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Conserved domains on  [gi|654546383|ref|WP_028014089|]
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MULTISPECIES: phosphatidylglycerophosphatase C [Enterobacter]

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 ...
 2-211 5.98e-129

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 TIGR01545:

Pssm-ID: 473868  Cd Length: 210  Bit Score: 361.56  E-value: 5.98e-129
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 654546383    2 ANHERRVVFFDLDGTLHQQDMFGTFMRYLLRRQPLNALLVLPLLPLIGIALLVKGRAARWPMSLLLWGCTFGHSEARLKQ 81
Cdd:TIGR01545   1 AAGAKRIIFFDLDGTLHQQDMFGSFLRFLLRHLPLNALLVIPLLPIIAIALLIGGRAARWPMSLLLWACTFGHREAHLQD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 654546383   82 LEKEFALWFRGHVAAFPVVQARLTSYLDANDADIWLITGSPQTLVEQVYFDTPWLPRVNLIATQISRGYGGWVLTMRCLG 161
Cdd:TIGR01545  81 LEADFVAAFRDKVTAFPLVAERLRQYLESSDADIWLITGSPQPLVEAVYFDSNFIHRLNLIASQIERGNGGWVLPLRCLG 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 654546383  162 HEKVVQLEKRIGTPLRLYSGYSDSKQDNPLLYFCQHRWRVTPLGELQQLE 211
Cdd:TIGR01545 161 HEKVAQLEQKIGSPLKLYSGYSDSKQDNPLLAFCEHRWRVSKRGELQQLE 210
 
Name Accession Description Interval E-value
YfhB_g-proteo TIGR01545
haloacid dehalogenase superfamily, subfamily IF hydrolase, YfhB; This model describes a clade ...
 2-211 5.98e-129

haloacid dehalogenase superfamily, subfamily IF hydrolase, YfhB; This model describes a clade of sequences limited to the gamma proteobacteria. This group is a member of the haloacid dehalogenase (HAD) superfamily of aspartate-dependent hydrolases and all of the conserved catalytic motifs are present. Although structurally similar to subfamily IA in that the variable domain is predicted to consist of five consecutive alpha helices (by PSI-PRED), it is sufficiently divergent to warrant being regarded as a separate sub-family (IF). The gene name comes from the E. coli gene. There is currently no information regarding the function of this gene.


Pssm-ID: 130608  Cd Length: 210  Bit Score: 361.56  E-value: 5.98e-129
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 654546383    2 ANHERRVVFFDLDGTLHQQDMFGTFMRYLLRRQPLNALLVLPLLPLIGIALLVKGRAARWPMSLLLWGCTFGHSEARLKQ 81
Cdd:TIGR01545   1 AAGAKRIIFFDLDGTLHQQDMFGSFLRFLLRHLPLNALLVIPLLPIIAIALLIGGRAARWPMSLLLWACTFGHREAHLQD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 654546383   82 LEKEFALWFRGHVAAFPVVQARLTSYLDANDADIWLITGSPQTLVEQVYFDTPWLPRVNLIATQISRGYGGWVLTMRCLG 161
Cdd:TIGR01545  81 LEADFVAAFRDKVTAFPLVAERLRQYLESSDADIWLITGSPQPLVEAVYFDSNFIHRLNLIASQIERGNGGWVLPLRCLG 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 654546383  162 HEKVVQLEKRIGTPLRLYSGYSDSKQDNPLLYFCQHRWRVTPLGELQQLE 211
Cdd:TIGR01545 161 HEKVAQLEQKIGSPLKLYSGYSDSKQDNPLLAFCEHRWRVSKRGELQQLE 210
HAD_PGPPase cd02612
phosphatidylglycerol-phosphate phosphatase, similar to Escherichia coli K-12 ...
 9-203 7.33e-37

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: 127.42  E-value: 7.33e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 654546383   9 VFFDLDGTLHQQDMFGTFMRYLLRRQPLNALLVLPLLPLigIALLVKGRAARWPMSLLLWGCTFGHSEaRLKQLEKEFAL 88
Cdd:cd02612    2 AFFDLDGTLIAGDSFFAFLRFKGIAERRAPLEELLLLRL--MALYALGRLDGAGMEALLGFATAGLAG-ELAALVEEFVE 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 654546383  89 WFRGHVaAFPVVQARLTSYLDANDaDIWLITGSPqTLVEQVYFDTPWLPrvNLIATQ--ISRGYGGWVLTMR-CLGHEKV 165
Cdd:cd02612   79 EYILRV-LYPEARELIAWHKAAGH-DVVLISASP-EELVAPIARKLGID--NVLGTQleTEDGRYTGRIIGPpCYGEGKV 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 654546383 166 VQLEKRI---GTPLRLYSGYSDSKQDNPLLYFCQHRWRVTP 203
Cdd:cd02612  154 KRLREWLaeeGIDLKDSYAYSDSINDLPMLEAVGHPVAVNP 194
HAD pfam12710
haloacid dehalogenase-like hydrolase;
9-192 4.00e-10

haloacid dehalogenase-like hydrolase;


Pssm-ID: 432733 [Multi-domain]  Cd Length: 188  Bit Score: 56.77  E-value: 4.00e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 654546383    9 VFFDLDGTLHQQDMFGTFMRYLLRRQPLNALLVLPLLPLIGIALLVkGRAARWPMSLLLWGCTFGHSEARLKQLEKEFAL 88
Cdd:pfam12710   1 ALFDLDGTLLDGDSLFLLIRALLRRGGPDLWRALLVLLLLALLRLL-GRLSRAGARELLRALLAGLPEEDAAELERFVAE 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 654546383   89 WFRGhvAAFPVVQARLTSYLDANDAdIWLITGSPQTLVEqvyfdtPWLPRV---NLIATQISRGY----GGWVLTMR-CL 160
Cdd:pfam12710  80 VALP--RLHPGALELLAAHRAAGDR-VVVVTGGLRPLVE------PVLAELgfdEVLATELEVDDgrftGELRLIGPpCA 150

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 654546383  161 GHEKVVQLEKRIG------TPLRLYsGYSDSKQDNPLL 192
Cdd:pfam12710 151 GEGKVRRLRAWLAarglglDLADSV-AYGDSPSDLPML 187
SerB COG0560
Phosphoserine phosphatase [Amino acid transport and metabolism]; Phosphoserine phosphatase is ...
 5-192 2.49e-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: 46.37  E-value: 2.49e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 654546383   5 ERRVVFFDLDGTLHQQDMFGTFMRYLLRRQPLNALLVLPLLPLIgIALLVKGRAARWPMSLLLWGCTFGHSEARLKQLEK 84
Cdd:COG0560    2 KMRLAVFDLDGTLIAGESIDELARFLGRRGLVDRREVLEEVAAI-TERAMAGELDFEESLRFRVALLAGLPEEELEELAE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 654546383  85 EFalwFRGHVAAFPVVQARLTSYLDANDaDIWLITGSPQTLVEqvyfdtPWLPRVNL---IATQ--ISRG-YGGWVLTMR 158
Cdd:COG0560   81 RL---FEEVPRLYPGARELIAEHRAAGH-KVAIVSGGFTFFVE------PIAERLGIdhvIANEleVEDGrLTGEVVGPI 150

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 654546383 159 CLGHEKVVQLE---KRIGTPLRLYSGYSDSKQDNPLL 192
Cdd:COG0560  151 VDGEGKAEALRelaAELGIDLEQSYAYGDSANDLPML 187
 
Name Accession Description Interval E-value
YfhB_g-proteo TIGR01545
haloacid dehalogenase superfamily, subfamily IF hydrolase, YfhB; This model describes a clade ...
 2-211 5.98e-129

haloacid dehalogenase superfamily, subfamily IF hydrolase, YfhB; This model describes a clade of sequences limited to the gamma proteobacteria. This group is a member of the haloacid dehalogenase (HAD) superfamily of aspartate-dependent hydrolases and all of the conserved catalytic motifs are present. Although structurally similar to subfamily IA in that the variable domain is predicted to consist of five consecutive alpha helices (by PSI-PRED), it is sufficiently divergent to warrant being regarded as a separate sub-family (IF). The gene name comes from the E. coli gene. There is currently no information regarding the function of this gene.


Pssm-ID: 130608  Cd Length: 210  Bit Score: 361.56  E-value: 5.98e-129
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 654546383    2 ANHERRVVFFDLDGTLHQQDMFGTFMRYLLRRQPLNALLVLPLLPLIGIALLVKGRAARWPMSLLLWGCTFGHSEARLKQ 81
Cdd:TIGR01545   1 AAGAKRIIFFDLDGTLHQQDMFGSFLRFLLRHLPLNALLVIPLLPIIAIALLIGGRAARWPMSLLLWACTFGHREAHLQD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 654546383   82 LEKEFALWFRGHVAAFPVVQARLTSYLDANDADIWLITGSPQTLVEQVYFDTPWLPRVNLIATQISRGYGGWVLTMRCLG 161
Cdd:TIGR01545  81 LEADFVAAFRDKVTAFPLVAERLRQYLESSDADIWLITGSPQPLVEAVYFDSNFIHRLNLIASQIERGNGGWVLPLRCLG 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 654546383  162 HEKVVQLEKRIGTPLRLYSGYSDSKQDNPLLYFCQHRWRVTPLGELQQLE 211
Cdd:TIGR01545 161 HEKVAQLEQKIGSPLKLYSGYSDSKQDNPLLAFCEHRWRVSKRGELQQLE 210
HAD_PGPPase cd02612
phosphatidylglycerol-phosphate phosphatase, similar to Escherichia coli K-12 ...
 9-203 7.33e-37

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: 127.42  E-value: 7.33e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 654546383   9 VFFDLDGTLHQQDMFGTFMRYLLRRQPLNALLVLPLLPLigIALLVKGRAARWPMSLLLWGCTFGHSEaRLKQLEKEFAL 88
Cdd:cd02612    2 AFFDLDGTLIAGDSFFAFLRFKGIAERRAPLEELLLLRL--MALYALGRLDGAGMEALLGFATAGLAG-ELAALVEEFVE 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 654546383  89 WFRGHVaAFPVVQARLTSYLDANDaDIWLITGSPqTLVEQVYFDTPWLPrvNLIATQ--ISRGYGGWVLTMR-CLGHEKV 165
Cdd:cd02612   79 EYILRV-LYPEARELIAWHKAAGH-DVVLISASP-EELVAPIARKLGID--NVLGTQleTEDGRYTGRIIGPpCYGEGKV 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 654546383 166 VQLEKRI---GTPLRLYSGYSDSKQDNPLLYFCQHRWRVTP 203
Cdd:cd02612  154 KRLREWLaeeGIDLKDSYAYSDSINDLPMLEAVGHPVAVNP 194
HAD pfam12710
haloacid dehalogenase-like hydrolase;
9-192 4.00e-10

haloacid dehalogenase-like hydrolase;


Pssm-ID: 432733 [Multi-domain]  Cd Length: 188  Bit Score: 56.77  E-value: 4.00e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 654546383    9 VFFDLDGTLHQQDMFGTFMRYLLRRQPLNALLVLPLLPLIGIALLVkGRAARWPMSLLLWGCTFGHSEARLKQLEKEFAL 88
Cdd:pfam12710   1 ALFDLDGTLLDGDSLFLLIRALLRRGGPDLWRALLVLLLLALLRLL-GRLSRAGARELLRALLAGLPEEDAAELERFVAE 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 654546383   89 WFRGhvAAFPVVQARLTSYLDANDAdIWLITGSPQTLVEqvyfdtPWLPRV---NLIATQISRGY----GGWVLTMR-CL 160
Cdd:pfam12710  80 VALP--RLHPGALELLAAHRAAGDR-VVVVTGGLRPLVE------PVLAELgfdEVLATELEVDDgrftGELRLIGPpCA 150

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 654546383  161 GHEKVVQLEKRIG------TPLRLYsGYSDSKQDNPLL 192
Cdd:pfam12710 151 GEGKVRRLRAWLAarglglDLADSV-AYGDSPSDLPML 187
HAD-SF-IB-hyp1 TIGR01490
HAD-superfamily subfamily IB hydrolase, TIGR01490; This hypothetical equivalog is a member of ...
 9-207 1.32e-06

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: 46.95  E-value: 1.32e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 654546383    9 VFFDLDGTLHQQDMFGTFMRYLLRRQPLNALLVLPLLPLIGIALLVKGRAARWPMSLLLWGCTFGHSEARLKQLEKEFA- 87
Cdd:TIGR01490   2 AFFDFDGTLTAKDTLFIFLKFLASKNILFEELRLPKVLARFEFFLNRGLDYMAYYRAFALDALAGLLEEDVRAIVEEFVn 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 654546383   88 LWFRGHVaaFPVVQARLTSYLDANDaDIWLITGSPQTLVEQVY----FDtpwlprvNLIATQISRG----YGGWVLTMRC 159
Cdd:TIGR01490  82 QKIESIL--YPEARDLIRWHKAEGH-TIVLVSASLTILVKPLArilgID-------NAIGTRLEESedgiYTGNIDGNNC 151

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 654546383  160 LGHEKVVQL-----EKRIgtPLRLYSGYSDSKQDNPLLYFCQHRWRVTPLGEL 207
Cdd:TIGR01490 152 KGEGKVHALaellaEEQI--DLKDSYAYGDSISDLPLLSLVGHPYVVNPDKKL 202
SerB COG0560
Phosphoserine phosphatase [Amino acid transport and metabolism]; Phosphoserine phosphatase is ...
 5-192 2.49e-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: 46.37  E-value: 2.49e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 654546383   5 ERRVVFFDLDGTLHQQDMFGTFMRYLLRRQPLNALLVLPLLPLIgIALLVKGRAARWPMSLLLWGCTFGHSEARLKQLEK 84
Cdd:COG0560    2 KMRLAVFDLDGTLIAGESIDELARFLGRRGLVDRREVLEEVAAI-TERAMAGELDFEESLRFRVALLAGLPEEELEELAE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 654546383  85 EFalwFRGHVAAFPVVQARLTSYLDANDaDIWLITGSPQTLVEqvyfdtPWLPRVNL---IATQ--ISRG-YGGWVLTMR 158
Cdd:COG0560   81 RL---FEEVPRLYPGARELIAEHRAAGH-KVAIVSGGFTFFVE------PIAERLGIdhvIANEleVEDGrLTGEVVGPI 150

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 654546383 159 CLGHEKVVQLE---KRIGTPLRLYSGYSDSKQDNPLL 192
Cdd:COG0560  151 VDGEGKAEALRelaAELGIDLEQSYAYGDSANDLPML 187
 
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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