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 446822652  10 IQALTFDLDDTLYDNRPVIKQVEEKVTEWLlsEHPITATRPLAWWLAMKRDIARRFPEQCHDVSQWrylqVQHGLLELGY 89
Cdd:COG1011    1 IKAVLFDLDGTLLDFDPVIAEALRALAERL--GLLDEAEELAEAYRAIEYALWRRYERGEITFAEL----LRRLLEELGL 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446822652  90 AQPEAEQAAsetleQVMRWRNQVDVPAETHRVLAQLAAK-VPLIAITNGNV-----QIEKIGLSGYFQTVLRAGPDGRAK 163
Cdd:COG1011   75 DLAEELAEA-----FLAALPELVEPYPDALELLEALKARgYRLALLTNGSAelqeaKLRRLGLDDLFDAVVSSEEVGVRK 149

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446822652 164 PYPDLFAQAAQQLQLEPRSILHVGDHLQTDVLGARQNGFQACWFNDQGQSirrlAKASVLPDVEIERLSELLLIV 238
Cdd:COG1011  150 PDPEIFELALERLGVPPEEALFVGDSPETDVAGARAAGMRTVWVNRSGEP----APAEPRPDYVISDLAELLELL 220

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 446822652   10 IQALTFDLDDTLYDNRPVIKQVEEKvtewLLSEHPItATRPLAWwlamkrdiARRFPEQCHDVSQWRYLQVQHGLLELGY 89
Cdd:pfam00702   1 IKAVVFDLDGTLTDGEPVVTEAIAE----LASEHPL-AKAIVAA--------AEDLPIPVEDFTARLLLGKRDWLEELDI 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446822652   90 AQPEAEQAASETLEQVMR-------WRNQVDVPAETHRVLAQL-AAKVPLIAITNGNVQI-----EKIGLSGYFQTVLRA 156
Cdd:pfam00702  68 LRGLVETLEAEGLTVVLVellgviaLADELKLYPGAAEALKALkERGIKVAILTGDNPEAaeallRLLGLDDYFDVVISG 147

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 446822652  157 GPDGRAKPYPDLFAQAAQQLQLEPRSILHVGDHLqTDVLGARQNG 201
Cdd:pfam00702 148 DDVGVGKPKPEIYLAALERLGVKPEEVLMVGDGV-NDIPAAKAAG 191

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 446822652  10 IQALTFDLDDTLYDNRPVIKQVEEKVTEWLlsEHPITATRPLAWWLAMKRDIARRFPEQCHDVSQWrylqVQHGLLELGY 89
Cdd:COG1011    1 IKAVLFDLDGTLLDFDPVIAEALRALAERL--GLLDEAEELAEAYRAIEYALWRRYERGEITFAEL----LRRLLEELGL 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446822652  90 AQPEAEQAAsetleQVMRWRNQVDVPAETHRVLAQLAAK-VPLIAITNGNV-----QIEKIGLSGYFQTVLRAGPDGRAK 163
Cdd:COG1011   75 DLAEELAEA-----FLAALPELVEPYPDALELLEALKARgYRLALLTNGSAelqeaKLRRLGLDDLFDAVVSSEEVGVRK 149

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446822652 164 PYPDLFAQAAQQLQLEPRSILHVGDHLQTDVLGARQNGFQACWFNDQGQSirrlAKASVLPDVEIERLSELLLIV 238
Cdd:COG1011  150 PDPEIFELALERLGVPPEEALFVGDSPETDVAGARAAGMRTVWVNRSGEP----APAEPRPDYVISDLAELLELL 220

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 446822652   10 IQALTFDLDDTLYDNRPVIKQVEEKvtewLLSEHPItATRPLAWwlamkrdiARRFPEQCHDVSQWRYLQVQHGLLELGY 89
Cdd:pfam00702   1 IKAVVFDLDGTLTDGEPVVTEAIAE----LASEHPL-AKAIVAA--------AEDLPIPVEDFTARLLLGKRDWLEELDI 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446822652   90 AQPEAEQAASETLEQVMR-------WRNQVDVPAETHRVLAQL-AAKVPLIAITNGNVQI-----EKIGLSGYFQTVLRA 156
Cdd:pfam00702  68 LRGLVETLEAEGLTVVLVellgviaLADELKLYPGAAEALKALkERGIKVAILTGDNPEAaeallRLLGLDDYFDVVISG 147

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 446822652  157 GPDGRAKPYPDLFAQAAQQLQLEPRSILHVGDHLqTDVLGARQNG 201
Cdd:pfam00702 148 DDVGVGKPKPEIYLAALERLGVKPEEVLMVGDGV-NDIPAAKAAG 191

dUMP phosphatase; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446822652 121 VLAQLAAKVPLIAITNG-----NVQIEKIGLSGYFQTVLRAGPDGRAKPYPDLFAQAAQQLQLEPRS-ILHVGDHLQTDV 194
Cdd:PRK09449 103 LLNALRGKVKMGIITNGftelqQVRLERTGLRDYFDLLVISEQVGVAKPDVAIFDYALEQMGNPDRSrVLMVGDNLHSDI 182

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 446822652 195 LGARQNGFQACWFNDQGQSirrlAKASVLPDVEIERLSELLLIV 238
Cdd:PRK09449 183 LGGINAGIDTCWLNAHGRE----QPEGIAPTYQVSSLSELEQLL 222

2-haloalkanoic acid dehalogenase, type II; Catalyzes the hydrolytic dehalogenation of small L-2-haloalkanoic acids to yield the corresponding D-2-hydroxyalkanoic acids. Belongs to the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases (pfam00702), class (subfamily) I. Note that the Type I HAD enzymes have not yet been fully characterized, but clearly utilize a substantially different catalytic mechanism and are thus unlikely to be related.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446822652   10 IQALTFDLDDTLYDNRPVIKQVEEKVTEwlLSEHPITATRP--LAW-WLamkRDIARRFP--EQCHDVSqWRYLQVQHGL 84
Cdd:TIGR01428   1 IKALVFDVYGTLFDVHSVAERAAELYGG--RGEALSQLWRQkqLEYsWL---RTLMGPYKdfWDLTREA-LRYLLGRLGL 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446822652   85 lelgyaqPEAEQAASETLEQVMRWRNQVDVPAethrVLAQLA-AKVPLIAITNGNVQ-----IEKIGLSGYFQTVLRAGP 158
Cdd:TIGR01428  75 -------EDDESAADRLAEAYLRLPPHPDVPA----GLRALKeRGYRLAILSNGSPAmlkslVKHAGLDDPFDAVLSADA 143

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 446822652  159 DGRAKPYPDLFAQAAQQLQLEPRSILHVGDHLQtDVLGARQNGFQACWFNDQGQ 212
Cdd:TIGR01428 144 VRAYKPAPQVYQLALEALGVPPDEVLFVASNPW-DLGGAKKFGFKTAWINRPGE 196

haloacid dehalogenase superfamily, subfamily IA, variant 1 with third motif having Dx(3-4)D or Dx(3-4)E; 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/E), (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 1 (this model) is found in the enzymes phosphoglycolate phosphatase (TIGR01449) and enolase-phosphatase. These three variant models (see also TIGR01493 and TIGR01509) were created withthe 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 relatedHAD subfamilies caused by an overly broad single model. [Unknown function, Enzymes of unknown specificity]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446822652   12 ALTFDLDDTLYDNRPVIKQVE----EKVTEWLLSEHPITATRPLAwwlamkrdiarrfPEQCHDVSQWRYLQVQhGLLEL 87
Cdd:TIGR01549   1 AILFDIDGTLVDIKFAIRRAFpqtfEEFGLDPASFKALKQAGGLA-------------EEEWYRIATSALEELQ-GRFWS 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446822652   88 GYaqpEAEQAASETLEQVM-RWRnqvdvpaethrvlaqlAAKVPLIAITNGNVQIEKI-----GLSGYFQTVLRAGpDGR 161
Cdd:TIGR01549  67 EY---DAEEAYIRGAADLLaRLK----------------SAGIKLGIISNGSLRAQKLllrlfGLGDYFELILVSD-EPG 126

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 446822652  162 AKPYPDLFAQAAQQLQLEPRsILHVGDHLqTDVLGAR 198
Cdd:TIGR01549 127 SKPEPEIFLAALESLGVPPE-VLHVGDNL-NDIEGAR 161

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 446822652   12 ALTFDLDDTLYDnrpvikqveekvtewllSEHPITATRplawWLAMKRDIARRFPEQCHDVSQW--RYLQVQHGLLElgy 89
Cdd:TIGR01509   1 AILFDLDGVLVD-----------------TEFAIAKLI----NREELGLVPDELGVSAVGRLELalRRFKAQYGRTI--- 56

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446822652   90 AQPEAEQAASETLEQVMRWRNQVDVPAETHRVLAQL-AAKVPLIAITNGN----VQIEKIGLSGYFQTVLRAGPDGRAKP 164
Cdd:TIGR01509  57 SPEDAQLLYKQLFYEQIEEEAKLKPLPGVRALLEALrARGKKLALLTNSPrahkLVLALLGLRDLFDVVIDSSDVGLGKP 136

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 446822652  165 YPDLFAQAAQQLQLEPRSILHVGDhLQTDVLGARQNGFQACW 206
Cdd:TIGR01509 137 DPDIYLQALKALGLEPSECVFVDD-SPAGIEAAKAAGMHTVG 177

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

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446822652 163 KPYPDLFAQAAQQLQLEPRSILHVGDHLQTDVLGARQNGFQACW-----FNDqgqsiRRLAKASVLPDVEIERLSELLL 236
Cdd:COG0647  186 KPSPPIYELALERLGVDPERVLMVGDRLDTDILGANAAGLDTLLvltgvTTA-----EDLEAAPIRPDYVLDSLAELLL 259

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 446822652 118 THRVLAQLAAK-VPLIAITNGNVQ-----IEKIGLSGYFQTVLRAGPDGRAKPYPDLFAQAAQQLQLEPRSILHVGDHlQ 191
Cdd:cd01427   12 AVELLKRLRAAgIKLAIVTNRSREalralLEKLGLGDLFDGIIGSDGGGTPKPKPKPLLLLLLKLGVDPEEVLFVGDS-E 90

                         90
                 ....*....|....*.
gi 446822652 192 TDVLGARQNGFQACWF 207
Cdd:cd01427   91 NDIEAARAAGGRTVAV 106

HAD-hyrolase-like;

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446822652  163 KPYPDLFAQAAQQLQLEPRSILHVGDHLQTDVLGARQNGFQACWFNDQGQSIRRLAKASVLPDVEIERLSEL 234
Cdd:pfam13242   4 KPNPGMLERALARLGLDPERTVMIGDRLDTDILGAREAGARTILVLTGVTRPADLEKAPIRPDYVVDDLAEA 75

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 446822652 122 LAQLAAK-VPLIAITNGNVQ-----IEKIGLSGYFQTVLraGPDGRA--KPYPDLFAQAAQQLQLEPRSILHVGDHlQTD 193
Cdd:cd16417   96 LAALKAQgYPLACVTNKPERfvaplLEALGISDYFSLVL--GGDSLPekKPDPAPLLHACEKLGIAPAQMLMVGDS-RND 172

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 446822652 194 VLGARQNGFQACW----FNDqGQSIRRLAkasvlPDVEIERLSELL 235
Cdd:cd16417  173 ILAARAAGCPSVGltygYNY-GEDIAASG-----PDAVIDSLAELL 212

N-terminal lipase phosphatase domain of human soluble epoxide hydrolase, Escherichia coli YihX/HAD4 alpha-D-glucose 1-phosphate phosphatase, and related domains, may be inactive; This family includes the N-terminal phosphatase domain of human soluble epoxide hydrolase (sEH). sEH is a bifunctional enzyme with two distinct enzyme activities, the C-terminal domain has epoxide hydrolysis activity and the N-terminal domain (Ntermphos), which belongs to this family, has lipid phosphatase activity. The latter prefers mono-phosphate esters, and lysophosphatidic acids (LPAs) are the best natural substrates found to date. In addition this family includes Gallus gallus sEH and Xenopus sEH which appears to lack phosphatase activity, and Escherichia coli YihX/HAD4 which selectively hydrolyzes alpha-Glucose-1-P, phosphatase, has significant phosphatase activity against pyridoxal phosphate, and has low beta phosphoglucomutase activity. 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 446822652  10 IQALTFDLDDTLYDNRP--VIKQVEEKVTEwlLSEHPITATRPLAWWLAMKRDI--ARRFPEQCHDvsqwrylqvqhgll 85
Cdd:cd02603    1 IRAVLFDFGGVLIDPDPaaAVARFEALTGE--PSEFVLDTEGLAGAFLELERGRitEEEFWEELRE-------------- 64

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446822652  86 ELGYaqpeaeQAASETLEQVmrWRNQVDVPAETHRVLAQL-AAKVPLIAITNGNVQIEKIGLS------GYFQTVLRAGP 158
Cdd:cd02603   65 ELGR------PLSAELFEEL--VLAAVDPNPEMLDLLEALrAKGYKVYLLSNTWPDHFKFQLEllprrgDLFDGVVESCR 136

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446822652 159 DGRAKPYPDLFAQAAQQLQLEPRSILHVgDHLQTDVLGARQNGFQACWFNDQGQSIRRLA 218
Cdd:cd02603  137 LGVRKPDPEIYQLALERLGVKPEEVLFI-DDREENVEAARALGIHAILVTDAEDALRELA 195

Predicted sugar hydrolase, contains GT1 and HAD domains [General function prediction only];

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 446822652 168 LFAQAAQQLQLEPRSILHVGDHLQTDVLGARQNGFQACWFNDQGQSIRRLAKASVLPD 225
Cdd:COG5610  178 LFDYVLEEEGVDPKQILHIGDNPRSDVQRPRKLGIQALHYPRASLSRIESLEREGLSL 235

Haloacid Dehalogenase Superfamily Class (subfamily) IIA; This model represents one structural subclass of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. The superfamily is defined by the presence of three short catalytic motifs. The classes 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. Class I consists of sequences in which the capping domain is found in between the first and second catalytic motifs. Class II consists of sequences in which the capping domain is found between the second and third motifs. Class III sequences have no capping domain in iether of these positions. The Class IIA capping domain is predicted by PSI-PRED to consist of a mixed alpha-beta fold with the basic pattern: Helix-Helix-Helix-Sheet-Helix-Loop-Sheet-Helix-Sheet-Helix. Presently, this subfamily encompasses a single equivalog model (TIGR01452) for the eukaryotic phosphoglycolate phosphatase, as well as four hypothetical equivalogs covering closely related sequences (TIGR01456 and TIGR01458 in eukaryotes, TIGR01457 in gram positive bacteria and TIGR01459 in gram negative bacteria). The Escherishia coli NagD gene and the Bacillus subtilus AraL gene are members of this subfamily but are not members of the any of the presently defined equivalogs within it. NagD is part of the NAG operon responsible for N-acetylglucosamine metabolism. The function of this gene is unknown. Genes from several organisms have been annotated as NagD, or NagD-like. However, without data on the presence of other members of this pathway, (such as in the case of Yersinia pestis) these assignments should not be given great weight. The AraL gene is similar: it is part of the L-arabinose operon, but the function is unknown. A gene from Halobacterium has been annotated as AraL, but no other Ara operon genes have been annotated. Many of the genes in this subfamily have been annotated as "pNPPase" "4-nitrophenyl phosphatase" or "NPPase". These all refer to the same activity versus a common lab test compound used to determine phosphatase activity. There is no evidence that this activity is physiologically relevant. [Unknown function, Enzymes of unknown specificity]

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 446822652  163 KPYPDLFAQAAQQLQLEP-RSILHVGDHLQTDVLGARQNGFQACW 206
Cdd:TIGR01460 188 KPSPAIYRAALNLLQARPeRRDVMVGDNLRTDILGAKNAGFDTLL 232

N-acetylmuramic acid 6-phosphate phosphatase MupP;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446822652 122 LAQLAAK-VPLIAITNGNVQ-----IEKIGLSGYFQTVLraGPD--GRAKPYPDLFAQAAQQLQLEPRSILHVGDHLqTD 193
Cdd:PRK13222 102 LAALKAAgYPLAVVTNKPTPfvaplLEALGIADYFSVVI--GGDslPNKKPDPAPLLLACEKLGLDPEEMLFVGDSR-ND 178

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 446822652 194 VLGARQNGFQACWF----NDqGQSIRRLAkasvlPDVEIERLSELLLIV 238
Cdd:PRK13222 179 IQAARAAGCPSVGVtygyNY-GEPIALSE-----PDVVIDHFAELLPLL 221

HAD superfamily (subfamily IIIA) phosphatase, TIGR01668; This family of hypothetical proteins is a member of the IIIA subfamily of the haloacid dehalogenase (HAD) superfamily of hydrolases. All characterized members of this subfamily (TIGR01662) and most characterized members of the HAD superfamily are phosphatases. HAD superfamily phosphatases contain active site residues in several conserved catalytic motifs, all of which are found conserved here. This family consists of sequences from fungi, plants, cyanobacteria, gram-positive bacteria and Deinococcus. There is presently no characterization of any sequence in this family.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 446822652  160 GRAKPYPDLFAQAAQQLQLEPRSILHVGDHLQTDVLGARQNGFQACW 206
Cdd:TIGR01668  88 HAVKPPGCAFRRAHPEMGLTSEQVAVVGDRLFTDVMGGNRNGSYTIL 134

haloacid dehalogenase-like superfamily phosphatases, UmpH/NagD family; Phosphatases in this UmpH/NagD family include Escherichia coli UmpH UMP phosphatase/NagD nucleotide phosphatase , Mycobacterium tuberculosis Rv1692 glycerol 3-phosphate phosphatase, human PGP phosphoglycolate phosphatase, Schizosaccharomyces pombe PHO2 p-nitrophenylphosphatase, Bacillus AraL a putative sugar phosphatase, and Plasmodium falciparum para nitrophenyl phosphate phosphatase PNPase. 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
                 ....*....|....*....|....*....|....*....|.
gi 446822652 163 KPYPDLFAQAAQQLQLEPRSILHVGDHLQTDVLGARQNGFQ 203
Cdd:cd07508  197 KPSPWLGELALEKFGIDPERVLFVGDRLATDVLFGKACGFQ 237

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
                 ....*....|....*....|....*....|....*....
gi 446822652 163 KPYPDLFAQAAQQLQLEPRSILHVGDHLQTDVLGARQNG 201
Cdd:cd07530  177 KPEPIMMRAALEKLGLKSEETLMVGDRLDTDIAAGIAAG 215

uncharacterized family of the haloacid dehalogenase-like (HAD) hydrolase superfamily, similar to Parvibaculum lavamentivorans HAD-superfamily hydrolase, subfamily IA, variant 1; 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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446822652 122 LAQLAAKVPLIAITNG------NVQIEKIGLSGYFQTVlRAGPDGRAKPYPDLFAQAAQQLQLEPRSILHVGD 188
Cdd:cd07533   93 LDALAAQGVLLAVATGksrrglDRVLEQHGLGGYFDAT-RTADDTPSKPHPEMLREILAELGVDPSRAVMVGD 164

subfamily of beta-phosphoglucomutase-like family, similar to Escherichia coli 6-phosphogluconate phosphatase YieH; This subfamily includes Escherichia coli YieH/HAD3 an 6-phosphogluconate phosphatase, which can hydrolyzed purines and pyrimidines as secondary substrates. It belongs to the beta-phosphoglucomutase-like family whose other 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. 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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446822652 121 VLAQLAakVPLIAITNG-----NVQIEKIGLSGYFQTVLRAGPD-GRAKPYPDLFAQAAQQLQLEPRSILHVGD 188
Cdd:cd07526   50 ALSALT--LPFCVASNSsrerlTHSLGLAGLLAYFEGRIFSASDvGRGKPAPDLFLHAAAQMGVAPERCLVIED 121

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 446822652 145 GLSGYFQTVlrAGPD--GRAKPYPDLFAQAAQQLQLEPRSILHVGDHLQtDVLGARQNGFQAC---WfndqgqSIRRLAK 219
Cdd:cd02616  118 GLDKYFDVI--VGGDdvTHHKPDPEPVLKALELLGAEPEEALMVGDSPH-DILAGKNAGVKTVgvtW------GYKGREY 188

                         90
                 ....*....|....*....
gi 446822652 220 -ASVLPDVEIERLSELLLI 237
Cdd:cd02616  189 lKAFNPDFIIDKMSDLLTI 207

UmpH/NagD family phosphatase para nitrophenyl phosphate phosphatase, similar to Plasmodium falciparum PNPase; Plasmodium falciparum para nitrophenyl phosphate phosphatase (PNPase) catalyzes the dephosphorylation of thiamine monophosphate to thiamine, other substrates on which its active are nucleotides, phosphorylated sugars, pyridoxal-5-phosphate, and paranitrophenyl phosphate. 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        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446822652 163 KPYPDLFAQAAQQLQLEPRSILHVGDHLQTDVLGARQNGFQACWF---NDQGQSIRRL------AKASVLPDVEIERLSE 233
Cdd:cd07532  206 KPNPQILNFLMKSGVIKPERTLMIGDRLKTDILFANNCGFQSLLVgtgVNSLEDAEKIkkegdpKKKDLVPDTYLPSLGH 285

                 .
gi 446822652 234 L 234
Cdd:cd07532  286 L 286