3-deoxy-manno-octulosonate-8-phosphatase KdsC;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1799318089   4 THYTPIPADVAERAARVRVAVFDVDGTLTDGRLWYAEDGRETKVFHVHDGLGLKRLQENGVKVAIITARISHPVSLRAEE 83
Cdd:PRK09484    5 TCYGPVSDDVMAKAENIRLLICDVDGVFSDGLIYMGNNGEELKAFNVRDGYGIRCLLTSGIEVAIITGRKSKLVEDRMTT 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1799318089  84 LGIQHVYQGQKDKRACLKELLDALRLTPEQAAFVGDDLPDLPAMGIAGLAVATANAHPWVAERAHWRTRLSGGYGAAREV 163
Cdd:PRK09484   85 LGITHLYQGQSNKLIAFSDLLEKLAIAPEQVAYIGDDLIDWPVMEKVGLSVAVADAHPLLLPRADYVTRIAGGRGAVREV 164

                         170
                  ....*....|..
gi 1799318089 164 ADMILAAQGKAE 175
Cdd:PRK09484  165 CDLLLLAQGKLD 176

3-deoxy-D-manno-octulosonate 8-phosphate phosphatase, YrbI family; This family of 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. One member of this family, the YrbI protein from H. influenzae has been cloned, expressed, purified and found to be an active 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase. Furthermore, its crystal structure has been determined. This family consists of sequences from beta, gamma and epsilon proteobacteria, Aquifex, Fusobacterium, Porphyromonas and Methanosarcina. The Methanosarcina sequence is distinctive in that it is linked to an N-terminal cytidylyltransferase domain (pfam02348) and is annotated as acylneuraminate cytidylyltransferase. This may give some clue as the function of these phosphatases. Several eukaryotic sequences scoring between trusted and noise are also closely related to this function such as the CMP-N-acetylneuraminic acid synthetase from mouse, but in these cases the phosphatase domain is clearly inactive as many of the active site residues are not conserved. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1799318089  20 VRVAVFDVDGTLTDGRLWYAEDGRETKVFHVHDGLGLKRLQENGVKVAIITARISHPVSLRAEELGIQHVYQGQKDKRAC 99
Cdd:TIGR01670   1 IRLLILDVDGVLTDGKIYYTNNGEEIKAFNVRDGYGIRCALKSGIEVAIITGRKAKLVEDRCKTLGITHLYQGQSNKLIA 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1799318089 100 LKELLDALRLTPEQAAFVGDDLPDLPAMGIAGLAVATANAHPWVAERAHWRTRLSGGYGAAREVADMILAAQGK 173
Cdd:TIGR01670  81 FSDILEKLALAPENVAYIGDDLIDWPVMEKVGLSVAVADAHPLLIPRADYVTRIAGGRGAVREVCELLLLAQGK 154

3-deoxy-manno-octulosonate-8-phosphatase KdsC;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1799318089   4 THYTPIPADVAERAARVRVAVFDVDGTLTDGRLWYAEDGRETKVFHVHDGLGLKRLQENGVKVAIITARISHPVSLRAEE 83
Cdd:PRK09484    5 TCYGPVSDDVMAKAENIRLLICDVDGVFSDGLIYMGNNGEELKAFNVRDGYGIRCLLTSGIEVAIITGRKSKLVEDRMTT 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1799318089  84 LGIQHVYQGQKDKRACLKELLDALRLTPEQAAFVGDDLPDLPAMGIAGLAVATANAHPWVAERAHWRTRLSGGYGAAREV 163
Cdd:PRK09484   85 LGITHLYQGQSNKLIAFSDLLEKLAIAPEQVAYIGDDLIDWPVMEKVGLSVAVADAHPLLLPRADYVTRIAGGRGAVREV 164

                         170
                  ....*....|..
gi 1799318089 164 ADMILAAQGKAE 175
Cdd:PRK09484  165 CDLLLLAQGKLD 176

3-deoxy-D-manno-octulosonate 8-phosphate phosphatase, YrbI family; This family of 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. One member of this family, the YrbI protein from H. influenzae has been cloned, expressed, purified and found to be an active 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase. Furthermore, its crystal structure has been determined. This family consists of sequences from beta, gamma and epsilon proteobacteria, Aquifex, Fusobacterium, Porphyromonas and Methanosarcina. The Methanosarcina sequence is distinctive in that it is linked to an N-terminal cytidylyltransferase domain (pfam02348) and is annotated as acylneuraminate cytidylyltransferase. This may give some clue as the function of these phosphatases. Several eukaryotic sequences scoring between trusted and noise are also closely related to this function such as the CMP-N-acetylneuraminic acid synthetase from mouse, but in these cases the phosphatase domain is clearly inactive as many of the active site residues are not conserved. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1799318089  20 VRVAVFDVDGTLTDGRLWYAEDGRETKVFHVHDGLGLKRLQENGVKVAIITARISHPVSLRAEELGIQHVYQGQKDKRAC 99
Cdd:TIGR01670   1 IRLLILDVDGVLTDGKIYYTNNGEEIKAFNVRDGYGIRCALKSGIEVAIITGRKAKLVEDRCKTLGITHLYQGQSNKLIA 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1799318089 100 LKELLDALRLTPEQAAFVGDDLPDLPAMGIAGLAVATANAHPWVAERAHWRTRLSGGYGAAREVADMILAAQGK 173
Cdd:TIGR01670  81 FSDILEKLALAPENVAYIGDDLIDWPVMEKVGLSVAVADAHPLLIPRADYVTRIAGGRGAVREVCELLLLAQGK 154

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 1799318089  21 RVAVFDVDGTLTDGRLWYAEDGRETKVFHVHDglGLKRLQENGVKVAIIT-----------ARISHPVSLRAEELGIQH- 88
Cdd:TIGR01662   1 KAVVLDLDGTLTDDVPYVSDEDERILYPEVPD--ALAELKEAGYKVVIVTnqsgigrgyfsRSFSGRVARRLEELGVPId 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1799318089  89 ---VYQGQKDKR--ACLKELLDALRLTPEQAAFVGD-DLPDLPAMGIAGLAVA 135
Cdd:TIGR01662  79 ilyACPGCRKPKpgMFLEALKRFNEIDPEESVYVGDqDLTDLQAAKRVGLATI 131

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 1799318089  22 VAVFDVDGTLTDGRLwyaedgretkvfhvhdglgLKRLQENGVKVAIITARISHPVSLRAEELGIQHVYQGQ-------- 93
Cdd:cd01427     1 AVLFDLDGTLLAVEL-------------------LKRLRAAGIKLAIVTNRSREALRALLEKLGLGDLFDGIigsdgggt 61

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1799318089  94 -KDKRACLKELLDALRLTPEQAAFVGDDLPDLPAMGIAG 131
Cdd:cd01427    62 pKPKPKPLLLLLLKLGVDPEEVLFVGDSENDIEAARAAG 100

P-type heavy metal-transporting ATPase; Heavy metal-transporting ATPases (Type IB ATPases) transport heavy metal ions (Cu(+), Cu(2+), Zn(2+), Cd(2+), Co(2+), etc.) across biological membranes. These ATPases include mammalian copper-transporting ATPases, ATP7A and ATP7B, Bacillus subtilis CadA which transports cadmium, zinc and cobalt out of the cell, Bacillus subtilis ZosA/PfeT which transports copper, and perhaps also zinc and ferrous iron, Archaeoglobus fulgidus CopA and CopB, Staphylococcus aureus plasmid pI258 CadA, a cadmium-efflux ATPase, and Escherichia coli ZntA which is selective for Pb(2+), Zn(2+), and Cd(2+). The characteristic N-terminal heavy metal associated (HMA) domain of this group is essential for the binding of metal ions. This family belongs to the P-type ATPases, a large family of integral membrane transporters that are of critical importance in all kingdoms of life. They generate and maintain (electro-) chemical gradients across cellular membranes, by translocating cations, heavy metals and lipids, and are distinguished from other main classes of transport ATPases (F- , V- , and ABC- type) by the formation of a phosphorylated (P-) intermediate state in the catalytic cycle.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1799318089  11 ADVAERAARVRVAVFDVDGTLTdGRLWYAEDGRETKVFHVHDGL------GLKRLQENGVKVAIIT-------ARIshpv 77
Cdd:cd02079   407 LSFAEEEGLVEAADALSDAGKT-SAVYVGRDGKLVGLFALEDQLrpeakeVIAELKSGGIKVVMLTgdneaaaQAV---- 481

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1799318089  78 slrAEELGIQHVYQGQK--DKRACLKELLDALRltpeQAAFVGDDLPDLPAMGIAGLAVAtanahpwvaerahwrtrLSG 155
Cdd:cd02079   482 ---AKELGIDEVHAGLLpeDKLAIVKALQAEGG----PVAMVGDGINDAPALAQADVGIA-----------------MGS 537

                         170
                  ....*....|...
gi 1799318089 156 GYGAAREVADMIL 168
Cdd:cd02079   538 GTDVAIETADIVL 550

Phosphoglycolate phosphatase, HAD superfamily [Energy production and conversion];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1799318089  56 LKRLQENGVKVAIITARISHPVSLRAEELGIQH---VYQGQ------KDKRACLKELLDALRLTPEQAAFVGDDLPDL-- 124
Cdd:COG0546    93 LEALKARGIKLAVVTNKPREFAERLLEALGLDDyfdAIVGGddvppaKPKPEPLLEALERLGLDPEEVLMVGDSPHDIea 172

                          90
                  ....*....|...
gi 1799318089 125 -PAMGIAGLAVAT 136
Cdd:COG0546   173 aRAAGVPFIGVTW 185

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 1799318089  24 VFDVDGTLTDgrLWYAEDGRETKVFhvhdglgLKRLQENGVKVAIITARISHPVSLRAEELGIQHVYQGQKDKRACLKEL 103
Cdd:cd16416     3 ITDLDNTLLA--WDNPDLTPEVKAW-------LADLKEAGIKVVLVSNNNERRVAKVIEKLDLPFVARAGKPRPRAFRRA 73

                          90
                  ....*....|....*...
gi 1799318089 104 LDALRLTPEQAAFVGDDL 121
Cdd:cd16416    74 LKEMDLPPEQVAMVGDQL 91

phosphoglycolate phosphatase, TA0175-type; This group of Archaeal sequences, now known to be phosphoglycolate phosphatases, is most closely related to the sucrose-phosphate phosphatases from plants and cyanobacteria (TIGR01485). Together, these two models comprise a subfamily model (TIGR01482). TIGR01482, in turn, is a member of the IIB subfamily (TIGR01484) of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1799318089  81 AEELGIQHVYQGQK--------DKRACLKELLDALRLTPEQAAFVGDDLPDLPAMGIAGLAVATANAHPWVAERAHWRTR 152
Cdd:TIGR01487 125 IKERGLNLVASGFAihimkkgvDKGVGVEKLKELLGIKPEEVAAIGDSENDIDLFRVVGFKVAVANADDQLKEIADYVTS 204

                  ....*.
gi 1799318089 153 LSGGYG 158
Cdd:TIGR01487 205 NPYGEG 210

phosphoserine phosphatase (PSP), similar to Methanococcus Jannaschii PSP and Saccharomyces cerevisiae SER2p; This family includes Methanococcus jannaschii PSP, and Saccharomyces cerevisiae phosphoserine phosphatase SER2p, EC 3.1.3.3, which participates in a pathway whereby serine and glycine are synthesized from the glycolytic intermediate 3-phosphoglycerate; phosphoserine phosphatase catalyzes the hydrolysis of phospho-L-serine to L-serine and inorganic phosphate, the third reaction in this pathway. 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 1799318089  56 LKRLQENGVKVAIITARISHPVSLRAEELGIQHVYQ-------------------GQKDKRACLKELLDALRLTPEQAAF 116
Cdd:cd07500    79 IQTLKAKGYKTAVVSGGFTYFTDRLAEELGLDYAFAneleikdgkltgkvlgpivDAQRKAETLQELAARLGIPLEQTVA 158

                          90
                  ....*....|....*....
gi 1799318089 117 VGDDLPDLPAMGIAGLAVA 135
Cdd:cd07500   159 VGDGANDLPMLKAAGLGIA 177

Cation-transporting P-type ATPase [Inorganic ion transport and metabolism];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1799318089  36 LWYAEDGRETKVFHVHDGL------GLKRLQENGVKVAIIT-------ARIshpvslrAEELGIQHVYQGQK--DKRACL 100
Cdd:COG2217   524 VYVAVDGRLLGLIALADTLrpeaaeAIAALKALGIRVVMLTgdnertaEAV-------ARELGIDEVRAEVLpeDKAAAV 596

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1799318089 101 KELLDALRLTpeqaAFVGDDLPDLPAM-----GIAglavatanahpwvaerahwrtrLSGGYGAAREVADMIL 168
Cdd:COG2217   597 RELQAQGKKV----AMVGDGINDAPALaaadvGIA----------------------MGSGTDVAIEAADIVL 643

phosphoglycolate phosphatase, similar to Synechococcus elongates phosphoglycolate phosphatase PGP/CbbZ; Phosphoglycolate phosphatase catalyzes the dephosphorylation of phosphoglycolate; its activity requires divalent cations, especially Mg++. 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 1799318089  15 ERAARVRVAVFDVDGTLTDGRLWYAEDGRETKVFHVHDGLgLKRLQENGVKVAIITA-------RISHPVSLRAeelgIQ 87
Cdd:cd04303    48 EILKQLGVPLWKLPLIAKDFRRLMAEAAPELALFPGVEDM-LRALHARGVRLAVVSSnseenirRVLGPEELIS----LF 122

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1799318089  88 HVYQGQK--DKRACLKELLDALRLTPEQAAFVGDDLPDLPAMGIAGLAVA 135
Cdd:cd04303   123 AVIEGSSlfGKAKKIRRVLRRTKITAAQVIYVGDETRDIEAARKVGLAFA 172

haloacid dehalogenase-like hydrolase; This family contains haloacid dehalogenase-like hydrolase enzymes.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1799318089  24 VFDVDGTLTDgrlwyaEDGR---ETKVfhvhdglGLKRLQENGVKVAIITARisHPVSLR--AEELGIQ 87
Cdd:pfam08282   2 ASDLDGTLLN------SDKKiseKTKE-------AIKKLKEKGIKFVIATGR--PYRAILpvIKELGLD 55

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
                  ....*....|....*....|....*....|....*....|....*....
gi 1799318089  24 VFDVDGTLTDGRLWYAEDGRETKvfhvhdglgLKRLQENGVKVAIITAR 72
Cdd:TIGR01484   3 FFDLDGTLLDPNAHELSPETIEA---------LERLREAGVKVVIVTGR 42

P-type heavy metal-transporting ATPase, similar to human copper-transporting ATPases, ATP7A and ATP7B; The mammalian copper-transporting P-type ATPases, ATP7A and ATP7B are key molecules required for the regulation and maintenance of copper homeostasis. Menkes and Wilson diseases are caused by mutation in ATP7A and ATP7B respectively. This subfamily includes other copper-transporting ATPases such as: Bacillus subtilis CopA , Archeaoglobus fulgidus CopA, and Saccharomyces cerevisiae Ccc2p. This subclass of P-type ATPase is also referred to as CPx-type ATPases because their amino acid sequences contain a characteristic CPC or CPH motif associated with a stretch of hydrophobic amino acids and N-terminal ion-binding sequences. This subfamily belongs to the P-type ATPases, a large family of integral membrane transporters that are of critical importance in all kingdoms of life. They generate and maintain (electro-) chemical gradients across cellular membranes, by translocating cations, heavy metals and lipids, and are distinguished from other main classes of transport ATPases (F- , V- , and ABC- type) by the formation of a phosphorylated (P-) intermediate state in the catalytic cycle.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1799318089  36 LWYAEDGRETKVFHVHDGL------GLKRLQENGVKVAIITARISHPVSLRAEELGIQHVYQGQK--DKRACLKELLDAL 107
Cdd:cd02094   451 VLVAVDGELAGLIAVADPLkpdaaeAIEALKKMGIKVVMLTGDNRRTARAIAKELGIDEVIAEVLpeDKAEKVKKLQAQG 530

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1799318089 108 RLTpeqaAFVGDDLPDLPAMGIA--GLAVAT 136
Cdd:cd02094   531 KKV----AMVGDGINDAPALAQAdvGIAIGS 557

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 1799318089  22 VAVFDVDGTLTDGRLWYAEDGRETKVFHVHDGLGLKRLQENGVKVAIITARISHPvSLRAEELGIQHVYQGQKDKRACLK 101
Cdd:TIGR01549   1 AILFDIDGTLVDIKFAIRRAFPQTFEEFGLDPASFKALKQAGGLAEEEWYRIATS-ALEELQGRFWSEYDAEEAYIRGAA 79

                  ....*..
gi 1799318089 102 ELLDALR 108
Cdd:TIGR01549  80 DLLARLK 86

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.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1799318089  23 AVFDVDGTLTD-----GRLWYAEDGRETKVFHVHDGLG----------LKRLQENGVKVAIITARISHPVSLRAEELGIQ 87
Cdd:cd07505     2 VIFDMDGVLIDteplhRQAWQLLERKNALLLELIASEGlklkpgvvelLDALKAAGIPVAVATSSSRRNVELLLLELGLL 81

                  ...
gi 1799318089  88 HVY 90
Cdd:cd07505    82 RGY 84

copper-(or silver)-translocating P-type ATPase; This model describes the P-type ATPase primarily responsible for translocating copper ions accross biological membranes. These transporters are found in prokaryotes and eukaryotes. This model encompasses those species which pump copper ions out of cells or organelles (efflux pumps such as CopA of Escherichia coli) as well as those which pump the ion into cells or organelles either for the purpose of supporting life in extremely low-copper environments (for example CopA of Enterococcus hirae) or for the specific delivery of copper to a biological complex for which it is a necessary component (for example FixI of Bradyrhizobium japonicum, or CtaA and PacS of Synechocystis). The substrate specificity of these transporters may, to a varying degree, include silver ions (for example, CopA from Archaeoglobus fulgidus). Copper transporters from this family are well known as the genes which are mutated in two human disorders of copper metabolism, Wilson's and Menkes' diseases. The sequences contributing to the seed of this model are all experimentally characterized. The copper P-type ATPases have been characterized as Type IB based on a phylogenetic analysis which combines the copper-translocating ATPases with the cadmium-translocating species. This model and that describing the cadmium-ATPases (TIGR01512) are well separated, and thus we further type the copper-ATPases as IB1 (and the cadmium-ATPases as IB2). Several sequences which have not been characterized experimentally fall just below the cutoffs for both of these models (SP|Q9CCL1 from Mycobacterium leprae, GP|13816263 from Sulfolobus solfataricus, OMNI|NTL01CJ01098 from Campylobacter jejuni, OMNI|NTL01HS01687 from Halobacterium sp., GP|6899169 from Ureaplasma urealyticum and OMNI|HP1503 from Helicobacter pylori). Accession PIR|A29576 from Enterococcus faecalis scores very high against this model, but yet is annotated as an "H+/K+ exchanging ATPase". BLAST of this sequence does not hit anything else annotated in this way. This error may come from the characterization paper published in 1987. Accession GP|7415611 from Saccharomyces cerevisiae appears to be mis-annotated as a cadmium resistance protein. Accession OMNI|NTL01HS00542 from Halobacterium which scores above trusted for this model is annotated as "molybdenum-binding protein" although no evidence can be found for this classification. [Cellular processes, Detoxification, Transport and binding proteins, Cations and iron carrying compounds]

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1799318089  11 ADVAERAARVRVAVFDVDGTLTDGRLwyaedgretKVFHVH---DGLGLKRLQengvKVAIITARISHPVS 78
Cdd:TIGR01511 268 GDALERAANIDTVVFDKTGTLTQGKP---------TVTDVHvfgDRDRTELLA----LAAALEAGSEHPLA 325