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 1080115061   3 YKFLLFDLDHTLLDFDAAEDVALTQLLKEEGVAD-IQAYKDYYVPMNKALWKNLEQKKISKQELvitrFSRLFDHFGLEk 81
Cdd:COG1011     1 IKAVLFDLDGTLLDFDPVIAEALRALAERLGLLDeAEELAEAYRAIEYALWRRYERGEITFAEL----LRRLLEELGLD- 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080115061  82 DGILLAQRYQCYLAQQGQTFSGAHELLDSLIERDYELYAATNGITAIQTGRLAQSGLAPYFNQVFISEQLQTQKPDALFY 161
Cdd:COG1011    76 LAEELAEAFLAALPELVEPYPDALELLEALKARGYRLALLTNGSAELQEAKLRRLGLDDLFDAVVSSEEVGVRKPDPEIF 155

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1080115061 162 EKIgQQITGFDKEKTLMIGDSLTADIQGGNNAGIDTVWYNPYHLENKTQAQPTYEVHSYQDLLDCL 227
Cdd:COG1011   156 ELA-LERLGVPPEEALFVGDSPETDVAGARAAGMRTVWVNRSGEPAPAEPRPDYVISDLAELLELL 220

human N-acetylneuraminate-9-phosphate phosphatase, Escherichia coli house-cleaning phosphatase YjjG, and related phosphatases; N-acetylneuraminate-9- phosphatase (Neu5Ac-9-Pase; E.C. 3.1.3.29) catalyzes the dephosphorylation of N-acylneuraminate 9-phosphate during the synthesis of N-acetylneuraminate; Escherichia coli nucleotide phosphatase YjjG has a broad pyrimidine nucleotide activity spectrum and functions as an in vivo house-cleaning phosphatase for noncanonical pyrimidine nucleotides. 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 1080115061 103 GAHELLDSLIERdYELYAATNGITAIQTGRLAQSGLAPYFNQVFISEQLQTQKPDALFYEKIGQQItGFDKEKTLMIGDS 182
Cdd:cd04305    13 GAKELLEELKKG-YKLGIITNGPTEVQWEKLEQLGIHKYFDHIVISEEVGVQKPNPEIFDYALNQL-GVKPEETLMVGDS 90

                          90
                  ....*....|....*....
gi 1080115061 183 LTADIQGGNNAGIDTVWYN 201
Cdd:cd04305    91 LESDILGAKNAGIKTVWFN 109

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 1080115061   3 YKFLLFDLDHTLLDFDAAEDVALTQLLKEEGVAD-IQAYKDYYVPMNKALWKNLEQKKISKQELvitrFSRLFDHFGLEk 81
Cdd:COG1011     1 IKAVLFDLDGTLLDFDPVIAEALRALAERLGLLDeAEELAEAYRAIEYALWRRYERGEITFAEL----LRRLLEELGLD- 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080115061  82 DGILLAQRYQCYLAQQGQTFSGAHELLDSLIERDYELYAATNGITAIQTGRLAQSGLAPYFNQVFISEQLQTQKPDALFY 161
Cdd:COG1011    76 LAEELAEAFLAALPELVEPYPDALELLEALKARGYRLALLTNGSAELQEAKLRRLGLDDLFDAVVSSEEVGVRKPDPEIF 155

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1080115061 162 EKIgQQITGFDKEKTLMIGDSLTADIQGGNNAGIDTVWYNPYHLENKTQAQPTYEVHSYQDLLDCL 227
Cdd:COG1011   156 ELA-LERLGVPPEEALFVGDSPETDVAGARAAGMRTVWVNRSGEPAPAEPRPDYVISDLAELLELL 220

human N-acetylneuraminate-9-phosphate phosphatase, Escherichia coli house-cleaning phosphatase YjjG, and related phosphatases; N-acetylneuraminate-9- phosphatase (Neu5Ac-9-Pase; E.C. 3.1.3.29) catalyzes the dephosphorylation of N-acylneuraminate 9-phosphate during the synthesis of N-acetylneuraminate; Escherichia coli nucleotide phosphatase YjjG has a broad pyrimidine nucleotide activity spectrum and functions as an in vivo house-cleaning phosphatase for noncanonical pyrimidine nucleotides. 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 1080115061 103 GAHELLDSLIERdYELYAATNGITAIQTGRLAQSGLAPYFNQVFISEQLQTQKPDALFYEKIGQQItGFDKEKTLMIGDS 182
Cdd:cd04305    13 GAKELLEELKKG-YKLGIITNGPTEVQWEKLEQLGIHKYFDHIVISEEVGVQKPNPEIFDYALNQL-GVKPEETLMVGDS 90

                          90
                  ....*....|....*....
gi 1080115061 183 LTADIQGGNNAGIDTVWYN 201
Cdd:cd04305    91 LESDILGAKNAGIKTVWFN 109

Beta-phosphoglucomutase, HAD superfamily [Carbohydrate transport and metabolism];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080115061   2 PYKFLLFDLDHTLLDFDAAEDVALTQLLKEEGVaDIQAyKDYYVPMNKALWKNLEqkkiskqelvitrfsRLFDHFGLEK 81
Cdd:COG0637     1 MIKAVIFDMDGTLVDSEPLHARAWREAFAELGI-DLTE-EEYRRLMGRSREDILR---------------YLLEEYGLDL 63

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080115061  82 DGILLAQRY-----QCYLAQQGQTFSGAHELLDSLIERDYELYAATNGITAIQTGRLAQSGLAPYFNQVFISEQLQTQKP 156
Cdd:COG0637    64 PEEELAARKeelyrELLAEEGLPLIPGVVELLEALKEAGIKIAVATSSPRENAEAVLEAAGLLDYFDVIVTGDDVARGKP 143

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1080115061 157 DALFYEKIGQQItGFDKEKTLMIGDSLtADIQGGNNAGIDTVWYNPYHLENKTQAQPTYEVHSYQDL 223
Cdd:COG0637   144 DPDIYLLAAERL-GVDPEECVVFEDSP-AGIRAAKAAGMRVVGVPDGGTAEEELAGADLVVDDLAEL 208

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 1080115061   6 LLFDLDHTLLDFDAAEDVALTQLL--KEEGVADIQAYKDYYVPMnKALWKNLEQKKISKQELVITRFSRLFDHFGLEKDG 83
Cdd:pfam00702   4 VVFDLDGTLTDGEPVVTEAIAELAseHPLAKAIVAAAEDLPIPV-EDFTARLLLGKRDWLEELDILRGLVETLEAEGLTV 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080115061  84 ILLAQRYQCYLAQQGQTFSGAHELLDSLIERDYELYAATNGITAIQTGRLAQSGLAPYFNQVFISEQLQTQKPDALFYEK 163
Cdd:pfam00702  83 VLVELLGVIALADELKLYPGAAEALKALKERGIKVAILTGDNPEAAEALLRLLGLDDYFDVVISGDDVGVGKPKPEIYLA 162

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1080115061 164 IGQQItGFDKEKTLMIGDSLtADIQGGNNAG 194
Cdd:pfam00702 163 ALERL-GVKPEEVLMVGDGV-NDIPAAKAAG 191

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 1080115061 104 AHELLDSLIERDYELYAATNGITAIQTGRLAQSGLAPYFNQVFISEQLQTQKPDALFYEKIGQQItGFDKEKTLMIGDSL 183
Cdd:cd01427    12 AVELLKRLRAAGIKLAIVTNRSREALRALLEKLGLGDLFDGIIGSDGGGTPKPKPKPLLLLLLKL-GVDPEEVLFVGDSE 90

                          90
                  ....*....|....*..
gi 1080115061 184 TaDIQGGNNAGIDTVWY 200
Cdd:cd01427    91 N-DIEAARAAGGRTVAV 106

N-acetylmuramic acid 6-phosphate phosphatase MupP;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080115061   1 MPYKFLLFDLDHTLLD----FDAAEDVALTQL-LKEEGVADIQAYKDYYVPMnkaLWKN---LEQKKISKQELVITRfsR 72
Cdd:PRK13222    4 MDIRAVAFDLDGTLVDsapdLAAAVNAALAALgLPPAGEERVRTWVGNGADV---LVERaltWAGREPDEELLEKLR--E 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080115061  73 LFDHFglekdgillaqrYQCYLAQQGQTFSGAHELLDSLIERDYELYAATNGITAIQTGRLAQSGLAPYFNQVFISEQLQ 152
Cdd:PRK13222   79 LFDRH------------YAENVAGGSRLYPGVKETLAALKAAGYPLAVVTNKPTPFVAPLLEALGIADYFSVVIGGDSLP 146

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080115061 153 TQKPDAL-FYEKIGQqiTGFDKEKTLMIGDSLTaDIQGGNNAGIDTVW----YNpyHLENKTQAQPTYEVHSYQDLLDCL 227
Cdd:PRK13222  147 NKKPDPApLLLACEK--LGLDPEEMLFVGDSRN-DIQAARAAGCPSVGvtygYN--YGEPIALSEPDVVIDHFAELLPLL 221

                  .
gi 1080115061 228 D 228
Cdd:PRK13222  222 G 222

L-2-haloacid dehalogenase; L-2-Haloacid dehalogenase catalyzes the hydrolytic dehalogenation of L-2-haloacids to produce the corresponding D-2-hydroxyacids with an inversion of the C2-configuration. 2-haloacid dehalogenases are of interest for their potential to degrade recalcitrant halogenated environmental pollutants and their use in the synthesis of industrial chemicals. 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 1080115061   4 KFLLFDLDHTLLDFDAAEDVALtQLLKEEGVADIQAYKDYYVP-----MNKALWKNLEQkkiskqelvITRFS--RLFDH 76
Cdd:cd02588     1 KALVFDVYGTLIDWHSGLAAAE-RAFPGRGEELSRLWRQKQLEytwlvTLMGPYVDFDE---------LTRDAlrATAAE 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080115061  77 FGL---EKDGILLAQRYQCYLAqqgqtFSGAHELLDSLIERDYELYAATNGITAIQTGRLAQSGLAPYFNQVFISEQLQT 153
Cdd:cd02588    71 LGLeldESDLDELGDAYLRLPP-----FPDVVAGLRRLREAGYRLAILSNGSPDLIEDVVANAGLRDLFDAVLSAEDVRA 145

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1080115061 154 QKPDALFYEKIGQQItGFDKEKTLMIGDSlTADIQGGNNAGIDTVWYN-PYHLENKTQAQPTYEVHSYQDLLD 225
Cdd:cd02588   146 YKPAPAVYELAAERL-GVPPDEILHVASH-AWDLAGARALGLRTAWINrPGEVPDPLGPAPDFVVPDLGELAD 216

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 1080115061   6 LLFDLDHTLLdfDAAEDVALTQLLKEEGVADIQAYKDYYvpmnkalwknleqkkiSKQELVITRFSRLFDHFGLEKDG-I 84
Cdd:TIGR01509   2 ILFDLDGVLV--DTEFAIAKLINREELGLVPDELGVSAV----------------GRLELALRRFKAQYGRTISPEDAqL 63

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080115061  85 LLAQRYQCYLAQQGQTFS--GAHELLDSLIERDYELYAATNGITAIQTgRLAQSGLAPYFNQVFISEQLQTQKPDALFYE 162
Cdd:TIGR01509  64 LYKQLFYEQIEEEAKLKPlpGVRALLEALRARGKKLALLTNSPRAHKL-VLALLGLRDLFDVVIDSSDVGLGKPDPDIYL 142

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1080115061 163 KiGQQITGFDKEKTLMIGDSLtADIQGGNNAGIDTVWY 200
Cdd:TIGR01509 143 Q-ALKALGLEPSECVFVDDSP-AGIEAAKAAGMHTVGV 178

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 1080115061   3 YKFLLFDLDHTLLdfDAAEDV--ALTQLLKE---EGVADIQAYKDYYVPMNKALWKNLEQKKISKQELVITRFSRLFDHF 77
Cdd:cd02616     1 ITTILFDLDGTLI--DTNELIikSFNHTLKEyglEGYTREEVLPFIGPPLRETFEKIDPDKLEDMVEEFRKYYREHNDDL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080115061  78 GLEkdgillaqryqcylaqqgqtFSGAHELLDSLIERDYELYAATNGI--TAIQTgrLAQSGLAPYFNQVFISEQLQTQK 155
Cdd:cd02616    79 TKE--------------------YPGVYETLARLKSQGIKLGVVTTKLreTALKG--LKLLGLDKYFDVIVGGDDVTHHK 136

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1080115061 156 PDALFYEKiGQQITGFDKEKTLMIGDSlTADIQGGNNAGIDTV---W-YNPyhLENKTQAQPTYEVHSYQDLLD 225
Cdd:cd02616   137 PDPEPVLK-ALELLGAEPEEALMVGDS-PHDILAGKNAGVKTVgvtWgYKG--REYLKAFNPDFIIDKMSDLLT 206

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        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1080115061 155 KPDALFYEKiGQQITGFDKEKTLMIGDSLTADIQGGNNAGIDTVWY-----NPYHLENKTQaQPTYEVHSYQD 222
Cdd:cd07530   177 KPEPIMMRA-ALEKLGLKSEETLMVGDRLDTDIAAGIAAGIDTLLVltgvtTREDLAKPPY-RPTYIVPSLRE 247

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 1080115061 104 AHELLDSLIERDYELYAATNgITAIQTGRLAQSGLAPYFNQVFISEQLQTQKPDALFYEKIGQQItGFDKEKTLMIGDSL 183
Cdd:cd16415    12 AVETLKDLKEKGLKLAVVSN-FDRRLRELLEALGLDDYFDFVVFSYEVGYEKPDPRIFQKALERL-GVSPEEALHVGDDL 89

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1080115061 184 TADIQGGNNAGIDTVWYNPyhlenktqAQPTYEVHSYQDLLDCLD 228
Cdd:cd16415    90 KNDYLGARAVGWHALLVDR--------EGALHELPSLANLLERLL 126

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 1080115061 155 KPDALFYEKIGQQITGFDKEKTLMIGDSLTADIQGGNNAGIDTVW 199
Cdd:TIGR01460 188 KPSPAIYRAALNLLQARPERRDVMVGDNLRTDILGAKNAGFDTLL 232

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 1080115061  90 YQCYLAQQG----QTFSGAHELLDSLIERDYELYAAT--NGITAIQTgrLAQSGLAPYFNQVFISEQLQTQ--KPDAlfy 161
Cdd:cd04302    68 YREYYKEKGlfenEVYPGIPELLEKLKAAGYRLYVATskPEVFARRI--LEHFGLDEYFDGIAGASLDGSRvhKADV--- 142

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1080115061 162 ekIGQQIT--GFDKEKTLMIGDSLTaDIQGGNNAGIDTV---W-YNPYhlENKTQAQPTYEVHSYQDLL 224
Cdd:cd04302   143 --IRYALDtlGIAPEQAVMIGDRKH-DIIGARANGIDSIgvlYgYGSE--DELEEAGATYIVETPAELL 206

Predicted phosphohydrolase YqeG, HAD superfamily [General function prediction only];

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1080115061 167 QITGFDKEKTLMIGDSLTADIQGGNNAGIDTVWYNPY 203
Cdd:COG2179   102 KLMGLPPEETAVVGDQLFTDVLGGNRAGLYTILVKPL 138

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 1080115061   4 KFLLFDLDHTLLDFDAAEDVA-LTQL--LKEEGVADIQAYKDYYVPMNKALWKNLEQKKISKQELVITRFSRLFDHFGLE 80
Cdd:cd02603     2 RAVLFDFGGVLIDPDPAAAVArFEALtgEPSEFVLDTEGLAGAFLELERGRITEEEFWEELREELGRPLSAELFEELVLA 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080115061  81 KDGILLAQRyqcylaqqgqtfsgahELLDSLIERDYELYAATNgitAIQTGRLAQSGLAP----YFNQVFISEQLQTQKP 156
Cdd:cd02603    82 AVDPNPEML----------------DLLEALRAKGYKVYLLSN---TWPDHFKFQLELLPrrgdLFDGVVESCRLGVRKP 142

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1080115061 157 DALFYEkIGQQITGFDKEKTLMIGDSLtADIQGGNNAGIDTVwynpyHLENKTQA 211
Cdd:cd02603   143 DPEIYQ-LALERLGVKPEEVLFIDDRE-ENVEAARALGIHAI-----LVTDAEDA 190

UmpH/NagD family phosphatase, similar to human PGP phosphoglycolate phosphatase and Schizosaccharomyces pombe PHO2 p-nitrophenylphosphatase; This subfamily includes the phosphoglycolate phosphatases (human PGP and Arabidopsis thaliana PGLP2) and p-nitrophenylphosphatases (Schizosaccharomyces pombe PHO2 and Saccharomyces PHO13p). It 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
                  ....*....|....*....|....*....|....*....|....
gi 1080115061 155 KPDALFYEKIGQQItGFDKEKTLMIGDSLTADIQGGNNAGIDTV 198
Cdd:cd07510   204 KPSRFMFDCISSKF-SIDPARTCMVGDRLDTDILFGQNCGLKTL 246

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
                  ....*....|....*....|....*.
gi 1080115061 173 KEKTLMIGDSLTADIQGGNNAGIDTV 198
Cdd:cd16416    81 PEQVAMVGDQLFTDILGGNRAGLYTI 106

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
                  ....*....|....*....|....*....|
gi 1080115061 170 GFDKEKTLMIGDSLTADIQGGNNAGIDTVW 199
Cdd:cd07532   220 VIKPERTLMIGDRLKTDILFANNCGFQSLL 249

Phosphoserine phosphatase [Amino acid transport and metabolism]; Phosphoserine phosphatase is part of the Pathway/BioSystem: Serine biosynthesis

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080115061   1 MPYKFLLFDLDHTLLDFDAaeDVALTQLLKEEGVADIQAYKDyyvpMNKALWKNLEQKKISKQELVITRFSRLfdhFGLE 80
Cdd:COG0560     1 RKMRLAVFDLDGTLIAGES--IDELARFLGRRGLVDRREVLE----EVAAITERAMAGELDFEESLRFRVALL---AGLP 71

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1080115061  81 KDgiLLAQRYQCYLAQQGQTFSGAHELLDSLIERDYELYAATNGITAIqTGRLAQ 135
Cdd:COG0560    72 EE--ELEELAERLFEEVPRLYPGARELIAEHRAAGHKVAIVSGGFTFF-VEPIAE 123

5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YigB;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080115061 105 HELLDSLIERdYELYAATNGitaiqTGRLAQSGLAPYFNQVFISEQLQTQKPDALFYEKIGQQItGFDKEKTLMIGDSLT 184
Cdd:PRK10748  119 HDTLKQLAKK-WPLVAITNG-----NAQPELFGLGDYFEFVLRAGPHGRSKPFSDMYHLAAEKL-NVPIGEILHVGDDLT 191