Vancomycin resistance protein YoaR (function unknown), contains peptidoglycan-binding and VanW domains [Defense mechanisms];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613254598 229 ANKLLSYKLPNLVYQHESDMiktgrgidPGLQENKAFNLELSSSKMNQLEIKPGESFSFWHLVGKADKKHGYKDGRVIIN 308
Cdd:COG2720  216 TEDLEALGIKEVIGEFTTPF--------DGSQANRTTNIRLAAEKLNGTLVKPGETFSFNKTVGPRTAANGYKEAPVIVN 287

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613254598 309 DKVKSGTGGGLCNLANTINLLIIHSPLTITEVHYHSdalAPDSGVrkPLSNGTSVAYNYVDYRFNNTTDQTFQLCVWCED 388
Cdd:COG2720  288 GKLVPGVGGGVCQVSTTLYNAALFAGLEIVERHPHS---YPVSYY--PAGRDATVAYGYIDLKFKNDTDYPVLIQAYVTG 362

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 613254598 389 KQLKAELRSERDiPYQYRIVEEDHHF------------------VQEHGIYYRKSRIYKVTEEKGtsKEIKRKL 444
Cdd:COG2720  363 GSLTVEIYGTKP-YDTVEIETEVTNVtppktvykedslppgeecVPQEGAPGFTVTVYRVVYDNG--KVVKREI 433

Vancomycin resistance protein YoaR (function unknown), contains peptidoglycan-binding and VanW domains [Defense mechanisms];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613254598 229 ANKLLSYKLPNLVYQHESDMiktgrgidPGLQENKAFNLELSSSKMNQLEIKPGESFSFWHLVGKADKKHGYKDGRVIIN 308
Cdd:COG2720  216 TEDLEALGIKEVIGEFTTPF--------DGSQANRTTNIRLAAEKLNGTLVKPGETFSFNKTVGPRTAANGYKEAPVIVN 287

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613254598 309 DKVKSGTGGGLCNLANTINLLIIHSPLTITEVHYHSdalAPDSGVrkPLSNGTSVAYNYVDYRFNNTTDQTFQLCVWCED 388
Cdd:COG2720  288 GKLVPGVGGGVCQVSTTLYNAALFAGLEIVERHPHS---YPVSYY--PAGRDATVAYGYIDLKFKNDTDYPVLIQAYVTG 362

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 613254598 389 KQLKAELRSERDiPYQYRIVEEDHHF------------------VQEHGIYYRKSRIYKVTEEKGtsKEIKRKL 444
Cdd:COG2720  363 GSLTVEIYGTKP-YDTVEIETEVTNVtppktvykedslppgeecVPQEGAPGFTVTVYRVVYDNG--KVVKREI 433

Uncharacterized family of the the haloacid dehalogenase-like superfamily, similar to the uncharacterized protein Bacillus subtilis YqeG; The haloacid dehalogenase-like (HAD) hydrolases are a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members include 2-L-haloalkanoic acid dehalogenase (C-Cl bond hydrolysis), azetidine hydrolase (C-N bond hydrolysis); phosphonoacetaldehyde hydrolase (C-P bond hydrolysis), phosphoserine phosphatase and phosphomannomutase (CO-P bond hydrolysis), P-type ATPases (PO-P bond hydrolysis) and many others. Members are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613254598  40 GLIFDIDSTLVPHGS-EVTDEVNELFKQLHDIGFKTVFLSNNSVERILEFNKEIKTDFIGMANKPHPKNFFRALDKLGVE 118
Cdd:cd16416    1 GVITDLDNTLLAWDNpDLTPEVKAWLADLKEAGIKVVLVSNNNERRVAKVIEKLDLPFVARAGKPRPRAFRRALKEMDLP 80

                         90       100
                 ....*....|....*....|....*...
gi 613254598 119 KSKVLLIGDQIFTDILGANKCNIDNVLV 146
Cdd:cd16416   81 PEQVAMVGDQLFTDILGGNRAGLYTILV 108

haloacid dehalogenase-like hydrolase; This family is structurally different from the alpha/beta hydrolase family (pfam00561). This family includes L-2-haloacid dehalogenase, epoxide hydrolases and phosphatases. The structure of the family consists of two domains. One is an inserted four helix bundle, which is the least well conserved region of the alignment, between residues 16 and 96 of Swiss:P24069. The rest of the fold is composed of the core alpha/beta domain. Those members with the characteriztic DxD triad at the N-terminus are probably phosphatidylglycerolphosphate (PGP) phosphatases involved in cardiolipin biosynthesis in the mitochondria.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613254598   10 KDMIKRLLPNLYIKSVYDIDFKEVYRLGYEGLIFDIDStlvphgSEVTDEVNELFKQLHDIGFKTVFLSNNS---VERIL 86
Cdd:pfam00702  59 RDWLEELDILRGLVETLEAEGLTVVLVELLGVIALADE------LKLYPGAAEALKALKERGIKVAILTGDNpeaAEALL 132

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 613254598   87 E-------FNKEIKTDFIGMAnKPHPKNFFRALDKLGVEKSKVLLIGDQIfTDILGANKCN 140
Cdd:pfam00702 133 RllglddyFDVVISGDDVGVG-KPKPEIYLAALERLGVKPEEVLMVGDGV-NDIPAAKAAG 191

Vancomycin resistance protein YoaR (function unknown), contains peptidoglycan-binding and VanW domains [Defense mechanisms];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613254598 229 ANKLLSYKLPNLVYQHESDMiktgrgidPGLQENKAFNLELSSSKMNQLEIKPGESFSFWHLVGKADKKHGYKDGRVIIN 308
Cdd:COG2720  216 TEDLEALGIKEVIGEFTTPF--------DGSQANRTTNIRLAAEKLNGTLVKPGETFSFNKTVGPRTAANGYKEAPVIVN 287

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613254598 309 DKVKSGTGGGLCNLANTINLLIIHSPLTITEVHYHSdalAPDSGVrkPLSNGTSVAYNYVDYRFNNTTDQTFQLCVWCED 388
Cdd:COG2720  288 GKLVPGVGGGVCQVSTTLYNAALFAGLEIVERHPHS---YPVSYY--PAGRDATVAYGYIDLKFKNDTDYPVLIQAYVTG 362

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 613254598 389 KQLKAELRSERDiPYQYRIVEEDHHF------------------VQEHGIYYRKSRIYKVTEEKGtsKEIKRKL 444
Cdd:COG2720  363 GSLTVEIYGTKP-YDTVEIETEVTNVtppktvykedslppgeecVPQEGAPGFTVTVYRVVYDNG--KVVKREI 433

Uncharacterized family of the the haloacid dehalogenase-like superfamily, similar to the uncharacterized protein Bacillus subtilis YqeG; The haloacid dehalogenase-like (HAD) hydrolases are a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members include 2-L-haloalkanoic acid dehalogenase (C-Cl bond hydrolysis), azetidine hydrolase (C-N bond hydrolysis); phosphonoacetaldehyde hydrolase (C-P bond hydrolysis), phosphoserine phosphatase and phosphomannomutase (CO-P bond hydrolysis), P-type ATPases (PO-P bond hydrolysis) and many others. Members are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613254598  40 GLIFDIDSTLVPHGS-EVTDEVNELFKQLHDIGFKTVFLSNNSVERILEFNKEIKTDFIGMANKPHPKNFFRALDKLGVE 118
Cdd:cd16416    1 GVITDLDNTLLAWDNpDLTPEVKAWLADLKEAGIKVVLVSNNNERRVAKVIEKLDLPFVARAGKPRPRAFRRALKEMDLP 80

                         90       100
                 ....*....|....*....|....*...
gi 613254598 119 KSKVLLIGDQIFTDILGANKCNIDNVLV 146
Cdd:cd16416   81 PEQVAMVGDQLFTDILGGNRAGLYTILV 108

FMN and 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YigB, HAD superfamily (riboflavin biosynthesis) [Coenzyme transport and metabolism];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613254598  28 IDFKEVYRLGYEGLIFDIDSTLV-------PHGSEVTDEVNELFKQLHDIGFKTVFLSNNS---VERILE-------FNK 90
Cdd:COG1011   59 ITFAELLRRLLEELGLDLAEELAeaflaalPELVEPYPDALELLEALKARGYRLALLTNGSaelQEAKLRrlglddlFDA 138

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 613254598  91 EIKTDFIGMAnKPHPKNFFRALDKLGVEKSKVLLIGDQIFTDILGANKCNIDNVLVK 147
Cdd:COG1011  139 VVSSEEVGVR-KPDPEIFELALERLGVPPEEALFVGDSPETDVAGARAAGMRTVWVN 194

Haloacid dehalogenase-like hydrolases; The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others. This superfamily includes a variety of enzymes that catalyze the cleavage of substrate C-Cl, P-C, and P-OP bonds via nucleophilic substitution pathways. All of which use a nucleophilic aspartate in their phosphoryl transfer reaction. They catalyze nucleophilic substitution reactions at phosphorus or carbon centers, using a conserved Asp carboxylate in covalent catalysis. All members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. Members of this superfamily are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613254598  40 GLIFDIDSTLVphgsevtdeVNELFKQLHDIGFKTVFLSNNS---VERILE-FNKEIKTDFI-----GMANKPHPKNFFR 110
Cdd:cd01427    1 AVLFDLDGTLL---------AVELLKRLRAAGIKLAIVTNRSreaLRALLEkLGLGDLFDGIigsdgGGTPKPKPKPLLL 71

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 613254598 111 ALDKLGVEKSKVLLIGDQIfTDILGANKCNIDNVLV 146
Cdd:cd01427   72 LLLKLGVDPEEVLFVGDSE-NDIEAARAAGGRTVAV 106

Ribonucleotide monophosphatase NagD, HAD superfamily [Nucleotide transport and metabolism];

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 613254598  96 FIGmanKPHPkNFFR-ALDKLGVEKSKVLLIGDQIFTDILGANKCNIDNVLV 146
Cdd:COG0647  183 VVG---KPSP-PIYElALERLGVDPERVLMVGDRLDTDILGANAAGLDTLLV 230

HAD-hyrolase-like;

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 613254598  102 KPHPKNFFRALDKLGVEKSKVLLIGDQIFTDILGANKCNIDNVLVK 147
Cdd:pfam13242   4 KPNPGMLERALARLGLDPERTVMIGDRLDTDILGAREAGARTILVL 49

HAD-superfamily hydrolase, subfamily IIIA; This subfamily falls within the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. The Class III subfamilies are characterized by the lack of any domains located between either between the first and second conserved catalytic motifs (as in the Class I subfamilies, TIGR01493, TIGR01509, TIGR01488 and TIGR01494) or between the second and third conserved catalytic motifs (as in the Class II subfamilies, TIGR01460 and TIGR01484) of the superfamily domain. The IIIA subfamily contains five major clades: histidinol-phosphatase (TIGR01261) and histidinol-phosphatase-related protein (TIGR00213) which together form a subfamily (TIGR01656), DNA 3'-phosphatase (TIGR01663, TIGR01664), YqeG (TIGR01668) and YrbI (TIGR01670). In the case of histidinol phosphatase and PNK-3'-phosphatase, this model represents a domain of a bifunctional system. In the histidinol phosphatase HisB, a C-terminal domain is an imidazoleglycerol-phosphate dehydratase which catalyzes a related step in histidine biosynthesis. In PNK-3'-phosphatase, N- and C-terminal domains constitute the polynucleotide kinase and DNA-binding components of the enzyme. [Unknown function, Enzymes of unknown specificity]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613254598   40 GLIFDIDSTLV-------PHG-SEVTDEVNELFKQLHDIGFKTVFLSNNSV-----------ERILEFNKEIKTDF---- 96
Cdd:TIGR01662   2 AVVLDLDGTLTddvpyvsDEDeRILYPEVPDALAELKEAGYKVVIVTNQSGigrgyfsrsfsGRVARRLEELGVPIdily 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 613254598   97 -IGMANKPHPKNFFRALDKL-GVEKSKVLLIGDQIFTDILGANKC 139
Cdd:TIGR01662  82 aCPGCRKPKPGMFLEALKRFnEIDPEESVYVGDQDLTDLQAAKRV 126

UmpH/NagD family phosphatase, similar to Escherichia coli UmpH UMP phosphatase/NagD nucleotide phosphatase and Mycobacterium tuberculosis Rv1692 glycerol 3-phosphate phosphatase; Escherichia coli UmpH/NagD is a ribonucleoside tri-, di-, and monophosphatase with a preference for purines, it shows peak activity with UMP and functions in UMP-degradation. It is also an effective phosphatase with AMP, GMP and CMP. Mycobacterium tuberculosis phosphatase, Rv1692 is a glycerol 3-phosphate phosphatase. Rv1692 is the final enzyme involved in glycerophospholipid recycling/catabolism. This subfamily belongs to the UmpH/NagD phosphatase family, and to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 613254598  79 NNSVERILEFNKEIKTDFIGmanKPHPKNFFRALDKLGVEKSKVLLIGDQIFTDILGANKCNIDNVLV 146
Cdd:cd07530  157 NGSVVAALEAATGVKPLFIG---KPEPIMMRAALEKLGLKSEETLMVGDRLDTDIAAGIAAGIDTLLV 221

pyrophosphatase similar to Bacillus subtilis PpaX; This family includes Bacillus subtilis PpaX which hydrolyzes pyrophosphate formed during serine-46-phosphorylated HPr (P-Ser-HPr) dephosphorylation by the bifunctional enzyme HPr kinase/phosphorylase. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613254598  54 SEVTDEVNELFKQLHDIGFKTVFLSNNSVERILEFNKEIKTD-----FIGM----ANKPHPKNFFRALDKLGVEKSKVLL 124
Cdd:cd02616   79 TKEYPGVYETLARLKSQGIKLGVVTTKLRETALKGLKLLGLDkyfdvIVGGddvtHHKPDPEPVLKALELLGAEPEEALM 158

                         90       100       110
                 ....*....|....*....|....*....|.
gi 613254598 125 IGDQIFtDILGANKCNIDNVLVKYLLHEGEM 155
Cdd:cd02616  159 VGDSPH-DILAGKNAGVKTVGVTWGYKGREY 188

uncharacterized family of the haloacid dehalogenase-like superfamily, similar to uncharacterized Drosophila melanogaster rhythmically expressed gene 2 protein and human haloacid dehalogenase-like hydrolase domain-containing protein 3; The haloacid dehalogenase-like (HAD) hydrolases are a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members include 2-L-haloalkanoic acid dehalogenase (C-Cl bond hydrolysis), azetidine hydrolase (C-N bond hydrolysis); phosphonoacetaldehyde hydrolase (C-P bond hydrolysis), phosphoserine phosphatase and phosphomannomutase (CO-P bond hydrolysis), P-type ATPases (PO-P bond hydrolysis) and many others. Members are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613254598  41 LIFDIDSTLVphgsevtdeVNELFKQLHDIGFKTVFLSN--NSVERILE-FNKEIKTDFI------GMAnKPHPKNFFRA 111
Cdd:cd16415    2 ITFDVTGTLL---------AVETLKDLKEKGLKLAVVSNfdRRLRELLEaLGLDDYFDFVvfsyevGYE-KPDPRIFQKA 71

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 613254598 112 LDKLGVEKSKVLLIGDQIFTDILGANKCNIDNVLV 146
Cdd:cd16415   72 LERLGVSPEEALHVGDDLKNDYLGARAVGWHALLV 106

haloacid dehalogenase (HAD)-like 5'-nucleotidases similar to the Pseudomonas aeruginosa PA0065; 5'-nucleotidases dephosphorylate nucleoside 5'-monophosphates to nucleosides and inorganic phosphate. Purified Pseudomonas aeruginosa PA0065 displayed high activity toward 5'-UMP and 5'-IMP, significant activity against 5'-XMP and 5'-TMP, and low activity against 5'-CMP. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613254598  53 GSEVTDEVNELFKQLHDIGFK--------TVFLsnnsvERILEfNKEIKTDFIGMA------NKPHPKNFFR-ALDKLGV 117
Cdd:cd04302   79 ENEVYPGIPELLEKLKAAGYRlyvatskpEVFA-----RRILE-HFGLDEYFDGIAgasldgSRVHKADVIRyALDTLGI 152

                         90       100       110
                 ....*....|....*....|....*....|.
gi 613254598 118 EKSKVLLIGDQIFtDILGANKCNIDNVLVKY 148
Cdd:cd04302  153 APEQAVMIGDRKH-DIIGARANGIDSIGVLY 182

HAD-superfamily class IIA hydrolase, TIGR01459; This hypothetical equivalog is a member of the Class IIA subfamily of the haloacid dehalogenase superfamily of aspartate-nucleophile hydrolases. The sequences modelled by this equivalog are all gram negative and primarily alpha proteobacteria. Only one sequence hase been annotated as other than "hypothetical." That one, from Brucella, is annotated as related to NagD, but only by sequence similarity and should be treated with some skepticism. (See comments for Class IIA subfamily model)

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 613254598  102 KPHPKNFFRALDKLG-VEKSKVLLIGDQIFTDILGANKCNIDNVLV 146
Cdd:TIGR01459 195 KPYPAIFHKALKECSnIPKNRMLMVGDSFYTDILGANRLGIDTALV 240

beta-phosphoglucomutase-like family of the haloacid dehalogenase-like (HAD) hydrolase superfamily; This family represents the beta-phosphoglucomutase-like family of the haloacid dehalogenase-like (HAD) hydrolase superfamily. Family members include Lactococcus lactis beta-PGM, a mutase which catalyzes the interconversion of beta-D-glucose 1-phosphate (G1P) and D-glucose 6-phosphate (G6P), Saccharomyces cerevisiae phosphatases GPP1 and GPP2 that dephosphorylate DL-glycerol-3-phosphate and DOG1 and DOG2 that dephosphorylate 2-deoxyglucose-6-phosphate, and Escherichia coli 6-phosphogluconate phosphatase YieH. It belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613254598  40 GLIFDIDSTLV-------------------------PHGSEVTDEVNELFKQLHDIGFKTVFLSNNS---VERILEFNKE 91
Cdd:cd07505    1 AVIFDMDGVLIdteplhrqawqllerknallleliaSEGLKLKPGVVELLDALKAAGIPVAVATSSSrrnVELLLLELGL 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 613254598  92 IKTDFIGM-------ANKPHPKNFFRALDKLGVEKSKVLLIGD 127
Cdd:cd07505   81 LRGYFDVIvsgddveRGKPAPDIYLLAAERLGVDPERCLVFED 123

HAD-superfamily hydrolase, subfamily IIB; This subfamily falls within the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. The Class II subfamilies are characterized by a domain that is located between the second and third conserved catalytic motifs of the superfamily domain. The IIB subfamily is distinguished from the IIA subfamily (TIGR01460) by homology and the predicted secondary structure of this domain by PSI-PRED. The IIB subfamily's Class II domain has the following predicted structure: Helix-Sheet-Sheet-(Helix or Sheet)-Helix-Sheet-(variable)-Helix-Sheet-Sheet. The IIB subfamily consists of Trehalose-6-phosphatase (TIGR00685), plant and cyanobacterial Sucrose-phosphatase and a closely related group of bacterial and archaeal sequences, eukaryotic phosphomannomutase (pfam03332), a large subfamily ("Cof-like hydrolases", TIGR00099) containing many closely related bacterial sequences, a hypothetical equivalog containing the E. coli YedP protein, as well as two small clusters containing OMNI|TC0379 and OMNI|SA2196 whose relationship to the other groups is unclear. [Unknown function, Enzymes of unknown specificity]

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 613254598   41 LIFDIDSTLVPHGS-EVTDEVNELFKQLHDIGFKTVFLSNNSVERILEFNKEIKTDFI 97
Cdd:TIGR01484   2 LFFDLDGTLLDPNAhELSPETIEALERLREAGVKVVIVTGRSLAEIKELLKQLNLPLP 59

pyrophosphatase PpaX; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613254598  52 HGSEVT--DEVNELFKQLHDIGFKTVFLSN---NSVERILE-------FNKEIKTDFIGMAnKPHPKNFFRALDKLGVEK 119
Cdd:PRK13288  77 HDELVTeyETVYETLKTLKKQGYKLGIVTTkmrDTVEMGLKltgldefFDVVITLDDVEHA-KPDPEPVLKALELLGAKP 155

                         90       100
                 ....*....|....*....|....*....
gi 613254598 120 SKVLLIGDQiFTDILGANKCNIDNVLVKY 148
Cdd:PRK13288 156 EEALMVGDN-HHDILAGKNAGTKTAGVAW 183

Escherichia coli Gph phosphoglycolate phosphatase and related proteins; belongs to the haloacid dehalogenase-like superfamily; Phosphoglycolate phosphatase (PGP; EC 3.1.3.18) catalyzes the conversion of 2-phosphoglycolate into glycolate and phosphate. Members of this family belong to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase (C-Cl bond hydrolysis), azetidine hydrolase (C-N bond hydrolysis); phosphonoacetaldehyde hydrolase (C-P bond hydrolysis), phosphoserine phosphatase and phosphomannomutase (CO-P bond hydrolysis), P-type ATPases (PO-P bond hydrolysis) and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613254598  52 HGSEVTDEVNELFKQLHDIGFKTVFLSNNSVErileFNKEIKTDFiGMAN--------------KPHPKNFFRALDKLGV 117
Cdd:cd16417   84 VHSHLYPGVKEGLAALKAQGYPLACVTNKPER----FVAPLLEAL-GISDyfslvlggdslpekKPDPAPLLHACEKLGI 158

                         90       100       110
                 ....*....|....*....|....*....|.
gi 613254598 118 EKSKVLLIGDQIfTDILGANKCNIDNVLVKY 148
Cdd:cd16417  159 APAQMLMVGDSR-NDILAARAAGCPSVGLTY 188

UmpH/NagD family phosphatase, similar to Bacillus AraL phosphatase, a putative sugar phosphatase; Bacillus subtilis AraL is a phosphatase displaying activity towards different sugar phosphate substrates; it is encoded by the arabinose metabolic operon araABDLMNPQ-abfA and may play a role in the dephosphorylation of substrates related to l-arabinose metabolism. This subfamily belongs to the UmpH/NagD phosphatase family, and to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 613254598  39 EGLIFDIDSTlVPHGSEVTDEVNELFKQLHDIGFKTVFLSNNS-------VERILEFNKEIKTDFI 97
Cdd:cd07531    1 KGYIIDLDGT-IGKGVTLIPGAVEGVKTLRRLGKKIIFLSNNStrsrrilLERLRSFGIEVGEDEI 65

haloacid dehalogenase superfamily, subfamily IA, variant 3 with third motif having DD or ED; This model represents part of one structural subfamily of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. The superfamily is defined by the presence of three short catalytic motifs. The subfamilies are defined based on the location and the observed or predicted fold of a so-called "capping domain", or the absence of such a domain. Subfamily I consists of sequences in which the capping domain is found in between the first and second catalytic motifs. Subfamily II consists of sequences in which the capping domain is found between the second and third motifs. Subfamily III sequences have no capping domain in either of these positions. The Subfamily IA and IB capping domains are predicted by PSI-PRED to consist of an alpha helical bundle. Subfamily I encompasses such a wide region of sequence space (the sequences are highly divergent) that representing it with a single model is impossible, resulting in an overly broad description which allows in many unrelated sequences. Subfamily IA and IB are separated based on an aparrent phylogenetic bifurcation. Subfamily IA is still too broad to model, but cannot be further subdivided into large chunks based on phylogenetic trees. Of the three motifs defining the HAD superfamily, the third has three variant forms: (1) hhhhsDxxx(x)D, (2) hhhhssxxx(x)D and (3) hhhhDDxxx(x)s where _s_ refers to a small amino acid and _h_ to a hydrophobic one. All three of these variants are found in subfamily IA. Individual models were made based on seeds exhibiting only one of the variants each. Variant 3 (this model) is found in the enzymes beta-phosphoglucomutase (TIGR01990) and deoxyglucose-6-phosphatase, while many other enzymes of subfamily IA exhibit this variant as well as variant 1 (TIGR01549). These three variant models were created with the knowledge that there will be overlap among them - this is by design and serves the purpose of eliminating the overlap with models of more distantly related HAD subfamilies caused by an overly broad single model. [Unknown function, Enzymes of unknown specificity]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613254598   58 DEVNELFKQLHDIGFKTVFLSNN-----SVERILE----FNKEIKTDFIGMAnKPHPKNFFRALDKLGVEKSKVLLIGDQ 128
Cdd:TIGR01509  83 PGVRALLEALRARGKKLALLTNSprahkLVLALLGlrdlFDVVIDSSDVGLG-KPDPDIYLQALKALGLEPSECVFVDDS 161

                          90
                  ....*....|....*...
gi 613254598  129 IfTDILGANKCNIDNVLV 146
Cdd:TIGR01509 162 P-AGIEAAKAAGMHTVGV 178