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Conserved domains on  [gi|492529894|ref|WP_005875092|]
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HAD-IB family hydrolase [Porphyromonas gingivalis]

Protein Classification

HAD-IB family hydrolase( domain architecture ID 10019258)

HAD (haloacid dehalogenase)-IB family hydrolase similar to Caulobacter vibrioides protein CicA which may be involved in essential phosphotransferase reactions and may play a role in cell wall biosynthesis, morphogenesis, and cell division

CATH:  3.30.1240.10
EC:  3.-.-.-
Gene Ontology:  GO:0016787
PubMed:  16889794|15337123|33940035|37786806

Graphical summary

 Zoom to residue level

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List of domain hits

 Name Accession Description Interval E-value
HAD-SF-IB-hyp1 TIGR01490
HAD-superfamily subfamily IB hydrolase, TIGR01490; This hypothetical equivalog is a member of ...
 6-197 9.83e-86

HAD-superfamily subfamily IB hydrolase, TIGR01490; This hypothetical equivalog is a member of the IB subfamily (TIGR01488) of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. The sequences modelled here are all bacterial. The IB subfamily includes the enzyme phosphoserine phosphatase (TIGR00338). Due to this relationship, several of these sequences have been annotated as "phosphoserine phosphatase related proteins," or "Phosphoserine phosphatase-family enzymes." There is presently no evidence that any of the enzymes in this model possess PSPase activity. OMNI|NTL01ML1250 is annotated as a "possible transferase," however this is due to the C-terminal domain found on this sequence which is homologous to a group of glycerol-phosphate acyltransferases (between trusted and noise to TIGR00530). A subset of these sequences including OMNI|CC1962, the Caulobacter crescentus CicA protein cluster together and may represent a separate equivalog. [Unknown function, Enzymes of unknown specificity]


:

Pssm-ID: 273654 [Multi-domain]  Cd Length: 202  Bit Score: 251.49  E-value: 9.83e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492529894    6 IAIFDFDGTLTRCDSLLPFLR-QAQPVILF-WLRLPFYLAMWMCYKLRLAPADRTKAAILSTVLKGKREVECRAMGQRFV 83
Cdd:TIGR01490   1 LAFFDFDGTLTAKDTLFIFLKfLASKNILFeELRLPKVLARFEFFLNRGLDYMAYYRAFALDALAGLLEEDVRAIVEEFV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492529894   84 PA-IESILRPEALRCLEWHRSEGHRLVLLTASLLPCVEPWAEKTGFHTVIAT-LPEIKSGILTGRFEGNNCKGKEKIHRL 161
Cdd:TIGR01490  81 NQkIESILYPEARDLIRWHKAEGHTIVLVSASLTILVKPLARILGIDNAIGTrLEESEDGIYTGNIDGNNCKGEGKVHAL 160

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 492529894  162 DRALPHWRDS--ISYGYGDSPSDRPLLSLCTHSYYRRF 197
Cdd:TIGR01490 161 AELLAEEQIDlkDSYAYGDSISDLPLLSLVGHPYVVNP 198
 
Name Accession Description Interval E-value
HAD-SF-IB-hyp1 TIGR01490
HAD-superfamily subfamily IB hydrolase, TIGR01490; This hypothetical equivalog is a member of ...
 6-197 9.83e-86

HAD-superfamily subfamily IB hydrolase, TIGR01490; This hypothetical equivalog is a member of the IB subfamily (TIGR01488) of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. The sequences modelled here are all bacterial. The IB subfamily includes the enzyme phosphoserine phosphatase (TIGR00338). Due to this relationship, several of these sequences have been annotated as "phosphoserine phosphatase related proteins," or "Phosphoserine phosphatase-family enzymes." There is presently no evidence that any of the enzymes in this model possess PSPase activity. OMNI|NTL01ML1250 is annotated as a "possible transferase," however this is due to the C-terminal domain found on this sequence which is homologous to a group of glycerol-phosphate acyltransferases (between trusted and noise to TIGR00530). A subset of these sequences including OMNI|CC1962, the Caulobacter crescentus CicA protein cluster together and may represent a separate equivalog. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 273654 [Multi-domain]  Cd Length: 202  Bit Score: 251.49  E-value: 9.83e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492529894    6 IAIFDFDGTLTRCDSLLPFLR-QAQPVILF-WLRLPFYLAMWMCYKLRLAPADRTKAAILSTVLKGKREVECRAMGQRFV 83
Cdd:TIGR01490   1 LAFFDFDGTLTAKDTLFIFLKfLASKNILFeELRLPKVLARFEFFLNRGLDYMAYYRAFALDALAGLLEEDVRAIVEEFV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492529894   84 PA-IESILRPEALRCLEWHRSEGHRLVLLTASLLPCVEPWAEKTGFHTVIAT-LPEIKSGILTGRFEGNNCKGKEKIHRL 161
Cdd:TIGR01490  81 NQkIESILYPEARDLIRWHKAEGHTIVLVSASLTILVKPLARILGIDNAIGTrLEESEDGIYTGNIDGNNCKGEGKVHAL 160

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 492529894  162 DRALPHWRDS--ISYGYGDSPSDRPLLSLCTHSYYRRF 197
Cdd:TIGR01490 161 AELLAEEQIDlkDSYAYGDSISDLPLLSLVGHPYVVNP 198
HAD_PGPPase cd02612
phosphatidylglycerol-phosphate phosphatase, similar to Escherichia coli K-12 ...
 7-195 4.51e-46

phosphatidylglycerol-phosphate phosphatase, similar to Escherichia coli K-12 phosphatidylglycerol-phosphate phosphatase C; This family includes Escherichia coli K-12 phosphatidylglycerol-phosphate phosphatase C, PgpC (previously named yfhB) which catalyzes the dephosphorylation of phosphatidylglycerol-phosphate (PGP) to phosphatidylglycerol (PG). 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: 319796 [Multi-domain]  Cd Length: 195  Bit Score: 150.53  E-value: 4.51e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492529894   7 AIFDFDGTLTRCDSLLPFLRQA----QPVILFWLRLPFYLAMwmcykLRLAPADRTKAAILSTVLKGKREVECRAMGQRF 82
Cdd:cd02612    2 AFFDLDGTLIAGDSFFAFLRFKgiaeRRAPLEELLLLRLMAL-----YALGRLDGAGMEALLGFATAGLAGELAALVEEF 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492529894  83 VPA-IESILRPEALRCLEWHRSEGHRLVLLTASLLPCVEPWAEKTGFHTVIATLPEIKSGILTGRFEGNNCKGKEKIHRL 161
Cdd:cd02612   77 VEEyILRVLYPEARELIAWHKAAGHDVVLISASPEELVAPIARKLGIDNVLGTQLETEDGRYTGRIIGPPCYGEGKVKRL 156

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 492529894 162 DR--ALPHWRDSISYGYGDSPSDRPLLSLCTHSYYR 195
Cdd:cd02612  157 REwlAEEGIDLKDSYAYSDSINDLPMLEAVGHPVAV 192
HAD pfam12710
haloacid dehalogenase-like hydrolase;
7-187 7.01e-39

haloacid dehalogenase-like hydrolase;


Pssm-ID: 432733 [Multi-domain]  Cd Length: 188  Bit Score: 131.89  E-value: 7.01e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492529894    7 AIFDFDGTLTRCDSLLPFLRQ--AQPVILFWlRLPFYLAMWMCYKLRLAPADRTKAAILSTVLKGKREVECRAMGQRFVP 84
Cdd:pfam12710   1 ALFDLDGTLLDGDSLFLLIRAllRRGGPDLW-RALLVLLLLALLRLLGRLSRAGARELLRALLAGLPEEDAAELERFVAE 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492529894   85 AIESILRPEALRCLEWHRSEGHRLVLLTASLLPCVEPWAEKTGFHTVIATLPEIKSGILTGR--FEGNNCKGKEKIHRLD 162
Cdd:pfam12710  80 VALPRLHPGALELLAAHRAAGDRVVVVTGGLRPLVEPVLAELGFDEVLATELEVDDGRFTGElrLIGPPCAGEGKVRRLR 159

                         170       180
                  ....*....|....*....|....*....
gi 492529894  163 RAL----PHWRDSISYGYGDSPSDRPLLS 187
Cdd:pfam12710 160 AWLaargLGLDLADSVAYGDSPSDLPMLR 188
SerB COG0560
Phosphoserine phosphatase [Amino acid transport and metabolism]; Phosphoserine phosphatase is ...
 6-193 1.89e-34

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: 121.48  E-value: 1.89e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492529894   6 IAIFDFDGTLTRCDSLLPFLRQA--QPVILFWLRLPFYLAMWMCYKLRLAPADRTKAAILSTvLKGKREVECRAMGQRFV 83
Cdd:COG0560    5 LAVFDLDGTLIAGESIDELARFLgrRGLVDRREVLEEVAAITERAMAGELDFEESLRFRVAL-LAGLPEEELEELAERLF 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492529894  84 pAIESILRPEALRCLEWHRSEGHRLVLLTASLLPCVEPWAEKTGFHTVIATLPEIKSGILTGRFEGNNCKGKEKIHRLDR 163
Cdd:COG0560   84 -EEVPRLYPGARELIAEHRAAGHKVAIVSGGFTFFVEPIAERLGIDHVIANELEVEDGRLTGEVVGPIVDGEGKAEALRE 162

                        170       180       190
                 ....*....|....*....|....*....|..
gi 492529894 164 --ALPHWRDSISYGYGDSPSDRPLLSLCTHSY 193
Cdd:COG0560  163 laAELGIDLEQSYAYGDSANDLPMLEAAGLPV 194
 
Name Accession Description Interval E-value
HAD-SF-IB-hyp1 TIGR01490
HAD-superfamily subfamily IB hydrolase, TIGR01490; This hypothetical equivalog is a member of ...
 6-197 9.83e-86

HAD-superfamily subfamily IB hydrolase, TIGR01490; This hypothetical equivalog is a member of the IB subfamily (TIGR01488) of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. The sequences modelled here are all bacterial. The IB subfamily includes the enzyme phosphoserine phosphatase (TIGR00338). Due to this relationship, several of these sequences have been annotated as "phosphoserine phosphatase related proteins," or "Phosphoserine phosphatase-family enzymes." There is presently no evidence that any of the enzymes in this model possess PSPase activity. OMNI|NTL01ML1250 is annotated as a "possible transferase," however this is due to the C-terminal domain found on this sequence which is homologous to a group of glycerol-phosphate acyltransferases (between trusted and noise to TIGR00530). A subset of these sequences including OMNI|CC1962, the Caulobacter crescentus CicA protein cluster together and may represent a separate equivalog. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 273654 [Multi-domain]  Cd Length: 202  Bit Score: 251.49  E-value: 9.83e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492529894    6 IAIFDFDGTLTRCDSLLPFLR-QAQPVILF-WLRLPFYLAMWMCYKLRLAPADRTKAAILSTVLKGKREVECRAMGQRFV 83
Cdd:TIGR01490   1 LAFFDFDGTLTAKDTLFIFLKfLASKNILFeELRLPKVLARFEFFLNRGLDYMAYYRAFALDALAGLLEEDVRAIVEEFV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492529894   84 PA-IESILRPEALRCLEWHRSEGHRLVLLTASLLPCVEPWAEKTGFHTVIAT-LPEIKSGILTGRFEGNNCKGKEKIHRL 161
Cdd:TIGR01490  81 NQkIESILYPEARDLIRWHKAEGHTIVLVSASLTILVKPLARILGIDNAIGTrLEESEDGIYTGNIDGNNCKGEGKVHAL 160

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 492529894  162 DRALPHWRDS--ISYGYGDSPSDRPLLSLCTHSYYRRF 197
Cdd:TIGR01490 161 AELLAEEQIDlkDSYAYGDSISDLPLLSLVGHPYVVNP 198
HAD_PGPPase cd02612
phosphatidylglycerol-phosphate phosphatase, similar to Escherichia coli K-12 ...
 7-195 4.51e-46

phosphatidylglycerol-phosphate phosphatase, similar to Escherichia coli K-12 phosphatidylglycerol-phosphate phosphatase C; This family includes Escherichia coli K-12 phosphatidylglycerol-phosphate phosphatase C, PgpC (previously named yfhB) which catalyzes the dephosphorylation of phosphatidylglycerol-phosphate (PGP) to phosphatidylglycerol (PG). 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: 319796 [Multi-domain]  Cd Length: 195  Bit Score: 150.53  E-value: 4.51e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492529894   7 AIFDFDGTLTRCDSLLPFLRQA----QPVILFWLRLPFYLAMwmcykLRLAPADRTKAAILSTVLKGKREVECRAMGQRF 82
Cdd:cd02612    2 AFFDLDGTLIAGDSFFAFLRFKgiaeRRAPLEELLLLRLMAL-----YALGRLDGAGMEALLGFATAGLAGELAALVEEF 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492529894  83 VPA-IESILRPEALRCLEWHRSEGHRLVLLTASLLPCVEPWAEKTGFHTVIATLPEIKSGILTGRFEGNNCKGKEKIHRL 161
Cdd:cd02612   77 VEEyILRVLYPEARELIAWHKAAGHDVVLISASPEELVAPIARKLGIDNVLGTQLETEDGRYTGRIIGPPCYGEGKVKRL 156

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 492529894 162 DR--ALPHWRDSISYGYGDSPSDRPLLSLCTHSYYR 195
Cdd:cd02612  157 REwlAEEGIDLKDSYAYSDSINDLPMLEAVGHPVAV 192
HAD pfam12710
haloacid dehalogenase-like hydrolase;
7-187 7.01e-39

haloacid dehalogenase-like hydrolase;


Pssm-ID: 432733 [Multi-domain]  Cd Length: 188  Bit Score: 131.89  E-value: 7.01e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492529894    7 AIFDFDGTLTRCDSLLPFLRQ--AQPVILFWlRLPFYLAMWMCYKLRLAPADRTKAAILSTVLKGKREVECRAMGQRFVP 84
Cdd:pfam12710   1 ALFDLDGTLLDGDSLFLLIRAllRRGGPDLW-RALLVLLLLALLRLLGRLSRAGARELLRALLAGLPEEDAAELERFVAE 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492529894   85 AIESILRPEALRCLEWHRSEGHRLVLLTASLLPCVEPWAEKTGFHTVIATLPEIKSGILTGR--FEGNNCKGKEKIHRLD 162
Cdd:pfam12710  80 VALPRLHPGALELLAAHRAAGDRVVVVTGGLRPLVEPVLAELGFDEVLATELEVDDGRFTGElrLIGPPCAGEGKVRRLR 159

                         170       180
                  ....*....|....*....|....*....
gi 492529894  163 RAL----PHWRDSISYGYGDSPSDRPLLS 187
Cdd:pfam12710 160 AWLaargLGLDLADSVAYGDSPSDLPMLR 188
SerB COG0560
Phosphoserine phosphatase [Amino acid transport and metabolism]; Phosphoserine phosphatase is ...
 6-193 1.89e-34

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: 121.48  E-value: 1.89e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492529894   6 IAIFDFDGTLTRCDSLLPFLRQA--QPVILFWLRLPFYLAMWMCYKLRLAPADRTKAAILSTvLKGKREVECRAMGQRFV 83
Cdd:COG0560    5 LAVFDLDGTLIAGESIDELARFLgrRGLVDRREVLEEVAAITERAMAGELDFEESLRFRVAL-LAGLPEEELEELAERLF 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492529894  84 pAIESILRPEALRCLEWHRSEGHRLVLLTASLLPCVEPWAEKTGFHTVIATLPEIKSGILTGRFEGNNCKGKEKIHRLDR 163
Cdd:COG0560   84 -EEVPRLYPGARELIAEHRAAGHKVAIVSGGFTFFVEPIAERLGIDHVIANELEVEDGRLTGEVVGPIVDGEGKAEALRE 162

                        170       180       190
                 ....*....|....*....|....*....|..
gi 492529894 164 --ALPHWRDSISYGYGDSPSDRPLLSLCTHSY 193
Cdd:COG0560  163 laAELGIDLEQSYAYGDSANDLPMLEAAGLPV 194
HAD-SF-IB TIGR01488
Haloacid Dehalogenase superfamily, subfamily IB, phosphoserine phosphatase-like; This model ...
 6-188 2.15e-26

Haloacid Dehalogenase superfamily, subfamily IB, phosphoserine phosphatase-like; This model represents a subfamily of the Haloacid Dehalogenase superfamily of aspartate-nucleophile hydrolases. Subfamily IA, B, C and D are distinguished from the rest of the superfamily by the presence of a variable domain between the first and second conserved catalytic motifs. In subfamilies IA and IB, this domain consists of an alpha-helical bundle. It was necessary to model these two subfamilies separately, breaking them at a an apparent phylogenetic bifurcation, so that the resulting model(s) are not so broadly defined that members of subfamily III (which lack the variable domain) are included. Subfamily IA includes the enzyme phosphoserine phosphatase (TIGR00338) as well as three hypothetical equivalogs. Many members of these hypothetical equivalogs have been annotated as PSPase-like or PSPase-family proteins. In particular, the hypothetical equivalog which appears to be most closely related to PSPase contains only Archaea (while TIGR00338 contains only eukaryotes and bacteria) of which some are annotated as PSPases. Although this is a reasonable conjecture, none of these sequences has sufficient evidence for this assignment. If such should be found, this model should be retired while the PSPase model should be broadened to include these sequences. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 273653 [Multi-domain]  Cd Length: 177  Bit Score: 99.35  E-value: 2.15e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492529894    6 IAIFDFDGTLTRCDSLLPFLRQAQPVILFWLRLpfyLAMWMCYKLRLAPADRTKAAILSTVLKGKREVECRAmgqrfvpa 85
Cdd:TIGR01488   1 LAIFDFDGTLTRQDSLIDLLAKLLGTNDEVIEL---TRLAPSGRISFEDALGRRLALLHRSRSEEVAKEFLA-------- 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492529894   86 IESILRPEALRCLEWHRSEGHRLVLLTASLLPCVEPWAEKTGFHTVIATLPEI-KSGILTGRFEG-----NNCKGKeKIH 159
Cdd:TIGR01488  70 RQVALRPGARELISWLKERGIDTVIVSGGFDFFVEPVAEKLGIDDVFANRLEFdDNGLLTGPIEGqvnpeGECKGK-VLK 148

                         170       180
                  ....*....|....*....|....*....
gi 492529894  160 RLDRALPHWRDSISYgYGDSPSDRPLLSL 188
Cdd:TIGR01488 149 ELLEESKITLKKIIA-VGDSVNDLPMLKL 176
 
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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