysekpgHRFTLNAD--FAAVDPADYDG 83
Cdd:cd03135    1 VLVILADGFEEIEAVTPVDVLRRAGIEVTTASLEK--KLAVGSS---------------HGIKVKADktLSDVNLDDYDA 63

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498314432  84 LVVAGGR-APEYLRLNERVIEVVRHFFTEDKPVAAICHGAQLLAAARVLEGRTCSAYPACrpEVELAGGRYADIAVddaV 162
Cdd:cd03135   64 IVIPGGLpGAQNLADNEKLIKLLKEFNAKGKLIAAICAAPAVLAKAGLLKGKKATCYPGF--EDKLGGANYVDEPV---V 138

                 ....*...
gi 498314432 163 TDGKLVTA 170
Cdd:cd03135  139 VDGNIITS 146

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 498314432   6 LLLLCGDFaEDYETMVPFQALQAVGHRVDAVCPDKRAGESiataihdfegdqtysekpghrftlnadfaAVDPADYDGLV 85
Cdd:cd01653    2 AVLLFPGF-EELELASPLDALREAGAEVDVVSPDGGPVES-----------------------------DVDLDDYDGLI 51

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 498314432  86 VAGGRA-PEYLRLNERVIEVVRHFFTEDKPVAAICHGAQLL 125
Cdd:cd01653   52 LPGGPGtPDDLARDEALLALLREAAAAGKPILGICLGAQLL 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 498314432   6 LLLLCGDFaEDYETMVPFQALQAVGHRVDAVCPDKRAGESiataihdfegdqtysekpghrftlnadfaAVDPADYDGLV 85
Cdd:cd03128    2 AVLLFGGS-EELELASPLDALREAGAEVDVVSPDGGPVES-----------------------------DVDLDDYDGLI 51

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 498314432  86 VAGGRA-PEYLRLNERVIEVVRHFFTEDKPVAAICHGAQLL 125
Cdd:cd03128   52 LPGGPGtPDDLAWDEALLALLREAAAAGKPVLGICLGAQLL 92

GMP synthase, glutamine amidotransferase domain [Nucleotide transport and metabolism]; GMP synthase, glutamine amidotransferase domain is part of the Pathway/BioSystem: Purine biosynthesis

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 498314432  76 VDPADYDGLVVAGGR--APEYLRLNERVIEVVRHFFTEDKPVAAICHGAQLLAAA 128
Cdd:COG0518   44 PDLEDPDGLILSGGPmsVYDEDPWLEDEPALIREAFELGKPVLGICYGAQLLAHA 98

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 498314432  67 FTLNADFAAVDPADYDGLVVAGGRAPEYLRLNERVIEVVRHFFTEDKPVAAICHGAQLLAAARVLEGRTCSAYPACRPev 146
Cdd:cd03137   51 LSLVADAGLDALAAADTVIVPGGPDVDGRPPPPALLAALRRAAARGARVASVCTGAFVLAEAGLLDGRRATTHWAYAE-- 128

                         90       100
                 ....*....|....*....|....*..
gi 498314432 147 ELAgGRYADIAVDDA---VTDGKLVTA 170
Cdd:cd03137  129 DLA-RRFPAVRVDPDvlyVDDGNVWTS 154

Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; This group of sequences represents the small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II. CPSase II catalyzes the production of carbomyl phosphate (CP) from bicarbonate, glutamine and two molecules of MgATP. The reaction is believed to proceed by a series of four biochemical reactions involving a minimum of three discrete highly reactive intermediates. The synthesis of CP is critical for the initiation of two separate biosynthetic pathways. In one CP is coupled to aspartate, its carbon and nitrogen nuclei ultimately incorporated into the aromatic moieties of pyrimidine nucleotides. In the second pathway CP is condensed with ornithine at the start of the urea cycle and is utilized for the detoxification of ammonia and biosynthesis of arginine. CPSases may be encoded by one or by several genes, depending on the species. The E.coli enzyme is a heterodimer consisting of two polypeptide chains referred to as the small and large subunit. Ammonia an intermediate during the biosynthesis of carbomyl phosphate produced by the hydrolysis of glutamine in the small subunit of the enzyme is delivered via a molecular tunnel between the remotely located carboxyphosphate active site in the large subunit. CPSase IIs belong to the triad family of amidotransferases having a conserved Cys-His-Glu catalytic triad in the glutaminase active site. This group also contains the sequence from the mammalian urea cycle form which has lost the active site Cys, resulting in an ammonia-dependent form, CPSase I.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 498314432  70 NADFAAVDPADYDGLVVAGGRA-PEYLrlnERVIEVVRHFFTEDKPVAAICHGAQLLAAArvLEGRT 135
Cdd:cd01744   29 NTDAEEILKLDPDGIFLSNGPGdPALL---DEAIKTVRKLLGKKIPIFGICLGHQLLALA--LGAKT 90

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 498314432  68 TLNADFAAVDPADYDGLVVAGGRAPEYlRLNERVIEVVRHFFTEDKPVAAICHGAQLLAAARVLEGRTCSAYPACR---- 143
Cdd:cd03136   52 RVAPDAALEDAPPLDYLFVVGGLGARR-AVTPALLAWLRRAARRGVALGGIDTGAFLLARAGLLDGRRATVHWEHLeafa 130

                         90       100       110
                 ....*....|....*....|....*....|
gi 498314432 144 ---PEVELAGGRYadiavddaVTDGKLVTA 170
Cdd:cd03136  131 eafPRVQVTRDLF--------EIDGDRLTC 152

isoprenoid biosynthesis glyoxalase ElbB;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498314432  72 DFAAVDPADYDGLVVAGG-----------RAPEYLRLNERVIEVVRHFFTEDKPVAAIChGAQLLaAARVLEGR---TCS 137
Cdd:PRK11780  77 DLAEADAEDFDALIVPGGfgaaknlsnfaVKGAECTVNPDVKALVRAFHQAGKPIGFIC-IAPAM-LPKILGAGvklTIG 154

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 498314432 138 AYPACRPEVELAGGRYADIAVDDAVTD--GKLVTAPAW 173
Cdd:PRK11780 155 NDEDTAAAIEKMGGEHVDCPVDDIVVDeeNKVVTTPAY 192

Type 1 glutamine amidotransferase (GATase1)-like domain found in zebrafish ES1; Type 1 glutamine amidotransferase (GATase1)-like domain found in zebrafish ES1. This group includes, proteins similar to ES1, Escherichia coli enhancing lycopene biosynthesis protein 2, Azospirillum brasilense iaaC and, human HES1. The catalytic triad typical of GATase1domains is not conserved in this GATase1-like domain. However, in common with GATase1domains a reactive cys residue is found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow. Zebrafish ES1 is expressed specifically in adult photoreceptor cells and appears to be a cytoplasmic protein. A. brasilense iaaC is involved in controlling IAA biosynthesis.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498314432  72 DFAAVDPADYDGLVVAGG------------RAPEYlRLNERVIEVVRHFFTEDKPVAAICHGAQLlaAARVLeGRTCSAY 139
Cdd:cd03133   74 DLAKLKAADFDALIFPGGfgaaknlsdfavKGADC-TVNPEVERLVREFHQAGKPIGAICIAPAL--AAKIL-GEGVEVT 149

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 498314432 140 PACRPEVELA----GGRYADIAVDDAVTD--GKLVTAPAW 173
Cdd:cd03133  150 IGNDAGTAAAiekmGAEHVNCPVEEIVVDekNKVVTTPAY 189