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Conserved domains on  [gi|488961356|ref|WP_002872380|]
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MULTISPECIES: HAD-IIIA family hydrolase [Campylobacter]

Protein Classification

HAD family hydrolase( domain architecture ID 229399)

HAD (haloacid dehalogenase) family hydrolase; the HAD family includes phosphoesterases, ATPases, phosphonatases, dehalogenases, and sugar phosphomutases acting on a remarkably diverse set of substrates

EC:  3.6.3.-
Gene Ontology:  GO:0005524|GO:0016887|GO:0005215

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HAD_like super family cl21460
Haloacid Dehalogenase-like Hydrolases; The haloacid dehalogenase (HAD) superfamily includes ...
 2-153 4.59e-81

Haloacid Dehalogenase-like Hydrolases; The haloacid dehalogenase (HAD) superfamily includes carbon and phosphorus hydrolases such as 2-haloalkonoate dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, among others. These proteins catalyze nucleophilic substitution reactions at phosphorus or carbon centers, using a conserved Asp carboxylate in covalent catalysis. All members possess a conserve alpha/beta core domain, and many also possess a small cap domain, with varying folds and functions.


The actual alignment was detected with superfamily member TIGR01670:

Pssm-ID: 473868 [Multi-domain]  Cd Length: 154  Bit Score: 236.27  E-value: 4.59e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488961356    2 TELIFLDVDGCLTDGKIIYTSNGEFIKEFDVKDGAAIEAWLKLGKKIAIITGRNCPCVEKRAKDLKIEILYQGIKDKLAC 81
Cdd:TIGR01670   1 IRLLILDVDGVLTDGKIYYTNNGEEIKAFNVRDGYGIRCALKSGIEVAIITGRKAKLVEDRCKTLGITHLYQGQSNKLIA 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488961356   82 AKEILQKLNLDFSQCAAIGDYFNDKALLESVGLSFKPKDGHKDLN--VDIVLSKKGGKAAVAQMIEILVEKNHL 153
Cdd:TIGR01670  81 FSDILEKLALAPENVAYIGDDLIDWPVMEKVGLSVAVADAHPLLIprADYVTRIAGGRGAVREVCELLLLAQGK 154
 
Name Accession Description Interval E-value
KdsC-phosphatas TIGR01670
3-deoxy-D-manno-octulosonate 8-phosphate phosphatase, YrbI family; This family of proteins is ...
 2-153 4.59e-81

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]


Pssm-ID: 130731 [Multi-domain]  Cd Length: 154  Bit Score: 236.27  E-value: 4.59e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488961356    2 TELIFLDVDGCLTDGKIIYTSNGEFIKEFDVKDGAAIEAWLKLGKKIAIITGRNCPCVEKRAKDLKIEILYQGIKDKLAC 81
Cdd:TIGR01670   1 IRLLILDVDGVLTDGKIYYTNNGEEIKAFNVRDGYGIRCALKSGIEVAIITGRKAKLVEDRCKTLGITHLYQGQSNKLIA 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488961356   82 AKEILQKLNLDFSQCAAIGDYFNDKALLESVGLSFKPKDGHKDLN--VDIVLSKKGGKAAVAQMIEILVEKNHL 153
Cdd:TIGR01670  81 FSDILEKLALAPENVAYIGDDLIDWPVMEKVGLSVAVADAHPLLIprADYVTRIAGGRGAVREVCELLLLAQGK 154
KdsC COG1778
3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC and related HAD superfamily ...
 4-162 2.07e-63

3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC and related HAD superfamily phosphatases [Cell wall/membrane/envelope biogenesis, General function prediction only];


Pssm-ID: 441384 [Multi-domain]  Cd Length: 170  Bit Score: 192.19  E-value: 2.07e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488961356   4 LIFLDVDGCLTDGKIIYTSNGEFIKEFDVKDGAAIEAWLKLGKKIAIITGRNCPCVEKRAKDLKIEILYQGIKDKLACAK 83
Cdd:COG1778   10 LLIFDVDGVLTDGRIYYDEDGEELKRFNVRDGLGIKLLRKAGIKVAIITGRDSPAVRRRAEELGITHVYQGVKDKLEALE 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488961356  84 EILQKLNLDFSQCAAIGDYFNDKALLESVGLSFKPKDGHKDL--NVDIVLSKKGGKAAVAQMIEILVEKNHLKEEWNKLW 161
Cdd:COG1778   90 ELLAKLGLSPEEVAYIGDDLPDLPVMRRVGLSVAPADAHPEVkaAADYVTTKPGGRGAVREVCELILKAQGKWDALLAAY 169


                 .
gi 488961356 162 L 162
Cdd:COG1778  170 L 170
HAD_KDO-like cd01630
haloacid dehalogenase-like (HAD) hydrolase, similar to Escherichia coli ...
 4-145 4.71e-49

haloacid dehalogenase-like (HAD) hydrolase, similar to Escherichia coli 3-deoxy-D-manno-octulosonate 8-phosphate (KDO 8-P) phosphatase KdsC, and rainbow trout N-acylneuraminate cytidylyltransferase; KDO 8-P phosphatase catalyzes the hydrolysis of KDO 8-P to KDO (3-deoxy-D-manno-octulosonate) and inorganic phosphate and is the last enzyme in the KDO biosynthetic pathway. KDO is an 8-carbon sugar that links the lipid A and polysaccharide moieties of the lipopolysaccharide region in Gram-negative bacteria. An interruption in KDO biosynthesis leads to the accumulation of lipid A precursors and subsequent arrest in cell growth. The KDO biosynthesis pathway involves five sequential enzymatic reactions. This family also includes rainbow trout CMP-sialic acid synthetase which effectively converts both deaminoneuraminic acid (KDN, 2-keto-3-deoxy-D-glycero-D-galacto-nononic acid) and N-acetylneuraminic acid (Neu5Ac) to CMP-KDN and CMP-Neu5Ac, respectively. 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.


Pssm-ID: 319769 [Multi-domain]  Cd Length: 146  Bit Score: 154.99  E-value: 4.71e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488961356   4 LIFLDVDGCLTDGKIIYTSNGEFIKEFDVKDGAAIEAWLKLGKKIAIITGRNCPCVEKRAKDLKIEILYQGIKDKLACAK 83
Cdd:cd01630    3 LLVLDVDGVLTDGRIYYDSNGEELKSFNVRDGLGIKLLQKSGIEVAIITGRQSEAVRRRAKELGIEDLFQGVKDKLEALE 82

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488961356  84 EILQKLNLDFSQCAAIGDYFNDKALLESVGLSFKPKDGHKDLN--VDIVLSKKGGKAAVAQMIE 145
Cdd:cd01630   83 ELLEKLGLSDEEVAYMGDDLPDLPVMKRVGLSVAPADAHPEVReaADYVTRARGGRGAVREVCE 146
PRK09484 PRK09484
3-deoxy-manno-octulosonate-8-phosphatase KdsC;
4-155 1.07e-31

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


Pssm-ID: 181898 [Multi-domain]  Cd Length: 183  Bit Score: 111.95  E-value: 1.07e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488961356   4 LIFLDVDGCLTDGKIIYTSNGEFIKEFDVKDGAAIEAWLKLGKKIAIITGRNCPCVEKRAKDLKIEILYQGIKDKLACAK 83
Cdd:PRK09484  23 LLICDVDGVFSDGLIYMGNNGEELKAFNVRDGYGIRCLLTSGIEVAIITGRKSKLVEDRMTTLGITHLYQGQSNKLIAFS 102

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488961356  84 EILQKLNLDFSQCAAIGDYFNDKALLESVGLSFKPKDGHKDL--NVDIVLSKKGGKAAVAQMIE-ILVEKNHLKE 155
Cdd:PRK09484 103 DLLEKLAIAPEQVAYIGDDLIDWPVMEKVGLSVAVADAHPLLlpRADYVTRIAGGRGAVREVCDlLLLAQGKLDE 177
Hydrolase_3 pfam08282
haloacid dehalogenase-like hydrolase; This family contains haloacid dehalogenase-like ...
 68-116 9.42e-05

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


Pssm-ID: 429897 [Multi-domain]  Cd Length: 255  Bit Score: 41.07  E-value: 9.42e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 488961356   68 IEILYQGIkDKLACAKEILQKLNLDFSQCAAIGDYFNDKALLESVGLSF 116
Cdd:pfam08282 179 LEIMPKGV-SKGTALKALAKHLNISLEEVIAFGDGENDIEMLEAAGLGV 226
 
Name Accession Description Interval E-value
KdsC-phosphatas TIGR01670
3-deoxy-D-manno-octulosonate 8-phosphate phosphatase, YrbI family; This family of proteins is ...
 2-153 4.59e-81

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]


Pssm-ID: 130731 [Multi-domain]  Cd Length: 154  Bit Score: 236.27  E-value: 4.59e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488961356    2 TELIFLDVDGCLTDGKIIYTSNGEFIKEFDVKDGAAIEAWLKLGKKIAIITGRNCPCVEKRAKDLKIEILYQGIKDKLAC 81
Cdd:TIGR01670   1 IRLLILDVDGVLTDGKIYYTNNGEEIKAFNVRDGYGIRCALKSGIEVAIITGRKAKLVEDRCKTLGITHLYQGQSNKLIA 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488961356   82 AKEILQKLNLDFSQCAAIGDYFNDKALLESVGLSFKPKDGHKDLN--VDIVLSKKGGKAAVAQMIEILVEKNHL 153
Cdd:TIGR01670  81 FSDILEKLALAPENVAYIGDDLIDWPVMEKVGLSVAVADAHPLLIprADYVTRIAGGRGAVREVCELLLLAQGK 154
KdsC COG1778
3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC and related HAD superfamily ...
 4-162 2.07e-63

3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC and related HAD superfamily phosphatases [Cell wall/membrane/envelope biogenesis, General function prediction only];


Pssm-ID: 441384 [Multi-domain]  Cd Length: 170  Bit Score: 192.19  E-value: 2.07e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488961356   4 LIFLDVDGCLTDGKIIYTSNGEFIKEFDVKDGAAIEAWLKLGKKIAIITGRNCPCVEKRAKDLKIEILYQGIKDKLACAK 83
Cdd:COG1778   10 LLIFDVDGVLTDGRIYYDEDGEELKRFNVRDGLGIKLLRKAGIKVAIITGRDSPAVRRRAEELGITHVYQGVKDKLEALE 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488961356  84 EILQKLNLDFSQCAAIGDYFNDKALLESVGLSFKPKDGHKDL--NVDIVLSKKGGKAAVAQMIEILVEKNHLKEEWNKLW 161
Cdd:COG1778   90 ELLAKLGLSPEEVAYIGDDLPDLPVMRRVGLSVAPADAHPEVkaAADYVTTKPGGRGAVREVCELILKAQGKWDALLAAY 169


                 .
gi 488961356 162 L 162
Cdd:COG1778  170 L 170
HAD_KDO-like cd01630
haloacid dehalogenase-like (HAD) hydrolase, similar to Escherichia coli ...
 4-145 4.71e-49

haloacid dehalogenase-like (HAD) hydrolase, similar to Escherichia coli 3-deoxy-D-manno-octulosonate 8-phosphate (KDO 8-P) phosphatase KdsC, and rainbow trout N-acylneuraminate cytidylyltransferase; KDO 8-P phosphatase catalyzes the hydrolysis of KDO 8-P to KDO (3-deoxy-D-manno-octulosonate) and inorganic phosphate and is the last enzyme in the KDO biosynthetic pathway. KDO is an 8-carbon sugar that links the lipid A and polysaccharide moieties of the lipopolysaccharide region in Gram-negative bacteria. An interruption in KDO biosynthesis leads to the accumulation of lipid A precursors and subsequent arrest in cell growth. The KDO biosynthesis pathway involves five sequential enzymatic reactions. This family also includes rainbow trout CMP-sialic acid synthetase which effectively converts both deaminoneuraminic acid (KDN, 2-keto-3-deoxy-D-glycero-D-galacto-nononic acid) and N-acetylneuraminic acid (Neu5Ac) to CMP-KDN and CMP-Neu5Ac, respectively. 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.


Pssm-ID: 319769 [Multi-domain]  Cd Length: 146  Bit Score: 154.99  E-value: 4.71e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488961356   4 LIFLDVDGCLTDGKIIYTSNGEFIKEFDVKDGAAIEAWLKLGKKIAIITGRNCPCVEKRAKDLKIEILYQGIKDKLACAK 83
Cdd:cd01630    3 LLVLDVDGVLTDGRIYYDSNGEELKSFNVRDGLGIKLLQKSGIEVAIITGRQSEAVRRRAKELGIEDLFQGVKDKLEALE 82

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488961356  84 EILQKLNLDFSQCAAIGDYFNDKALLESVGLSFKPKDGHKDLN--VDIVLSKKGGKAAVAQMIE 145
Cdd:cd01630   83 ELLEKLGLSDEEVAYMGDDLPDLPVMKRVGLSVAPADAHPEVReaADYVTRARGGRGAVREVCE 146
PRK09484 PRK09484
3-deoxy-manno-octulosonate-8-phosphatase KdsC;
4-155 1.07e-31

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


Pssm-ID: 181898 [Multi-domain]  Cd Length: 183  Bit Score: 111.95  E-value: 1.07e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488961356   4 LIFLDVDGCLTDGKIIYTSNGEFIKEFDVKDGAAIEAWLKLGKKIAIITGRNCPCVEKRAKDLKIEILYQGIKDKLACAK 83
Cdd:PRK09484  23 LLICDVDGVFSDGLIYMGNNGEELKAFNVRDGYGIRCLLTSGIEVAIITGRKSKLVEDRMTTLGITHLYQGQSNKLIAFS 102

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488961356  84 EILQKLNLDFSQCAAIGDYFNDKALLESVGLSFKPKDGHKDL--NVDIVLSKKGGKAAVAQMIE-ILVEKNHLKE 155
Cdd:PRK09484 103 DLLEKLAIAPEQVAYIGDDLIDWPVMEKVGLSVAVADAHPLLlpRADYVTRIAGGRGAVREVCDlLLLAQGKLDE 177
HAD_Pase cd07514
phosphatase, similar to Thermoplasma acidophilum TA0175 phosphoglycolate phosphatase (PCPase), ...
 4-147 2.50e-09

phosphatase, similar to Thermoplasma acidophilum TA0175 phosphoglycolate phosphatase (PCPase), and Pyrococcus horikoshii PH1421, a magnesium-dependent phosphatase; belongs to the haloacid dehalogenase-like superfamily; Thermoplasma acidophilum TA0175 phosphoglycolate phosphatase (PGPase) catalyzes the magnesium-dependent dephosphorylation of phosphoglycolate. This family also includes Pyrococcus horikoshii OT3 PH1421, a magnesium-dependent phosphatase. 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.


Pssm-ID: 319816 [Multi-domain]  Cd Length: 139  Bit Score: 52.59  E-value: 2.50e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488961356   4 LIFLDVDGCLTDGKiiytsngefikefDVKDGAAIEA---WLKLGKKIAIITGRNCPCVEKRAKDLKIE---ILYQGIKD 77
Cdd:cd07514    1 LIAVDIDGTLTDRR-------------RSIDLRAIEAirkLEKAGIPVVLVTGNSLPVARALAKYLGLSgpvVAENGGVD 67

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 488961356  78 KLACAKEILQKLNLDFSQCAAIGDYFNDKALLESVGLSFKPKDGHKDL--NVDIVLSKKGGKaAVAQMIEIL 147
Cdd:cd07514   68 KGTGLEKLAERLGIDPEEVLAIGDSENDIEMFKVAGFKVAVANADEELkeAADYVTDASYGD-GVLEAIDKL 138
HAD-SF-IIIA TIGR01662
HAD-superfamily hydrolase, subfamily IIIA; This subfamily falls within the Haloacid ...
 4-101 1.29e-07

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]


Pssm-ID: 273742 [Multi-domain]  Cd Length: 135  Bit Score: 47.78  E-value: 1.29e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488961356    4 LIFLDVDGCLTDGKIIYTSNGEFIKEFDVKDGAAIEAwlKLGKKIAIITGRNC-----------PCVEKRAKDLKIEIly 72
Cdd:TIGR01662   2 AVVLDLDGTLTDDVPYVSDEDERILYPEVPDALAELK--EAGYKVVIVTNQSGigrgyfsrsfsGRVARRLEELGVPI-- 77

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 488961356   73 QGI-------KDKLACAKEILQKLN-LDFSQCAAIGD 101
Cdd:TIGR01662  78 DILyacpgcrKPKPGMFLEALKRFNeIDPEESVYVGD 114
Cof COG0561
Hydroxymethylpyrimidine pyrophosphatase and other HAD family phosphatases [Coenzyme transport ...
 16-125 8.75e-07

Hydroxymethylpyrimidine pyrophosphatase and other HAD family phosphatases [Coenzyme transport and metabolism, General function prediction only];


Pssm-ID: 440327 [Multi-domain]  Cd Length: 192  Bit Score: 46.67  E-value: 8.75e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488961356  16 GKIIYTSNGEFIKE--FDVKDGAAIEAWL-KLGKKIAIITgrncpcvekRAKDLKIEILYQGIkDKLACAKEILQKLNLD 92
Cdd:COG0561   67 GALIYDPDGEVLYErpLDPEDVREILELLrEHGLHLQVVV---------RSGPGFLEILPKGV-SKGSALKKLAERLGIP 136

                         90       100       110
                 ....*....|....*....|....*....|...
gi 488961356  93 FSQCAAIGDYFNDKALLESVGLSFKPKDGHKDL 125
Cdd:COG0561  137 PEEVIAFGDSGNDLEMLEAAGLGVAMGNAPPEV 169
HAD_like cd01427
Haloacid dehalogenase-like hydrolases; The haloacid dehalogenase-like (HAD) superfamily ...
 4-116 1.30e-06

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.


Pssm-ID: 319763 [Multi-domain]  Cd Length: 106  Bit Score: 44.69  E-value: 1.30e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488961356   4 LIFLDVDGCLTdgkiiytsngefikefdVKDgaAIEAWLKLGKKIAIITGRNCPCVEKRAKDLKIEILYQGI-------- 75
Cdd:cd01427    1 AVLFDLDGTLL-----------------AVE--LLKRLRAAGIKLAIVTNRSREALRALLEKLGLGDLFDGIigsdgggt 61

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 488961356  76 -KDKLACAKEILQKLNLDFSQCAAIGDYFNDKALLESVGLSF 116
Cdd:cd01427   62 pKPKPKPLLLLLLKLGVDPEEVLFVGDSENDIEAARAAGGRT 103
SerB COG0560
Phosphoserine phosphatase [Amino acid transport and metabolism]; Phosphoserine phosphatase is ...
 36-120 3.36e-06

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


Pssm-ID: 440326 [Multi-domain]  Cd Length: 221  Bit Score: 45.21  E-value: 3.36e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488961356  36 AAIEAWLKLGKKIAIITGRNCPCVEKRAKDLKIE---------------------ILYQgiKDKLACAKEILQKLNLDFS 94
Cdd:COG0560   95 ELIAEHRAAGHKVAIVSGGFTFFVEPIAERLGIDhvianelevedgrltgevvgpIVDG--EGKAEALRELAAELGIDLE 172

                         90       100
                 ....*....|....*....|....*...
gi 488961356  95 QCAAIGDYFNDKALLESVGLS--FKPKD 120
Cdd:COG0560  173 QSYAYGDSANDLPMLEAAGLPvaVNPDP 200
HAD_Pase cd07516
phosphatase, similar to Escherichia coli Cof and Thermotoga maritima TM0651; belongs to the ...
 68-116 8.60e-05

phosphatase, similar to Escherichia coli Cof and Thermotoga maritima TM0651; belongs to the haloacid dehalogenase-like superfamily; Escherichia coli Cof is involved in the hydrolysis of HMP-PP (4-amino-2-methyl-5-hydroxymethylpyrimidine pyrophosphate, an intermediate in thiamin biosynthesis), Cof also has phosphatase activity against the coenzymes pyridoxal phosphate (PLP) and FMN. Thermotoga maritima TM0651 acts as a phosphatase with a phosphorylated carbohydrate molecule as a possible substrate. Escherichia coli YbhA is also a member of this family and catalyzes the dephosphorylation of PLP, YbhA can also hydrolyze erythrose-4-phosphate and fructose-1,6-bis-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, 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.


Pssm-ID: 319818 [Multi-domain]  Cd Length: 253  Bit Score: 41.43  E-value: 8.60e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 488961356  68 IEILYQGIkDKLACAKEILQKLNLDFSQCAAIGDYFNDKALLESVGLSF 116
Cdd:cd07516  175 LEIMPKGV-SKGNALKKLAEYLGISLEEVIAFGDNENDLSMLEYAGLGV 222
Hydrolase_3 pfam08282
haloacid dehalogenase-like hydrolase; This family contains haloacid dehalogenase-like ...
 68-116 9.42e-05

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


Pssm-ID: 429897 [Multi-domain]  Cd Length: 255  Bit Score: 41.07  E-value: 9.42e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 488961356   68 IEILYQGIkDKLACAKEILQKLNLDFSQCAAIGDYFNDKALLESVGLSF 116
Cdd:pfam08282 179 LEIMPKGV-SKGTALKALAKHLNISLEEVIAFGDGENDIEMLEAAGLGV 226
Cof-subfamily TIGR00099
Cof subfamily of IIB subfamily of haloacid dehalogenase superfamily; This subfamily of ...
 68-116 1.96e-04

Cof subfamily of IIB subfamily of haloacid dehalogenase superfamily; This subfamily of sequences falls within the Class-IIB subfamily (TIGR01484) of the Haloacid Dehalogenase superfamily of aspartate-nucleophile hydrolases. The use of the name "Cof" as an identifier here is arbitrary and refers to the E. coli Cof protein. This subfamily is notable for the large number of recent paralogs in many species. Listeria, for instance, has 12, Clostridium, Lactococcus and Streptococcus pneumoniae have 8 each, Enterococcus and Salmonella have 7 each, and Bacillus subtilus, Mycoplasma, Staphylococcus and E. coli have 6 each. This high degree of gene duplication is limited to the gamma proteobacteria and low-GC gram positive lineages. The profusion of genes in this subfamily is not coupled with a high degree of divergence, so it is impossible to determine an accurate phylogeny at the equivalog level. Considering the relationship of this subfamily to the other known members of the HAD-IIB subfamily (TIGR01484), sucrose and trehalose phosphatases and phosphomannomutase, it seems a reasonable hypothesis that these enzymes act on phosphorylated sugars. Possibly the diversification of genes in this subfamily represents the diverse sugars and polysaccharides that various bacteria find in their biological niches. The members of this subfamily are restricted almost exclusively to bacteria (one sequences from S. pombe scores above trusted, while another is between trusted and noise). It is notable that no archaea are found in this group, the closest relations to the archaea found here being two Deinococcus sequences. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 272905 [Multi-domain]  Cd Length: 256  Bit Score: 40.33  E-value: 1.96e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 488961356   68 IEILYQGIkDKLACAKEILQKLNLDFSQCAAIGDYFNDKALLESVGLSF 116
Cdd:TIGR00099 180 IEITAKGV-SKGSALQSLAEALGISLEDVIAFGDGMNDIEMLEAAGYGV 227
HAD_YbiV-Like cd07518
Escherichia coli YbiV sugar phosphatase/phosphotransferase and related proteins; belongs to ...
 68-116 2.45e-04

Escherichia coli YbiV sugar phosphatase/phosphotransferase and related proteins; belongs to the haloacid dehalogenase-like superfamily; Escherichia coli YbiV can act as both a sugar phosphatase and as a phosphotransferase. 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, 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.


Pssm-ID: 319820 [Multi-domain]  Cd Length: 184  Bit Score: 39.49  E-value: 2.45e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 488961356  68 IEILYQGIkDKLACAKEILQKLNLDFSQCAAIGDYFNDKALLESVGLSF 116
Cdd:cd07518  107 IDIIPPGV-NKATGLKQLLKHWGISPDEVMAFGDGGNDIEMLKYAGYSY 154
Hydrolase pfam00702
haloacid dehalogenase-like hydrolase; This family is structurally different from the alpha ...
 29-113 4.21e-04

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.


Pssm-ID: 459910 [Multi-domain]  Cd Length: 191  Bit Score: 39.11  E-value: 4.21e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488961356   29 EFDVKDGA--AIEAWLKLGKKIAIITGRNCPCVEKRAKDL----KIEILYQGIKDKLACAK-----EILQKLNLDFSQCA 97
Cdd:pfam00702  96 ELKLYPGAaeALKALKERGIKVAILTGDNPEAAEALLRLLglddYFDVVISGDDVGVGKPKpeiylAALERLGVKPEEVL 175

                          90
                  ....*....|....*.
gi 488961356   98 AIGDYFNDKALLESVG 113
Cdd:pfam00702 176 MVGDGVNDIPAAKAAG 191
Gph COG0546
Phosphoglycolate phosphatase, HAD superfamily [Energy production and conversion];
36-105 5.63e-04

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


Pssm-ID: 440312 [Multi-domain]  Cd Length: 214  Bit Score: 38.76  E-value: 5.63e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488961356  36 AAIEAWLKLGKKIAIITGRNCPCVEKRAKDLKIEILYQGI---------KDKLACAKEILQKLNLDFSQCAAIGDYFND 105
Cdd:COG0546   91 ELLEALKARGIKLAVVTNKPREFAERLLEALGLDDYFDAIvggddvppaKPKPEPLLEALERLGLDPEEVLMVGDSPHD 169
HAD-SF-IIB TIGR01484
HAD-superfamily hydrolase, subfamily IIB; This subfamily falls within the Haloacid ...
 39-116 1.67e-03

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]


Pssm-ID: 273651 [Multi-domain]  Cd Length: 207  Bit Score: 37.36  E-value: 1.67e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488961356   39 EAWLKLGKKIAIITGRNCPCVEKR--AKDLkIEILYQGIkDKLACAKEILQKLNLDFSQCAAIGDYFNDKALLESVGLSF 116
Cdd:TIGR01484 128 QELDSKMRERLEKIGRNDLELEAIysGKTD-LEVLPAGV-NKGSALQALLQELNGKKDEILAFGDSGNDEEMFEVAGLAV 205
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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