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Conserved domains on  [gi|2067386778|dbj|GJA64146|]
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phospholipase [Aeromonas caviae]

Protein Classification

phospholipase D-like domain-containing protein( domain architecture ID 11445347)

phospholipase D-like domain-containing protein; similar to Bacillus subtilis minor cardiolipin synthase ClsB involved in the biosynthesis of cardiolipin

EC:  3.1.4.-
Gene Ontology:  GO:0016780
PubMed:  10425395|15052340|10818442

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 5-411 3.76e-77

Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and metabolism]; Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase is part of the Pathway/BioSystem: Phospholipid biosynthesis


:

Pssm-ID: 441111 [Multi-domain]  Cd Length: 367  Bit Score: 243.70  E-value: 3.76e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778   5 DFALLADPGAALKARCQLIRQARHRILAQYYSWEEDGSGKLLLAELVRAARRGVVVQLLIDDL--YGGENRFLEAVAAeP 82
Cdd:COG1502    16 RVTLLVDGDEAFAALLEAIEAARRSIDLEYYIFDDDEVGRRLADALIAAARRGVKVRVLLDGIgsRALNRDFLRRLRA-A 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778  83 GIEVRLFNPFWLRgwrpltlllegvlsFRRINHRMHNKLLLVDGSQAVIGGRNIGDRYFGLGM-PPHFIDLDLVCRGPLC 161
Cdd:COG1502    95 GVEVRLFNPVRLL--------------FRRLNGRNHRKIVVIDGRVAFVGGANITDEYLGRDPgFGPWRDTHVRIEGPAV 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778 162 QQAEQGFALFWHSRWSHPvrrllrrpllpaetralndflltLTDPAMAAAYDLpatlfdecpvplcwhpgrgQCWFDRPG 241
Cdd:COG1502   161 ADLQAVFAEDWNFATGEA-----------------------LPFPEPAGDVRV-------------------QVVPSGPD 198

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778 242 KglvARPTTAPLLGRMLASNQGALRLVSPYLILTRGLRRRLKGQRRQGVDIEILTNslASTDVPLVYGAYRRHRPWLERQ 321
Cdd:COG1502   199 S---PRETIERALLAAIASARRRIYIETPYFVPDRSLLRALIAAARRGVDVRILLP--AKSDHPLVHWASRSYYEELLEA 273

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778 322 GVTLFELttEAFSLHAKLILMGKEEALLGSFNLDPRSLMLNTELMLHLHSPTLCDELQQLIDGWLQQA--VHPVAASPSA 399
Cdd:COG1502   274 GVRIYEY--EPGFLHAKVMVVDDEWALVGSANLDPRSLRLNFEVNLVIYDPEFAAQLRARFEEDLAHSreVTLEEWRKRP 351

                         410
                  ....*....|..
gi 2067386778 400 WRRLLAQLSDWL 411
Cdd:COG1502   352 LRRLRERLARLL 363
 
Name Accession Description Interval E-value
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 5-411 3.76e-77

Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and metabolism]; Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase is part of the Pathway/BioSystem: Phospholipid biosynthesis


Pssm-ID: 441111 [Multi-domain]  Cd Length: 367  Bit Score: 243.70  E-value: 3.76e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778   5 DFALLADPGAALKARCQLIRQARHRILAQYYSWEEDGSGKLLLAELVRAARRGVVVQLLIDDL--YGGENRFLEAVAAeP 82
Cdd:COG1502    16 RVTLLVDGDEAFAALLEAIEAARRSIDLEYYIFDDDEVGRRLADALIAAARRGVKVRVLLDGIgsRALNRDFLRRLRA-A 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778  83 GIEVRLFNPFWLRgwrpltlllegvlsFRRINHRMHNKLLLVDGSQAVIGGRNIGDRYFGLGM-PPHFIDLDLVCRGPLC 161
Cdd:COG1502    95 GVEVRLFNPVRLL--------------FRRLNGRNHRKIVVIDGRVAFVGGANITDEYLGRDPgFGPWRDTHVRIEGPAV 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778 162 QQAEQGFALFWHSRWSHPvrrllrrpllpaetralndflltLTDPAMAAAYDLpatlfdecpvplcwhpgrgQCWFDRPG 241
Cdd:COG1502   161 ADLQAVFAEDWNFATGEA-----------------------LPFPEPAGDVRV-------------------QVVPSGPD 198

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778 242 KglvARPTTAPLLGRMLASNQGALRLVSPYLILTRGLRRRLKGQRRQGVDIEILTNslASTDVPLVYGAYRRHRPWLERQ 321
Cdd:COG1502   199 S---PRETIERALLAAIASARRRIYIETPYFVPDRSLLRALIAAARRGVDVRILLP--AKSDHPLVHWASRSYYEELLEA 273

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778 322 GVTLFELttEAFSLHAKLILMGKEEALLGSFNLDPRSLMLNTELMLHLHSPTLCDELQQLIDGWLQQA--VHPVAASPSA 399
Cdd:COG1502   274 GVRIYEY--EPGFLHAKVMVVDDEWALVGSANLDPRSLRLNFEVNLVIYDPEFAAQLRARFEEDLAHSreVTLEEWRKRP 351

                         410
                  ....*....|..
gi 2067386778 400 WRRLLAQLSDWL 411
Cdd:COG1502   352 LRRLRERLARLL 363
PLDc_ymdC_like_1 cd09111
Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and ...
 9-173 7.76e-71

Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and similar proteins; Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and similar proteins. In Escherichia coli, there are two genes, f413 (ybhO) and o493 (ymdC), which are homologous to gene cls that encodes the Escherichia coli cardiolipin (CL) synthase. The prototype of this subfamily is an uncharacterized protein ymdC specified by the o493 (ymdC) gene. Although the functional characterization of ymdC and similar proteins remains unknown, members of this subfamily show high sequence homology to bacterial CL synthases, which catalyze the reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form CL and glycerol. Moreover, ymdC and its similar proteins contain two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characteriszes the phospholipase D (PLD) superfamily. The two motifs may be part of the active site and may be involved in phosphatidyl group transfer.


Pssm-ID: 197210 [Multi-domain]  Cd Length: 162  Bit Score: 220.10  E-value: 7.76e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778   9 LADPGAALKARCQLIRQARHRILAQYYSWEEDGSGKLLLAELVRAARRGVVVQLLIDDLY-GGENRFLEAVAAEPGIEVR 87
Cdd:cd09111     1 LEDGLDALAARLALIRSAERSIDLQYYIWHDDESGRLLLGELLEAADRGVRVRLLLDDLGtSGRDRLLAALDAHPNIEVR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778  88 LFNPFWLRGWRpltlLLEGVLSFRRINHRMHNKLLLVDGSQAVIGGRNIGDRYFGLGMPPHFIDLDLVCRGPLCQQAEQG 167
Cdd:cd09111    81 LFNPFRNRGGR----LLEFLTDFSRLNRRMHNKLFIVDGAVAIVGGRNIGDEYFGASPEVNFRDLDVLAVGPVVRQLSES 156


                  ....*.
gi 2067386778 168 FALFWH 173
Cdd:cd09111   157 FDTYWN 162
cls PRK01642
cardiolipin synthetase; Reviewed
 8-408 8.49e-28

cardiolipin synthetase; Reviewed


Pssm-ID: 234967 [Multi-domain]  Cd Length: 483  Bit Score: 114.49  E-value: 8.49e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778   8 LLADPGAALKARCQLIRQARHRILAQYYSWEEDGSGKLLLAELVRAARRGVVVQLLIDDLygGENRFLEAVAAE----PG 83
Cdd:PRK01642  120 LLTNGDETFQAIIRDIELARHYILMEFYIWRPDGLGDQVAEALIAAAKRGVRVRLLYDSI--GSFAFFRSPYPEelrnAG 197

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778  84 IEVRLF---NPFWLRgwrpltlllegvlsFRRINHRMHNKLLLVDGSQAVIGGRNIGD-RYFG----LGmppHFIDLDLV 155
Cdd:PRK01642  198 VEVVEFlkvNLGRVF--------------RRRLDLRNHRKIVVIDGYIAYTGSMNVVDpEYFKqdpgVG---QWRDTHVR 260

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778 156 CRGPLCQQAEQGFALFWHsrWshpvrrllrrpllpaETRALndflltltdpamaAAYDLPatlfdECPVPLCWHPGRGQC 235
Cdd:PRK01642  261 IEGPVVTALQLIFAEDWE--W---------------ETGER-------------ILPPPP-----DVLIMPFEEASGHTV 305

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778 236 WFDRPGKGlVARPTTAPLLGRMLASNQGALRLVSPYLILTRGLRRRLKGQRRQGVDIEILTNSLAstDVPLVYGAYRRHR 315
Cdd:PRK01642  306 QVIASGPG-DPEETIHQFLLTAIYSARERLWITTPYFVPDEDLLAALKTAALRGVDVRIIIPSKN--DSLLVFWASRAFF 382

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778 316 PWLERQGVTLFELtTEAFsLHAKLILMGKEEALLGSFNLDPRSLMLNTELMLHLHSPTLCDELQQLIDGWLQQAvHPVAA 395
Cdd:PRK01642  383 TELLEAGVKIYRY-EGGL-LHTKSVLVDDELALVGTVNLDMRSFWLNFEITLVIDDTGFAADLAAMQEDYFARS-RELDL 459

                         410
                  ....*....|....*..
gi 2067386778 396 SP----SAWRRLLAQLS 408
Cdd:PRK01642  460 EEwrkrPLWQRIAERVA 476
bac_cardiolipin TIGR04265
cardiolipin synthase; This model is based on experimentally characterized bacterial ...
 21-380 1.09e-27

cardiolipin synthase; This model is based on experimentally characterized bacterial cardiolipin synthases (cls) from E. coli, Staphylococcus aureus (two), and Bacillus pseudofirmus OF4. This model describes just one of several homologous but non-orthologous forms of cls. The cutoff score is set arbitrarily high to avoid false-positives. Note that there are two enzymatic activites called cardiolipin synthase. This model represents type 1, which does not rely on a CDP-linked donor, but instead does a reversible transfer of a phosphatidyl group from one phosphatidylglycerol molecule to another.


Pssm-ID: 211988 [Multi-domain]  Cd Length: 483  Bit Score: 114.50  E-value: 1.09e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778  21 QLIRQARHRILAQYYSWEEDGSGKLLLAELVRAARRGVVVQLLIDDLyGGENRFLEAVaaEP----GIEVRLFNPFWLrg 96
Cdd:TIGR04265 136 QDIKNARHYIHLEYYIWQPDGLGDQILESLMAKAKQGVHVRILYDDV-GSVALFKSWP--ELfrnaGGEVVAFFPVKL-- 210

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778  97 wrpltlllegVLSFRRINHRMHNKLLLVDGSQAVIGGRNIGDRYFGLGMP-PHFIDLDLVCRGPLCQQAEQGFALFWHSR 175
Cdd:TIGR04265 211 ----------PLLNLRMNNRNHRKIIVIDGQIGYVGGFNIGDEYLGKDAKfGYWRDTHLRIEGDAVTALQLIFILDWNSQ 280

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778 176 WSHPVRRLlrrpllpaETRALNDFLLTLTDPAMAAAYDLPATLfdecpvplcWHpgrgqcwfdrpgkglvarpTTAPLLG 255
Cdd:TIGR04265 281 TGRRIIPY--------DPDYFPMPNEQAGGHGIQIIASGPDFP---------WE-------------------QIKYGYL 324

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778 256 RMLASNQGALRLVSPYLILTRGLRRRLKGQRRQGVDIEILTNSlaSTDVPLVYGAYRRHRPWLERQGVTLFELttEAFSL 335
Cdd:TIGR04265 325 KMIYSAKKSIYIQSPYFIPDDDLLHAIKIAALSGVDVSIMIPN--KPDHPLVFWASRSNFTELLAAGVKIYQY--ENGFL 400

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*
gi 2067386778 336 HAKLILMGKEEALLGSFNLDPRSLMLNTELMLHLHSPTLCDELQQ 380
Cdd:TIGR04265 401 HSKSVLVDDEIASVGTANMDMRSFWLNFEVNAFIYDKGFAKDLAA 445
PLDc_2 pfam13091
PLD-like domain;
256-383 2.04e-18

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 80.80  E-value: 2.04e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778 256 RMLASNQGALRLVSPYLILTRGLRRRLKGQRRQGVDIEILTNSLAStDVPLVYGAYRRHRPWLERQGVTLFELTTEAFSL 335
Cdd:pfam13091   3 DLINSAKKSIDIATYYFVPDREIIDALIAAAKRGVDVRIILDSNKD-DAGGPKKASLKELRSLLRAGVEIREYQSFLRSM 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 2067386778 336 HAKLILMGKEEALLGSFNLDPRSLMLNTELMLHLHSPTLCDELQQLID 383
Cdd:pfam13091  82 HAKFYIIDGKTVIVGSANLTRRALRLNLENNVVIKDPELAQELEKEFD 129
PLDc smart00155
Phospholipase D. Active site motifs; Phosphatidylcholine-hydrolyzing phospholipase D (PLD) ...
 116-140 7.69e-04

Phospholipase D. Active site motifs; Phosphatidylcholine-hydrolyzing phospholipase D (PLD) isoforms are activated by ADP-ribosylation factors (ARFs). PLD produces phosphatidic acid from phosphatidylcholine, which may be essential for the formation of certain types of transport vesicles or may be constitutive vesicular transport to signal transduction pathways. PC-hydrolysing PLD is a homologue of cardiolipin synthase, phosphatidylserine synthase, bacterial PLDs, and viral proteins. Each of these appears to possess a domain duplication which is apparent by the presence of two motifs containing well-conserved histidine, lysine, aspartic acid, and/or asparagine residues which may contribute to the active site. An E. coli endonuclease (nuc) and similar proteins appear to be PLD homologues but possess only one of these motifs. The profile contained here represents only the putative active site regions, since an accurate multiple alignment of the repeat units has not been achieved.


Pssm-ID: 197546 [Multi-domain]  Cd Length: 28  Bit Score: 36.60  E-value: 7.69e-04
                           10        20
                   ....*....|....*....|....*
gi 2067386778  116 RMHNKLLLVDGSQAVIGGRNIGDRY 140
Cdd:smart00155   4 VLHTKLMIVDDEIAYIGSANLDGRS 28
 
Name Accession Description Interval E-value
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 5-411 3.76e-77

Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and metabolism]; Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase is part of the Pathway/BioSystem: Phospholipid biosynthesis


Pssm-ID: 441111 [Multi-domain]  Cd Length: 367  Bit Score: 243.70  E-value: 3.76e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778   5 DFALLADPGAALKARCQLIRQARHRILAQYYSWEEDGSGKLLLAELVRAARRGVVVQLLIDDL--YGGENRFLEAVAAeP 82
Cdd:COG1502    16 RVTLLVDGDEAFAALLEAIEAARRSIDLEYYIFDDDEVGRRLADALIAAARRGVKVRVLLDGIgsRALNRDFLRRLRA-A 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778  83 GIEVRLFNPFWLRgwrpltlllegvlsFRRINHRMHNKLLLVDGSQAVIGGRNIGDRYFGLGM-PPHFIDLDLVCRGPLC 161
Cdd:COG1502    95 GVEVRLFNPVRLL--------------FRRLNGRNHRKIVVIDGRVAFVGGANITDEYLGRDPgFGPWRDTHVRIEGPAV 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778 162 QQAEQGFALFWHSRWSHPvrrllrrpllpaetralndflltLTDPAMAAAYDLpatlfdecpvplcwhpgrgQCWFDRPG 241
Cdd:COG1502   161 ADLQAVFAEDWNFATGEA-----------------------LPFPEPAGDVRV-------------------QVVPSGPD 198

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778 242 KglvARPTTAPLLGRMLASNQGALRLVSPYLILTRGLRRRLKGQRRQGVDIEILTNslASTDVPLVYGAYRRHRPWLERQ 321
Cdd:COG1502   199 S---PRETIERALLAAIASARRRIYIETPYFVPDRSLLRALIAAARRGVDVRILLP--AKSDHPLVHWASRSYYEELLEA 273

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778 322 GVTLFELttEAFSLHAKLILMGKEEALLGSFNLDPRSLMLNTELMLHLHSPTLCDELQQLIDGWLQQA--VHPVAASPSA 399
Cdd:COG1502   274 GVRIYEY--EPGFLHAKVMVVDDEWALVGSANLDPRSLRLNFEVNLVIYDPEFAAQLRARFEEDLAHSreVTLEEWRKRP 351

                         410
                  ....*....|..
gi 2067386778 400 WRRLLAQLSDWL 411
Cdd:COG1502   352 LRRLRERLARLL 363
PLDc_ymdC_like_1 cd09111
Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and ...
 9-173 7.76e-71

Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and similar proteins; Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and similar proteins. In Escherichia coli, there are two genes, f413 (ybhO) and o493 (ymdC), which are homologous to gene cls that encodes the Escherichia coli cardiolipin (CL) synthase. The prototype of this subfamily is an uncharacterized protein ymdC specified by the o493 (ymdC) gene. Although the functional characterization of ymdC and similar proteins remains unknown, members of this subfamily show high sequence homology to bacterial CL synthases, which catalyze the reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form CL and glycerol. Moreover, ymdC and its similar proteins contain two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characteriszes the phospholipase D (PLD) superfamily. The two motifs may be part of the active site and may be involved in phosphatidyl group transfer.


Pssm-ID: 197210 [Multi-domain]  Cd Length: 162  Bit Score: 220.10  E-value: 7.76e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778   9 LADPGAALKARCQLIRQARHRILAQYYSWEEDGSGKLLLAELVRAARRGVVVQLLIDDLY-GGENRFLEAVAAEPGIEVR 87
Cdd:cd09111     1 LEDGLDALAARLALIRSAERSIDLQYYIWHDDESGRLLLGELLEAADRGVRVRLLLDDLGtSGRDRLLAALDAHPNIEVR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778  88 LFNPFWLRGWRpltlLLEGVLSFRRINHRMHNKLLLVDGSQAVIGGRNIGDRYFGLGMPPHFIDLDLVCRGPLCQQAEQG 167
Cdd:cd09111    81 LFNPFRNRGGR----LLEFLTDFSRLNRRMHNKLFIVDGAVAIVGGRNIGDEYFGASPEVNFRDLDVLAVGPVVRQLSES 156


                  ....*.
gi 2067386778 168 FALFWH 173
Cdd:cd09111   157 FDTYWN 162
PLDc_ymdC_like_2 cd09113
Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and ...
 236-413 4.41e-48

Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and similar proteins; Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and similar proteins. In Escherichia coli, there are two genes, f413 (ybhO) and o493 (ymdC), which are homologous to gene cls that encodes the Escherichia coli cardiolipin (CL) synthase. The prototype of this subfamily is an uncharacterized protein ymdC specified by the o493 (ymdC) gene. Although the functional characterization of ymdC and similar proteins remains unknown, members of this subfamily show high sequence homology to bacterial CL synthases, which catalyze the reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form CL and glycerol. Moreover, ymdC and its similar proteins contain two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characteriszes the phospholipase D (PLD) superfamily. The two motifs may be part of the active site and may be involved in phosphatidyl group transfer.


Pssm-ID: 197212 [Multi-domain]  Cd Length: 218  Bit Score: 163.16  E-value: 4.41e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778 236 WFDRPGKGLVARPTTAPLLGRMLASNQGA---LRLVSPYLILTRGLRRRLKGQRRQGVDIEILTNSLASTDVPLVYGAYR 312
Cdd:cd09113     1 LSDPPEKALKEAGPEPVLAYQLAELLKNAkreVLIVSPYFVPGDEGVALLAELARRGVRVRILTNSLAATDVPAVHSGYA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778 313 RHRPWLERQGVTLFEL--------------TTEAFSLHAKLILMGKEEALLGSFNLDPRSLMLNTELMLHLHSPTLCDEL 378
Cdd:cd09113    81 RYRKRLLKAGVELYELkpdaakrkrlrglfGSSRASLHAKSFVIDDRLVFVGSFNLDPRSAYLNTEMGLVIDSPELAAQL 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2067386778 379 QQLIDGWLQQAVHPVAASP-----------------------SAWRRLLAQLSDWLPL 413
Cdd:cd09113   161 RAAMEEDLAPSAYWVLLLDdgglvweteedgkekeydsepetSFWRRLGAWLLSLLPI 218
PLDc_CLS_1 cd09110
Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Catalytic ...
 14-173 3.94e-38

Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Catalytic domain, repeat 1, of bacterial cardiolipin (CL) synthase and a few homologs found in eukaryotes and archaea. Bacterial CL synthases catalyze the reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form CL and glycerol. The monomer of bacterial CL synthase consists of two catalytic domains. Each catalytic domain contains one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. Two HKD motifs from two domains form a single active site involved in phosphatidyl group transfer. Bacterial CL synthases can be stimulated by phosphate and inhibited by CL, the product of the reaction, and by phosphatidate. Phosphate stimulation may be unique to enzymes with CL synthase activity belonging to the PLD superfamily. Like other PLD enzymes, bacterial CL synthases utilize a common two-step ping-pong catalytic mechanism involving an enzyme-substrate intermediate to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine residue from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group.


Pssm-ID: 197209 [Multi-domain]  Cd Length: 154  Bit Score: 134.91  E-value: 3.94e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778  14 AALKARCQLIRQARHRILAQYYSWEEDGSGKLLLAELVRAARRGVVVQLLIDDL--YGGENRFLEAVAAEpGIEVRLFNP 91
Cdd:cd09110     5 EFFPALLEAIRAARHSIHLEYYIFRDDEIGRRFRDALIEKARRGVEVRLLYDGFgsLGLSRRFLRELREA-GVEVRAFNP 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778  92 FWLRgwrpltlllegvLSFRRINHRMHNKLLLVDGSQAVIGGRNIGDRYFGLGM-PPHFIDLDLVCRGPLCQQAEQGFAL 170
Cdd:cd09110    84 LSFP------------LFLLRLNYRNHRKILVIDGKIAFVGGFNIGDEYLGKDPgFGPWRDTHVRIEGPAVADLQAAFLE 151


                  ...
gi 2067386778 171 FWH 173
Cdd:cd09110   152 DWY 154
cls PRK01642
cardiolipin synthetase; Reviewed
 8-408 8.49e-28

cardiolipin synthetase; Reviewed


Pssm-ID: 234967 [Multi-domain]  Cd Length: 483  Bit Score: 114.49  E-value: 8.49e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778   8 LLADPGAALKARCQLIRQARHRILAQYYSWEEDGSGKLLLAELVRAARRGVVVQLLIDDLygGENRFLEAVAAE----PG 83
Cdd:PRK01642  120 LLTNGDETFQAIIRDIELARHYILMEFYIWRPDGLGDQVAEALIAAAKRGVRVRLLYDSI--GSFAFFRSPYPEelrnAG 197

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778  84 IEVRLF---NPFWLRgwrpltlllegvlsFRRINHRMHNKLLLVDGSQAVIGGRNIGD-RYFG----LGmppHFIDLDLV 155
Cdd:PRK01642  198 VEVVEFlkvNLGRVF--------------RRRLDLRNHRKIVVIDGYIAYTGSMNVVDpEYFKqdpgVG---QWRDTHVR 260

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778 156 CRGPLCQQAEQGFALFWHsrWshpvrrllrrpllpaETRALndflltltdpamaAAYDLPatlfdECPVPLCWHPGRGQC 235
Cdd:PRK01642  261 IEGPVVTALQLIFAEDWE--W---------------ETGER-------------ILPPPP-----DVLIMPFEEASGHTV 305

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778 236 WFDRPGKGlVARPTTAPLLGRMLASNQGALRLVSPYLILTRGLRRRLKGQRRQGVDIEILTNSLAstDVPLVYGAYRRHR 315
Cdd:PRK01642  306 QVIASGPG-DPEETIHQFLLTAIYSARERLWITTPYFVPDEDLLAALKTAALRGVDVRIIIPSKN--DSLLVFWASRAFF 382

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778 316 PWLERQGVTLFELtTEAFsLHAKLILMGKEEALLGSFNLDPRSLMLNTELMLHLHSPTLCDELQQLIDGWLQQAvHPVAA 395
Cdd:PRK01642  383 TELLEAGVKIYRY-EGGL-LHTKSVLVDDELALVGTVNLDMRSFWLNFEITLVIDDTGFAADLAAMQEDYFARS-RELDL 459

                         410
                  ....*....|....*..
gi 2067386778 396 SP----SAWRRLLAQLS 408
Cdd:PRK01642  460 EEwrkrPLWQRIAERVA 476
bac_cardiolipin TIGR04265
cardiolipin synthase; This model is based on experimentally characterized bacterial ...
 21-380 1.09e-27

cardiolipin synthase; This model is based on experimentally characterized bacterial cardiolipin synthases (cls) from E. coli, Staphylococcus aureus (two), and Bacillus pseudofirmus OF4. This model describes just one of several homologous but non-orthologous forms of cls. The cutoff score is set arbitrarily high to avoid false-positives. Note that there are two enzymatic activites called cardiolipin synthase. This model represents type 1, which does not rely on a CDP-linked donor, but instead does a reversible transfer of a phosphatidyl group from one phosphatidylglycerol molecule to another.


Pssm-ID: 211988 [Multi-domain]  Cd Length: 483  Bit Score: 114.50  E-value: 1.09e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778  21 QLIRQARHRILAQYYSWEEDGSGKLLLAELVRAARRGVVVQLLIDDLyGGENRFLEAVaaEP----GIEVRLFNPFWLrg 96
Cdd:TIGR04265 136 QDIKNARHYIHLEYYIWQPDGLGDQILESLMAKAKQGVHVRILYDDV-GSVALFKSWP--ELfrnaGGEVVAFFPVKL-- 210

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778  97 wrpltlllegVLSFRRINHRMHNKLLLVDGSQAVIGGRNIGDRYFGLGMP-PHFIDLDLVCRGPLCQQAEQGFALFWHSR 175
Cdd:TIGR04265 211 ----------PLLNLRMNNRNHRKIIVIDGQIGYVGGFNIGDEYLGKDAKfGYWRDTHLRIEGDAVTALQLIFILDWNSQ 280

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778 176 WSHPVRRLlrrpllpaETRALNDFLLTLTDPAMAAAYDLPATLfdecpvplcWHpgrgqcwfdrpgkglvarpTTAPLLG 255
Cdd:TIGR04265 281 TGRRIIPY--------DPDYFPMPNEQAGGHGIQIIASGPDFP---------WE-------------------QIKYGYL 324

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778 256 RMLASNQGALRLVSPYLILTRGLRRRLKGQRRQGVDIEILTNSlaSTDVPLVYGAYRRHRPWLERQGVTLFELttEAFSL 335
Cdd:TIGR04265 325 KMIYSAKKSIYIQSPYFIPDDDLLHAIKIAALSGVDVSIMIPN--KPDHPLVFWASRSNFTELLAAGVKIYQY--ENGFL 400

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*
gi 2067386778 336 HAKLILMGKEEALLGSFNLDPRSLMLNTELMLHLHSPTLCDELQQ 380
Cdd:TIGR04265 401 HSKSVLVDDEIASVGTANMDMRSFWLNFEVNAFIYDKGFAKDLAA 445
PLDc_CLS_unchar1_1 cd09156
Putative catalytic domain, repeat 1, of uncharacterized proteins similar to bacterial ...
 10-173 2.68e-26

Putative catalytic domain, repeat 1, of uncharacterized proteins similar to bacterial cardiolipin synthase; Putative catalytic domain, repeat 1, of uncharacterized proteins similar to bacterial cardiolipin (CL) synthases, which catalyze the reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form CL and glycerol. Members of this subfamily contain two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. The two motifs may be part of the active site and may be involved in phosphatidyl group transfer.


Pssm-ID: 197253 [Multi-domain]  Cd Length: 154  Bit Score: 103.49  E-value: 2.68e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778  10 ADPGAALKARCQLIRQARHRILAQYYSWEEDGSGKLLLAELVRAARRGVVVQLLIDDL--YGGENRFLEAVAAEpGIEVR 87
Cdd:cd09156     1 ADGVEAYQALIQLIESAKHSIDVCTFILGDDATGRRVIDALARKAREGVEVRLLLDALgsFFLSRRALKKLRAA-GGKVA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778  88 LFNPFWLrgwrpltlllegvLSFR-RINHRMHNKLLLVDGSQAVIGGRNIGDRYFGLGM-PPHFIDLDLVCRGPLCQQAE 165
Cdd:cd09156    80 FFMPVFR-------------LPFRgRTNLRNHRKIAIADGSTAISGGMNLANEYMGPEPdDGRWVDLSFLIEGPAVAQYQ 146


                  ....*...
gi 2067386778 166 QGFALFWH 173
Cdd:cd09156   147 EVFRSDWA 154
PLDc_CLS_unchar2_1 cd09157
Putative catalytic domain, repeat 1, of uncharacterized proteins similar to bacterial ...
 14-173 2.65e-22

Putative catalytic domain, repeat 1, of uncharacterized proteins similar to bacterial cardiolipin synthase; Putative catalytic domain, repeat 1, of uncharacterized proteins similar to bacterial cardiolipin (CL) synthases, which catalyze the reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form CL and glycerol. Members of this subfamily contain two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. The two motifs may be part of the active site and may be involved in phosphatidyl group transfer.


Pssm-ID: 197254 [Multi-domain]  Cd Length: 155  Bit Score: 92.63  E-value: 2.65e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778  14 AALKARCQLIRQARHRILAQYYSWEEDGSGKLLLAELVRAARRGVVVQLLIDDLYGG-ENRFLEAVAAEPGIEVRLFNPF 92
Cdd:cd09157     5 EAYPAMLEAIDAARHSIALSSYIFDNDGVGREFVDALAEAVARGVDVRVLIDGVGARySRPSIRRRLRRAGVPVARFLPP 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778  93 WLRGWRPLtlllegvlsfrrINHRMHNKLLLVDGSQAVIGGRNIGDRYFGLGMPPHFI-DLDLVCRGPLCQQAEQGFALF 171
Cdd:cd09157    85 RLPPRLPF------------INLRNHRKILVVDGRTGFTGGMNIRDGHLVADDPKNPVqDLHFRVEGPVVAQLQEVFAED 152


                  ..
gi 2067386778 172 WH 173
Cdd:cd09157   153 WY 154
PLDc_EcCLS_like_1 cd09152
Catalytic domain, repeat 1, of Escherichia coli cardiolipin synthase and similar proteins; ...
 8-173 1.21e-20

Catalytic domain, repeat 1, of Escherichia coli cardiolipin synthase and similar proteins; Catalytic domain, repeat 1, of Escherichia coli cardiolipin (CL) synthase and similar proteins. Escherichia coli CL synthase (EcCLS), specified by the cls gene, is the prototype of this family. EcCLS is a multi-pass membrane protein that catalyzes reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form cardiolipin (CL) and glycerol. The monomer of EcCLS consists of two catalytic domains. Each catalytic domain contains one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. Two HKD motifs from two domains form a single active site involved in phosphatidyl group transfer. EcCLS can be stimulated by phosphate and inhibited by CL, the product of the reaction, and by phosphatidate. Phosphate stimulation may be unique to enzymes with CL synthase activity belonging to the PLD superfamily. Like other PLD enzymes, EcCLS utilizes a common two-step ping-pong catalytic mechanism involving an enzyme-substrate intermediate to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine residue from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group.


Pssm-ID: 197250 [Multi-domain]  Cd Length: 163  Bit Score: 88.03  E-value: 1.21e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778   8 LLADPGAALKARCQLIRQARHRILAQYYSWEEDGSGKLLLAELVRAARRGVVVQLLIDDLyGGENRFLEAVA---AEPGI 84
Cdd:cd09152     6 LLTDYDAVIDRLIADIDAAKHHVHLLFYIWADDGTGDRVAEALERAAKRGVTCRLLLDAV-GSRAFFRSSLWkrlREAGV 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778  85 EVRL---FNPFWLRgwrpltlllegvlsFRRINHRMHNKLLLVDGSQAVIGGRNIGDRYFGLgMPPHFIDLDLVCR--GP 159
Cdd:cd09152    85 EVVEalpLRLFRRR--------------LARFDLRNHRKIAVIDGRIAYTGSQNIIDPEFFK-KAGGGPWVDLMVRveGP 149

                         170
                  ....*....|....
gi 2067386778 160 LCQQAEQGFALFWH 173
Cdd:cd09152   150 VVSQLQAVFASDWY 163
PLDc_PaCLS_like_1 cd09155
Putative catalytic domain, repeat 1, of Pseudomonas aeruginosa cardiolipin synthase and ...
 23-173 1.98e-20

Putative catalytic domain, repeat 1, of Pseudomonas aeruginosa cardiolipin synthase and similar proteins; Putative catalytic domain, repeat 1, of Pseudomonas aeruginosa cardiolipin (CL) synthase (PaCLS) and similar proteins. Although PaCLS and similar proteins have not been functionally characterized, members in this subfamily show high sequence homology to bacterial CL synthases, which catalyze the reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form CL and glycerol. Moreover, PaCLS and other members of this subfamily contain two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. The two motifs may be part of the active site and may be involved in phosphatidyl group transfer.


Pssm-ID: 197252 [Multi-domain]  Cd Length: 156  Bit Score: 87.30  E-value: 1.98e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778  23 IRQARHRILAQYYSWEEDGSGKLLLAELVRAARRGVVVQLLIDDL--YGGENRFLEAVAaEPGIEVRLFNPfwLRGWR-P 99
Cdd:cd09155    14 IASAEEYILVQFYIIRDDDLGRELKDALIARAQAGVRVYLLYDEIgsHSLSRSYIERLR-KAGVEVSAFNT--TRGWGnR 90

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2067386778 100 LtlllegvlsfrRINHRMHNKLLLVDGSQAVIGGRNIGDRYfgLGMPPHF---IDLDLVCRGPLCQQAEQGFALFWH 173
Cdd:cd09155    91 F-----------QLNFRNHRKIVVVDGQTAFVGGHNVGDEY--LGRDPRLgpwRDTHVKLEGPAVQQLQLSFAEDWY 154
PRK12452 PRK12452
cardiolipin synthase;
21-383 4.35e-20

cardiolipin synthase;


Pssm-ID: 171510 [Multi-domain]  Cd Length: 509  Bit Score: 92.29  E-value: 4.35e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778  21 QLIRQARHRILAQYYSWEEDGSGKLLLAELVRAARRGVVVQLLIDDL--YGGENRFLEAVaAEPGIEVRLFNPFWlrgwr 98
Cdd:PRK12452  157 QAIEQAKHHIHIQYYIYKSDEIGTKVRDALIKKAKDGVIVRFLYDGLgsNTLRRRFLQPM-KEAGIEIVEFDPIF----- 230

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778  99 pLTLLLEGVlsfrriNHRMHNKLLLVDGSQAVIGGRNIGDRYFGlgmpphfidldlvcrgplcqqAEQGFAlFWhsRWSH 178
Cdd:PRK12452  231 -SAWLLETV------NYRNHRKIVIVDGEIGFTGGLNVGDEYLG---------------------RSKKFP-VW--RDSH 279

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778 179 pvrrllrrplLPAETRALNDFLLTLTDPAMAAAYDLPATlfdecpvplCWHPGRGQCWFdrPGK------GLVARPTTAP 252
Cdd:PRK12452  280 ----------LKVEGKALYKLQAIFLEDWLYASSGLNTY---------SWDPFMNRQYF--PGKeisnaeGAVQIVASGP 338

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778 253 ----------LLGRMLaSNQGALRLVSPYLILTRGLRRRLKGQRRQGVDIEILTNslASTDVPLVYGAYRRHRPWLERQG 322
Cdd:PRK12452  339 ssddksirntLLAVMG-SAKKSIWIATPYFIPDQETLTLLRLSAISGIDVRILYP--GKSDSIISDQASQSYFTPLLKAG 415

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2067386778 323 VTLFelTTEAFSLHAKLILMGKEEALLGSFNLDPRSLMLNTELMLHLH-SPTLCDELQQLID 383
Cdd:PRK12452  416 ASIY--SYKDGFMHAKIVLVDDKIATIGTANMDVRSFELNYEIISVLYeSETVHDIKRDFED 475
PLDc_ybhO_like_2 cd09159
Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; ...
 265-411 5.36e-20

Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; Catalytic domain, repeat 2, of Escherichia coli cardiolipin (CL) synthase ybhO and similar proteins. In Escherichia coli, there are two genes, f413 (ybhO) and o493 (ymdC), which are homologous to gene cls that encodes the Escherichia coli CL synthase. The prototype of this subfamily is Escherichia coli CL synthase ybhO specified by the f413 (ybhO) gene. ybhO is a membrane-bound protein that catalyzes the formation of cardiolipin (CL) by transferring phosphatidyl group between two phosphatidylglycerol molecules. It can also catalyze phosphatidyl group transfer to water to form phosphatidate. In contrast to the Escherichia coli CL synthase encoded by the cls gene (EcCLS), ybhO does not hydrolyze CL. Moreover, ybhO lacks an N-terminal segment encoded by Escherichia coli cls, which makes ybhO easy to denature. The monomer of ybhO consists of two catalytic domains. Each catalytic domain contains one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. Two HKD motifs from two domains form a single active site involved in phosphatidyl group transfer. ybhO can be stimulated by phosphate and inhibited by CL, the product of the reaction, and by phosphatidate. Phosphate stimulation may be unique to enzymes with CL synthase activity belonging to the PLD superfamily.


Pssm-ID: 197256 [Multi-domain]  Cd Length: 170  Bit Score: 86.44  E-value: 5.36e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778 265 LRLVSPYLILTRGLRRRLKGQRRQGVDIEILTNSlASTDVPLVYGAYRRHRPWLERqGVTLFEltTEAFSLHAKLILMGK 344
Cdd:cd09159    27 IWIANAYFVPDRRLRRALIEAARRGVDVRLLLPG-KSDDPLTVAASRALYGKLLRA-GVRIFE--YQPSMLHAKTAVIDG 102

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2067386778 345 EEALLGSFNLDPRSLMLNTELMLHLHSPTLCDELQQLIDGWLQQAvhpVAASPSAW--RRLLAQLSDWL 411
Cdd:cd09159   103 DWATVGSSNLDPRSLRLNLEANLVVEDPAFAAQLEELFEEDLARS---REITLEEWrrRPLWQRLLEWL 168
PLDc_2 pfam13091
PLD-like domain;
256-383 2.04e-18

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 80.80  E-value: 2.04e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778 256 RMLASNQGALRLVSPYLILTRGLRRRLKGQRRQGVDIEILTNSLAStDVPLVYGAYRRHRPWLERQGVTLFELTTEAFSL 335
Cdd:pfam13091   3 DLINSAKKSIDIATYYFVPDREIIDALIAAAKRGVDVRIILDSNKD-DAGGPKKASLKELRSLLRAGVEIREYQSFLRSM 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 2067386778 336 HAKLILMGKEEALLGSFNLDPRSLMLNTELMLHLHSPTLCDELQQLID 383
Cdd:pfam13091  82 HAKFYIIDGKTVIVGSANLTRRALRLNLENNVVIKDPELAQELEKEFD 129
PRK11263 PRK11263
cardiolipin synthase ClsB;
23-415 7.57e-18

cardiolipin synthase ClsB;


Pssm-ID: 236888 [Multi-domain]  Cd Length: 411  Bit Score: 84.61  E-value: 7.57e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778  23 IRQARHRILAQYYSWEEDGSGKLLLAELVRAARRGVVVQLLIDDlYGGEN---RFLEAVAAEpGIEVRLFNPfwlrgwRP 99
Cdd:PRK11263   27 IAAAQEEILLETFILFEDKVGKQLHAALLAAAQRGVKVEVLVDG-YGSPDlsdEFVNELTAA-GVRFRYFDP------RP 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778 100 LTLlleGvlsfRRIN--HRMHNKLLLVDGSQAVIGGRNIGDRyfglgmppHFIDldlvcRGPlcqQAEQGFALfwhsRWS 177
Cdd:PRK11263   99 RLL---G----MRTNlfRRMHRKIVVIDGRIAFVGGINYSAD--------HLSD-----YGP---EAKQDYAV----EVE 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778 178 HPVrrllrrpllpaeTRALNDFLLtltdpamaaaydlpATLFDECPVPLCWHPGRGQCWFDRPGKG---LVARPTtapll 254
Cdd:PRK11263  152 GPV------------VADIHQFEL--------------EALPGQSAARRWWRRHHRAEENRQPGEAqalLVWRDN----- 200

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778 255 GR-----------MLASNQGALRLVSPYLILTRGLRRRLKGQRRQGVDIE-ILTnslASTDVPLVYGAYRRHRPWLERQG 322
Cdd:PRK11263  201 EEhrddierhylkALRQARREVIIANAYFFPGYRLLRALRNAARRGVRVRlILQ---GEPDMPIVRVGARLLYNYLLKGG 277

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778 323 VTLFELTTEAfsLHAKLILMGKEEALLGSFNLDPRSLMLNTELMLHLHSP----TLCDELQQLIDGWLQQaVHPVAASPS 398
Cdd:PRK11263  278 VQIYEYCRRP--LHGKVALMDDHWATVGSSNLDPLSLSLNLEANLIIRDRafnqTLRDNLNGLIAADCQQ-VDETMLPKR 354

                         410       420
                  ....*....|....*....|....*....
gi 2067386778 399 AWRRLLA------------QLSDWLPLHR 415
Cdd:PRK11263  355 TWWRLTKsvlafhflrhfpALAGWLPAHT 383
PLDc_CLS_unchar1_2 cd09162
Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial ...
 268-411 1.08e-16

Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial cardiolipin synthase; Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial cardiolipin (CL) synthases, which catalyze the reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form CL and glycerol. Members of this subfamily contain two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. The two motifs may be part of the active site and may be involved in phosphatidyl group transfer.


Pssm-ID: 197259 [Multi-domain]  Cd Length: 172  Bit Score: 77.30  E-value: 1.08e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778 268 VSPYLILTRGLRRRLKGQRRQGVDIEILT---NSLASTDvpLVYGAYRRHrpwLERQGVTLfeLTTEAFSLHAKLILMGK 344
Cdd:cd09162    30 VTPYFVPDEVLLRALRLAARRGVDVRLIVpkrSNHRIAD--LARGSYLRD---LQEAGAEI--YLYQPGMLHAKAVVVDD 102

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2067386778 345 EEALLGSFNLDPRSLMLNTELMLHLHSPTLCDELQQLIDGWLQQAvHPVAASPSAWRRLLAQLSDWL 411
Cdd:cd09162   103 KLALVGSANLDMRSLFLNYEVAVFFYSPADIKELSDWIESLISQC-TEGAPPPSALRDIAEGLMRLL 168
PLDc_CLS_unchar2_2 cd09163
Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial ...
 253-383 3.98e-16

Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial cardiolipin synthase; Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial cardiolipin (CL) synthases, which catalyze the reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form CL and glycerol. Members of this subfamily contain two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. The two motifs may be part of the active site and may be involved in phosphatidyl group transfer.


Pssm-ID: 197260 [Multi-domain]  Cd Length: 176  Bit Score: 75.67  E-value: 3.98e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778 253 LLGRMLASNQGALRLVSPYLILTRGLRRRLKGQRRQGVDIEILTNslASTDVPLVYGAYRRHRPWLERQGVTLFeLTTEA 332
Cdd:cd09163    15 TLLGAISAARHSIRIMTPYFLPDRTLITALQAAALRGVEVDIVLP--ERNNLPLVDWAMRANLWELLEHGVRIY-LQPPP 91

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2067386778 333 FSlHAKLILMGKEEALLGSFNLDPRSLMLNTELMLHLHSPTLCDELQQLID 383
Cdd:cd09163    92 FD-HSKLMVVDGAWALIGSANWDPRSLRLNFELNLEVYDTALAGQLDALFD 141
PLDc_CLS_2 cd09112
catalytic domain repeat 2 of bacterial cardiolipin synthase and similar proteins; This CD ...
 265-408 6.93e-16

catalytic domain repeat 2 of bacterial cardiolipin synthase and similar proteins; This CD corresponds to the catalytic domain repeat 2 of bacterial cardiolipin synthase (CL synthase, EC 2.7.8.-) and a few homologs found in eukaryotes and archea. Bacterial CL synthases catalyze reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form cardiolipin (CL) and glycerol. The monomer of bacterial CL synthase consists of two catalytic domains. Each catalytic domain contains one copy of conserved HKD motifs (H-X-K-X(4)-D, X represents any amino acid residue) that are the characteristic of the phospholipase D (PLD) superfamily. Two HKD motifs from two domains together form a single active site involving in phosphatidyl group transfer. Bacterial CL synthases can be stimulated by phosphate and inhibited by CL, the product of the reaction, and by phosphatidate. Phosphate stimulation may be unique to enzymes with CL synthase activity in PLD superfamily. Like other PLD enzymes, bacterial CL synthase utilize a common two-step ping-pong catalytic mechanism involving an enzyme-substrate intermediate to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine residue from one HKD motif could function as the nucleophile attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid stabilizing the leaving group.


Pssm-ID: 197211 [Multi-domain]  Cd Length: 174  Bit Score: 75.21  E-value: 6.93e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778 265 LRLVSPYLILTRGLRRRLKGQRRQGVDIEILTNSLAstDVPLVYGAYRRHRPWLERQGVTLFELTtEAFsLHAKLILMGK 344
Cdd:cd09112    27 IYIQTPYFIPDESLLEALKTAALSGVDVRIMIPGKP--DHKLVYWASRSYFEELLKAGVKIYEYN-KGF-LHSKTLIVDD 102

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2067386778 345 EEALLGSFNLDPRSLMLNTELMLHLHSPTLCDELQQLIDGWLQQAVHPVAAS---PSAWRRLLAQLS 408
Cdd:cd09112   103 EIASVGTANLDIRSFELNFEVNAVIYDKEVAKKLEEIFEEDLKDSELLTLEEwrkRSLWKRFKESLA 169
PLDc_PaCLS_like_2 cd09161
Putative catalytic domain, repeat 2, of Pseudomonas aeruginosa cardiolipin synthase and ...
 256-408 1.60e-14

Putative catalytic domain, repeat 2, of Pseudomonas aeruginosa cardiolipin synthase and similar proteins; Putative catalytic domain, repeat 2, of Pseudomonas aeruginosa cardiolipin (CL) synthase (PaCLS) and similar proteins. Although PaCLS and similar proteins have not been functionally characterized, members in this subfamily show high sequence homology to bacterial CL synthases, which catalyze the reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form CL and glycerol. Moreover, PaCLS and other members of this subfamily contain two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. The two motifs may be part of the active site and may be involved in phosphatidyl group transfer.


Pssm-ID: 197258 [Multi-domain]  Cd Length: 176  Bit Score: 71.17  E-value: 1.60e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778 256 RMLASNQGALRLVSPYLILTRGLRRRLKGQRRQGVDIEILTNSLAstDVPLVYGAYRRHRPWLERQGVTLFELTtEAFsL 335
Cdd:cd09161    18 QAINAAQKRLWIASPYFVPDEGVLAALQLAALRGVDVRILIPERP--DHLLVYLASFSYLPELIRAGVKVYRYQ-PGF-L 93

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2067386778 336 HAKLILMGKEEALLGSFNLDPRSLMLNTELMLHLHSPTLCDELQQLIDGWLQQAVHPVAAS---PSAWRRLLAQLS 408
Cdd:cd09161    94 HQKVVLVDDELAAVGTANLDNRSFRLNFEITALVADPGFAQEVEAMLEADFAASREVTAAElanRPLWFRLGARVA 169
PLDc_EcCLS_like_2 cd09158
Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase and similar proteins; ...
 267-404 2.18e-14

Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase and similar proteins; Catalytic domain, repeat 2, of Escherichia coli cardiolipin (CL) synthase and similar proteins. Escherichia coli CL synthase (EcCLS), specified by the cls gene, is the prototype of this family. EcCLS is a multi-pass membrane protein that catalyzes reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form cardiolipin (CL) and glycerol. The monomer of EcCLS consists of two catalytic domains. Each catalytic domain contains one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. Two HKD motifs from two domains form a single active site involved in phosphatidyl group transfer. EcCLS can be stimulated by phosphate and inhibited by CL, the product of the reaction, and by phosphatidate. Phosphate stimulation may be unique to enzymes with CL synthase activity belonging to the PLD superfamily. Like other PLD enzymes, EcCLS utilizes a common two-step ping-pong catalytic mechanism involving an enzyme-substrate intermediate to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine residue from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group.


Pssm-ID: 197255 [Multi-domain]  Cd Length: 174  Bit Score: 70.68  E-value: 2.18e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778 267 LVSPYLILTRGLRRRLKGQRRQGVDIEILTNslASTDVPLVYGAYRRHRPWLERQGVTLFELTtEAFsLHAKLILMGKEE 346
Cdd:cd09158    29 ITTPYFVPDESLLQALCTAALRGVEVTLILP--AKNDSFLVGAASRSYYEELLEAGVKIYLYR-GGL-LHAKTVTVDDEV 104

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2067386778 347 ALLGSFNLDPRSLMLNTELMLHLHSPTLCDELQQLIDGWLQQAvHPVAASP----SAWRRLL 404
Cdd:cd09158   105 ALVGSSNFDIRSFALNFEISLILYDKEFTAQLRAIQERYLARS-DPLTLEEwkkrPLWRRLL 165
PLDc_2 pfam13091
PLD-like domain;
20-172 2.89e-13

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 66.55  E-value: 2.89e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778  20 CQLIRQARHRI-LAQYYSWeedgSGKLLLAELVRAARRGVVVQLLIDDLYGG-------ENRFLEAVAAEpGIEVRLFNP 91
Cdd:pfam13091   2 IDLINSAKKSIdIATYYFV----PDREIIDALIAAAKRGVDVRIILDSNKDDaggpkkaSLKELRSLLRA-GVEIREYQS 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778  92 FWlrgwrpltlllegvlsfrrinHRMHNKLLLVDGSQAVIGGRNIGDRYFGLGMpphfiDLDLVCRGP-LCQQAEQGFAL 170
Cdd:pfam13091  77 FL---------------------RSMHAKFYIIDGKTVIVGSANLTRRALRLNL-----ENNVVIKDPeLAQELEKEFDR 130


                  ..
gi 2067386778 171 FW 172
Cdd:pfam13091 131 LW 132
PLDc_unchar1_2 cd09128
Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins; ...
 8-136 6.41e-11

Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins; Putative catalytic domain, repeat 2, of uncharacterized phospholipase D (PLD, EC 3.1.4.4)-like proteins. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze transphosphatidylation of phospholipids to acceptor alcohols. Members of this subfamily contain two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the PLD superfamily. The two motifs may be part of the active site and may be involved in phosphatidyl group transfer.


Pssm-ID: 197226 [Multi-domain]  Cd Length: 142  Bit Score: 59.98  E-value: 6.41e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778   8 LLADPGAALKARCQLIRQARHRIL--AQYYSWEEDgsgklLLAELVRAARRGVVVQLLIDDLYGGENRFLE--AVAAEPG 83
Cdd:cd09128     4 LLLSPDNAREALLALIDSAEESLLiqNEEMGDDAP-----ILDALVDAAKRGVDVRVLLPSAWSAEDERQArlRALEGAG 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2067386778  84 IEVRLfnpfwlRGWRPLtlllegvlsfrrinhRMHNKLLLVDGSQAVIGGRNI 136
Cdd:cd09128    79 VPVRL------LKDKFL---------------KIHAKGIVVDGKTALVGSENW 110
PLDc_SMU_988_like_1 cd09154
Putative catalytic domain, repeat 1, of Streptococcus mutans uncharacterized protein SMU_988 ...
 23-141 2.61e-10

Putative catalytic domain, repeat 1, of Streptococcus mutans uncharacterized protein SMU_988 and similar proteins; Putative catalytic domain, repeat 1, of Streptococcus mutans uncharacterized protein SMU_988 and similar proteins. Although SMU_988 and similar proteins have not been functionally characterized, members in this subfamily show high sequence homology to bacterial cardiolipin (CL) synthases, which catalyze the reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form CL and glycerol. Members of this subfamily contain two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. The two motifs may be part of the active site and may be involved in phosphatidyl group transfer.


Pssm-ID: 197251 [Multi-domain]  Cd Length: 155  Bit Score: 58.69  E-value: 2.61e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778  23 IRQARHRILAQYYSWEEdgsGKLL---LAELVRAARRGVVVQLLIDD------LYGGENRFLEAVaaepGIEVRLFNPFw 93
Cdd:cd09154    15 LKKAEKFIFMEYFIIEE---GYMWdsiLEILKEKAKEGVEVRIMYDDfgsittLPKDYPKELEKI----GIKCRVFNPF- 86

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 2067386778  94 lrgwRPltlllegVLSFRrINHRMHNKLLLVDGSQAVIGGRNIGDRYF 141
Cdd:cd09154    87 ----KP-------ILSLY-MNNRDHRKITVIDGKVAFTGGINLADEYI 122
PLDc_SMU_988_like_2 cd09160
Putative catalytic domain, repeat 2, of Streptococcus mutans uncharacterized protein SMU_988 ...
 269-364 1.25e-09

Putative catalytic domain, repeat 2, of Streptococcus mutans uncharacterized protein SMU_988 and similar proteins; Putative catalytic domain, repeat 2, of Streptococcus mutans uncharacterized protein SMU_988 and similar proteins. Although SMU_988 and similar proteins have not been functionally characterized, members in this subfamily show high sequence homology to bacterial cardiolipin (CL) synthases, which catalyze the reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form CL and glycerol. Members of this subfamily contain two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. The two motifs may be part of the active site and may be involved in phosphatidyl group transfer.


Pssm-ID: 197257 [Multi-domain]  Cd Length: 176  Bit Score: 57.12  E-value: 1.25e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778 269 SPYLILTRGLRRRLKGQRRQGVDIEILTNSLAstDVPLVYGAYRRHRPWLERQGVTLFELTtEAFsLHAKLILMGKEEAL 348
Cdd:cd09160    31 TPYLILDDEMLDALCLAAKRGVDVRIITPHIP--DKKYVFLVTRSNYPELLEAGVKIYEYT-PGF-IHAKTFVSDDKAAV 106

                          90
                  ....*....|....*.
gi 2067386778 349 LGSFNLDPRSLMLNTE 364
Cdd:cd09160   107 VGTINLDYRSLYLHFE 122
PLDc_SF cd00138
Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D ...
 21-135 3.02e-07

Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D (PLD) superfamily proteins. The PLD superfamily is composed of a large and diverse group of proteins including plant, mammalian and bacterial PLDs, bacterial cardiolipin (CL) synthases, bacterial phosphatidylserine synthases (PSS), eukaryotic phosphatidylglycerophosphate (PGP) synthase, eukaryotic tyrosyl-DNA phosphodiesterase 1 (Tdp1), and some bacterial endonucleases (Nuc and BfiI), among others. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze the transphosphatidylation of phospholipids to acceptor alcohols. The majority of members in this superfamily contain a short conserved sequence motif (H-x-K-x(4)-D, where x represents any amino acid residue), called the HKD signature motif. There are varying expanded forms of this motif in different family members. Some members contain variant HKD motifs. Most PLD enzymes are monomeric proteins with two HKD motif-containing domains. Two HKD motifs from two domains form a single active site. Some PLD enzymes have only one copy of the HKD motif per subunit but form a functionally active dimer, which has a single active site at the dimer interface containing the two HKD motifs from both subunits. Different PLD enzymes may have evolved through domain fusion of a common catalytic core with separate substrate recognition domains. Despite their various catalytic functions and a very broad range of substrate specificities, the diverse group of PLD enzymes can bind to a phosphodiester moiety. Most of them are active as bi-lobed monomers or dimers, and may possess similar core structures for catalytic activity. They are generally thought to utilize a common two-step ping-pong catalytic mechanism, involving an enzyme-substrate intermediate, to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group.


Pssm-ID: 197200 [Multi-domain]  Cd Length: 119  Bit Score: 49.05  E-value: 3.02e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778  21 QLIRQARHRILAQYYSWEEDGSGKLLlAELVRAARRGVVVQLLIDDLYGGENRFLEAVAAE---PGIEVRLFNpfwlrgw 97
Cdd:cd00138     5 ELLKNAKESIFIATPNFSFNSADRLL-KALLAAAERGVDVRLIIDKPPNAAGSLSAALLEAllrAGVNVRSYV------- 76

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 2067386778  98 rpltlllegvlSFRRINHRMHNKLLLVDGSQAVIGGRN 135
Cdd:cd00138    77 -----------TPPHFFERLHAKVVVIDGEVAYVGSAN 103
PLDc_unchar1_2 cd09128
Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins; ...
 243-381 5.89e-07

Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins; Putative catalytic domain, repeat 2, of uncharacterized phospholipase D (PLD, EC 3.1.4.4)-like proteins. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze transphosphatidylation of phospholipids to acceptor alcohols. Members of this subfamily contain two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the PLD superfamily. The two motifs may be part of the active site and may be involved in phosphatidyl group transfer.


Pssm-ID: 197226 [Multi-domain]  Cd Length: 142  Bit Score: 48.43  E-value: 5.89e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778 243 GLVARPTTAP-LLGRMLASNQGALRLVSPYLILTRGLRRRLKGQRRQGVDIEILTNSLAStdvplVYGAYRRHRPWLERQ 321
Cdd:cd09128     3 QLLLSPDNAReALLALIDSAEESLLIQNEEMGDDAPILDALVDAAKRGVDVRVLLPSAWS-----AEDERQARLRALEGA 77

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778 322 GVTLFELTTEAFSLHAKLILMGKEEALLGSFNLDPRSLMLNTELMLHLHSPTLCDELQQL 381
Cdd:cd09128    78 GVPVRLLKDKFLKIHAKGIVVDGKTALVGSENWSANSLDRNREVGLIFDDPEVAAYLQAV 137
PLDc_unchar3 cd09131
Putative catalytic domain of uncharacterized phospholipase D-like proteins; Putative catalytic ...
 21-135 1.24e-06

Putative catalytic domain of uncharacterized phospholipase D-like proteins; Putative catalytic domain of uncharacterized phospholipase D (PLD, EC 3.1.4.4)-like proteins. Members of this subfamily contain one copy of HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the PLD superfamily.


Pssm-ID: 197229 [Multi-domain]  Cd Length: 143  Bit Score: 47.72  E-value: 1.24e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778  21 QLIRQARHRI-----LAQYYSWEEDGSgKLLLAELVRAARRGVVVQLLIDD-----LYGGENRFLEAVAAEPGIEVRLFN 90
Cdd:cd09131    10 DLINNAKRSIyiamyMFKYYENPGNGV-NTLLEALIDAHKRGVDVKVVLEDsidddEVTEENDNTYRYLKDNGVEVRFDS 88

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 2067386778  91 PfwlrgwrpltlllegvlsfrriNHRMHNKLLLVDGSQAVIGGRN 135
Cdd:cd09131    89 P----------------------SVTTHTKLVVIDGRTVYVGSHN 111
PLDc_unchar1_1 cd09127
Putative catalytic domain, repeat 1, of uncharacterized phospholipase D-like proteins; ...
 12-141 1.26e-06

Putative catalytic domain, repeat 1, of uncharacterized phospholipase D-like proteins; Putative catalytic domain, repeat 1, of uncharacterized phospholipase D (PLD, EC 3.1.4.4)-like proteins. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze transphosphatidylation of phospholipids to acceptor alcohols. Members of this subfamily contain two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the PLD superfamily. The two motifs may be part of the active site and may be involved in phosphatidyl group transfer.


Pssm-ID: 197225 [Multi-domain]  Cd Length: 141  Bit Score: 47.64  E-value: 1.26e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778  12 PGAALKARCQLIRQARHRILAQYYSWEEDGsgklLLAELVRAARRGVVVQLLID-DLYGGENR--FLEAVAAEPGIEVRL 88
Cdd:cd09127     6 PDDGVAPVVDAIASAKRSILLKMYEFTDPA----LEKALAAAAKRGVRVRVLLEgGPVGGISRaeKLLDYLNEAGVEVRW 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2067386778  89 FNPfwlrgwrpltlllegvlSFRRINHrmHNKLLLVDGSQAVIGGRNIGDRYF 141
Cdd:cd09127    82 TNG-----------------TARYRYT--HAKYIVVDDERALVLTENFKPSGF 115
PLDc_Nuc cd09170
Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar ...
 13-133 2.91e-06

Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar proteins; Catalytic domain of an EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar proteins. Nuc is an endonuclease cleaving both single- and double-stranded DNA. It is the smallest known member of the phospholipase D (PLD, EC 3.1.4.4) superfamily that includes a diverse group of proteins with various catalytic functions. Most members of this superfamily have two copies of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) in a single polypeptide chain and both are required for catalytic activity. However, Nuc only has one copy of the HKD motif per subunit but form a functionally active homodimer (it is most likely also active in solution as a multimeric protein), which has a single active site at the dimer interface containing the HKD motifs from both subunits. Due to the lack of a distinct domain for DNA binding, Nuc cuts DNA non-specifically. It utilizes a two-step mechanism to cleave phosphodiester bonds: Upon substrate binding, the bond is first attacked by a histidine residue from one HKD motif to form a covalent phosphohistidine intermediate, which is then hydrolyzed by water with the aid of a second histidine residue from the other HKD motif in the opposite subunit.


Pssm-ID: 197267 [Multi-domain]  Cd Length: 142  Bit Score: 46.74  E-value: 2.91e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778  13 GAALKARCQLIRQARHRILAQYYSWEEDGsgkllLAE-LVRAARRGVVVQLLIDDLYGGENRFLEAVAAEPGIEVRL-FN 90
Cdd:cd09170    10 GGARELILDVIDSARRSIDVAAYSFTSPP-----IARaLIAAKKRGVDVRVVLDKSQAGGKYSALNYLANAGIPVRIdDN 84

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2067386778  91 PfwlrgwrpltlllegvlsfrrinHRMHNKLLLVDGsQAVIGG 133
Cdd:cd09170    85 Y-----------------------AIMHNKVMVIDG-KTVITG 103
PLDc_Nuc_like cd09116
Catalytic domain of EDTA-resistant nuclease Nuc, vertebrate phospholipase D6, and similar ...
 21-135 4.73e-06

Catalytic domain of EDTA-resistant nuclease Nuc, vertebrate phospholipase D6, and similar proteins; Catalytic domain of EDTA-resistant nuclease Nuc, vertebrate phospholipase D6 (PLD6, EC 3.1.4.4), and similar proteins. Nuc is an endonuclease from Salmonella typhimurium and the smallest known member of the PLD superfamily. It cleaves both single- and double-stranded DNA. PLD6 selectively hydrolyzes the terminal phosphodiester bond of phosphatidylcholine (PC), with the formation of phosphatidic acid and alcohols. Phosphatidic acid is an essential compound involved in signal transduction. PLD6 also catalyzes the transphosphatidylation of phospholipids to acceptor alcohols, by which various phospholipids can be synthesized. Both Nuc and PLD6 belong to the phospholipase D (PLD) superfamily. They contain a short conserved sequence motif, the HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue), which is essential for catalysis. PLDs utilize a two-step mechanism to cleave phosphodiester bonds: Upon substrate binding, the bond is first attacked by a histidine residue from one HKD motif to form a covalent phosphohistidine intermediate, which is then hydrolyzed by water with the aid of a second histidine residue from the other HKD motif in the opposite subunit. This subfamily also includes some uncharacterized hypothetical proteins, which have two HKD motifs in a single polypeptide chain.


Pssm-ID: 197215 [Multi-domain]  Cd Length: 138  Bit Score: 45.75  E-value: 4.73e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778  21 QLIRQARHRI-LAQYysweeDGSGKLLLAELVRAARRGVVVQLLIDDLYGGEN--RFLEAVAAEPGIEVRlfnpfwlrgw 97
Cdd:cd09116    16 ALIANAKSSIdVAMY-----ALTDPEIAEALKRAAKRGVRVRIILDKDSLADNlsITLLALLSNLGIPVR---------- 80

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 2067386778  98 rpltlllegVLSFRRInhrMHNKLLLVDGSQAVIGGRN 135
Cdd:cd09116    81 ---------TDSGSKL---MHHKFIIIDGKIVITGSAN 106
PLDc_SF cd00138
Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D ...
 256-367 6.13e-06

Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D (PLD) superfamily proteins. The PLD superfamily is composed of a large and diverse group of proteins including plant, mammalian and bacterial PLDs, bacterial cardiolipin (CL) synthases, bacterial phosphatidylserine synthases (PSS), eukaryotic phosphatidylglycerophosphate (PGP) synthase, eukaryotic tyrosyl-DNA phosphodiesterase 1 (Tdp1), and some bacterial endonucleases (Nuc and BfiI), among others. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze the transphosphatidylation of phospholipids to acceptor alcohols. The majority of members in this superfamily contain a short conserved sequence motif (H-x-K-x(4)-D, where x represents any amino acid residue), called the HKD signature motif. There are varying expanded forms of this motif in different family members. Some members contain variant HKD motifs. Most PLD enzymes are monomeric proteins with two HKD motif-containing domains. Two HKD motifs from two domains form a single active site. Some PLD enzymes have only one copy of the HKD motif per subunit but form a functionally active dimer, which has a single active site at the dimer interface containing the two HKD motifs from both subunits. Different PLD enzymes may have evolved through domain fusion of a common catalytic core with separate substrate recognition domains. Despite their various catalytic functions and a very broad range of substrate specificities, the diverse group of PLD enzymes can bind to a phosphodiester moiety. Most of them are active as bi-lobed monomers or dimers, and may possess similar core structures for catalytic activity. They are generally thought to utilize a common two-step ping-pong catalytic mechanism, involving an enzyme-substrate intermediate, to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group.


Pssm-ID: 197200 [Multi-domain]  Cd Length: 119  Bit Score: 45.20  E-value: 6.13e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778 256 RMLASNQGALRLVSPYLILTRG--LRRRLKGQRRQGVDIEILTNSlaSTDVPLVYGAYRRHRpwLERQGVTLFELTTE-- 331
Cdd:cd00138     5 ELLKNAKESIFIATPNFSFNSAdrLLKALLAAAERGVDVRLIIDK--PPNAAGSLSAALLEA--LLRAGVNVRSYVTPph 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2067386778 332 -AFSLHAKLILMGKEEALLGSFNLDPRSLMLNTELML 367
Cdd:cd00138    81 fFERLHAKVVVIDGEVAYVGSANLSTASAAQNREAGV 117
PLDc_vPLD3_4_5_like_1 cd09106
Putative catalytic domain, repeat 1, of vertebrate phospholipases, PLD3, PLD4 and PLD5, viral ...
 2-135 1.55e-04

Putative catalytic domain, repeat 1, of vertebrate phospholipases, PLD3, PLD4 and PLD5, viral envelope proteins K4 and p37, and similar proteins; Putative catalytic domain, repeat 1, of vertebrate phospholipases D, PLD3, PLD4, and PLD5 (EC 3.1.4.4), viral envelope proteins (vaccinia virus proteins K4 and p37), and similar proteins. Most family members contain two copies of the HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue), and have been classified into the phospholipase D (PLD) superfamily. Proteins in this subfamily are associated with Golgi membranes, altering their lipid content by the conversion of phospholipids into phosphatidic acid, which is thought to be involved in the regulation of lipid movement. ADP ribosylation factor (ARF), a small guanosine triphosphate binding protein, might be required activity. The vaccinia virus p37 protein, encoded by the F13L gene, is also associated with Golgi membranes and is required for the envelopment and spread of the extracellular enveloped virus (EEV). The vaccinia virus protein K4, encoded by the HindIII K4L gene, remains to be characterized. Sequence analysis indicates that the vaccinia virus proteins K4 and p37 might have evolved from one or more captured eukaryotic genes involved in cellular lipid metabolism. Up to date, no catalytic activity of PLD3 has been shown. Furthermore, due to the lack of functional important histidine and lysine residues in the HKD motif, mammalian PLD5 has been characterized as an inactive PLD. The poxvirus p37 proteins may also lack PLD enzymatic activity, since they contain only one partially conserved HKD motif (N-x-K-x(4)-D).


Pssm-ID: 197205 [Multi-domain]  Cd Length: 153  Bit Score: 41.85  E-value: 1.55e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778   2 IPADFALLADPGAALKARC--QLIRQARHRI-LAQYYsWEEDGS----------GKLLLAELVRAARRGVVVQLLIDdlY 68
Cdd:cd09106     5 IPEGLTFLSSSSHLSTFEAwmELISSAKKSIdIASFY-WNLRGTdtnpdssaqeGEDIFNALLEAAKRGVKIRILQD--K 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2067386778  69 GGENRF---LEAVAAEPGIEVR--LFNPFWLRGwrpltlllegvlsfrrinhRMHNKLLLVDGSQAVIGGRN 135
Cdd:cd09106    82 PSKDKPdedDLELAALGGAEVRslDFTKLIGGG-------------------VLHTKFWIVDGKHFYLGSAN 134
PLDc_Nuc_like_unchar1_1 cd09172
Putative catalytic domain, repeat 1, of uncharacterized hypothetical proteins similar to Nuc, ...
 15-132 3.78e-04

Putative catalytic domain, repeat 1, of uncharacterized hypothetical proteins similar to Nuc, an endonuclease from Salmonella typhimurium; Putative catalytic domain, repeat 1, of uncharacterized hypothetical proteins, which show high sequence homology to the endonuclease from Salmonella typhimurium and vertebrate phospholipase D6. Nuc and PLD6 belong to the phospholipase D (PLD) superfamily. They contain a short conserved sequence motif, the HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue), which characterizes the PLD superfamily and is essential for catalysis. Nuc and PLD6 utilize a two-step mechanism to cleave phosphodiester bonds: Upon substrate binding, the bond is first attacked by a histidine residue from one HKD motif to form a covalent phosphohistidine intermediate, which is then hydrolyzed by water with the aid of a second histidine residue from the other HKD motif in the opposite subunit. However, proteins in this subfamily have two HKD motifs in a single polypeptide chain.


Pssm-ID: 197269 [Multi-domain]  Cd Length: 144  Bit Score: 40.42  E-value: 3.78e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778  15 ALKARCQLIRQARH---RILAQYYSWEEDGsgklLLAELVRAARRGVVVQLLIDDlYGGENRFLEAVAAEPGIEVrlfnp 91
Cdd:cd09172     7 LREALLAFLDEARSagsSIRLAIYELDDPE----IIDALKAAKDRGVRVRIILDD-SSVTGDPTEESAAATLSKG----- 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 2067386778  92 fwlrgwrpltlllEGVLSFRRINHR-MHNKLLLVDGSQAVIG 132
Cdd:cd09172    77 -------------PGALVKRRHSSGlMHNKFLVVDRKDGPNR 105
PLDc_CLS_2 cd09112
catalytic domain repeat 2 of bacterial cardiolipin synthase and similar proteins; This CD ...
 22-132 4.33e-04

catalytic domain repeat 2 of bacterial cardiolipin synthase and similar proteins; This CD corresponds to the catalytic domain repeat 2 of bacterial cardiolipin synthase (CL synthase, EC 2.7.8.-) and a few homologs found in eukaryotes and archea. Bacterial CL synthases catalyze reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form cardiolipin (CL) and glycerol. The monomer of bacterial CL synthase consists of two catalytic domains. Each catalytic domain contains one copy of conserved HKD motifs (H-X-K-X(4)-D, X represents any amino acid residue) that are the characteristic of the phospholipase D (PLD) superfamily. Two HKD motifs from two domains together form a single active site involving in phosphatidyl group transfer. Bacterial CL synthases can be stimulated by phosphate and inhibited by CL, the product of the reaction, and by phosphatidate. Phosphate stimulation may be unique to enzymes with CL synthase activity in PLD superfamily. Like other PLD enzymes, bacterial CL synthase utilize a common two-step ping-pong catalytic mechanism involving an enzyme-substrate intermediate to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine residue from one HKD motif could function as the nucleophile attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid stabilizing the leaving group.


Pssm-ID: 197211 [Multi-domain]  Cd Length: 174  Bit Score: 40.92  E-value: 4.33e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778  22 LIRQARHRILAQ--YYSWEEDgsgklLLAELVRAARRGVVVQLLIDDL-------YGGENRFLEAVAAepGIEVRLFNPF 92
Cdd:cd09112    19 AINSAKKSIYIQtpYFIPDES-----LLEALKTAALSGVDVRIMIPGKpdhklvyWASRSYFEELLKA--GVKIYEYNKG 91

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 2067386778  93 WLrgwrpltlllegvlsfrrinhrmHNKLLLVDGSQAVIG 132
Cdd:cd09112    92 FL-----------------------HSKTLIVDDEIASVG 108
PLDc_PMFPLD_like_1 cd09108
Catalytic domain, repeat 1, of phospholipase D from Streptomyces Sp. Strain PMF and similar ...
 118-172 7.53e-04

Catalytic domain, repeat 1, of phospholipase D from Streptomyces Sp. Strain PMF and similar proteins; Catalytic domain, repeat 1, of phospholipases D (PLD, EC 3.1.4.4) from Streptomyces Sp. Strain PMF (PMFPLD) and similar proteins, which are generally extracellular and bear N-terminal signal sequences. PMFPLD hydrolyzes the terminal phosphodiester bond of phospholipids with the formation of phosphatidic acid and alcohols. Phosphatidic acid is an essential compound involved in signal transduction. It also catalyzes a transphosphatidylation of phospholipids to acceptor alcohols, by which various phospholipids can be synthesized. In contrast to eukaryotic PLDs, PMFPLD has a compact structure, which consists of two catalytic domains, but lacks the regulatory domains. Each catalytic domain contains one copy of the HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the PLD superfamily. Two HKD motifs from two domains form a single active site. Like other PLD enzymes, PMFPLD may utilize a common two-step ping-pong catalytic mechanism involving an enzyme-substrate intermediate to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine residue from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group. A calcium-dependent PLD from Streptomyce chromofuscus is excluded from this family, since it displays very little sequence homology with other Streptomyces PLDs. Moreover, it does not contain the conserved HKD motif and hydrolyzes the phospholipids via a different mechanism.


Pssm-ID: 197207 [Multi-domain]  Cd Length: 210  Bit Score: 40.49  E-value: 7.53e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2067386778 118 HNKLLLVDGSQAVIGGRNIGDRYFGLGMPPhFIDLDLVCRGPLCQQAEQGFALFW 172
Cdd:cd09108   157 HAKLLVVDGEELLTGGYNLWDDHYLDGGNP-VHDLSLVVRGPAARSGVRFFDDLW 210
PLDc smart00155
Phospholipase D. Active site motifs; Phosphatidylcholine-hydrolyzing phospholipase D (PLD) ...
 116-140 7.69e-04

Phospholipase D. Active site motifs; Phosphatidylcholine-hydrolyzing phospholipase D (PLD) isoforms are activated by ADP-ribosylation factors (ARFs). PLD produces phosphatidic acid from phosphatidylcholine, which may be essential for the formation of certain types of transport vesicles or may be constitutive vesicular transport to signal transduction pathways. PC-hydrolysing PLD is a homologue of cardiolipin synthase, phosphatidylserine synthase, bacterial PLDs, and viral proteins. Each of these appears to possess a domain duplication which is apparent by the presence of two motifs containing well-conserved histidine, lysine, aspartic acid, and/or asparagine residues which may contribute to the active site. An E. coli endonuclease (nuc) and similar proteins appear to be PLD homologues but possess only one of these motifs. The profile contained here represents only the putative active site regions, since an accurate multiple alignment of the repeat units has not been achieved.


Pssm-ID: 197546 [Multi-domain]  Cd Length: 28  Bit Score: 36.60  E-value: 7.69e-04
                           10        20
                   ....*....|....*....|....*
gi 2067386778  116 RMHNKLLLVDGSQAVIGGRNIGDRY 140
Cdd:smart00155   4 VLHTKLMIVDDEIAYIGSANLDGRS 28
PLDc_like_TrmB_middle cd09124
Middle phospholipase D-like domain of the transcriptional regulator TrmB and similar proteins; ...
 15-138 1.08e-03

Middle phospholipase D-like domain of the transcriptional regulator TrmB and similar proteins; Middle phospholipase D (PLD)-like domain of the transcriptional regulator TrmB and similar proteins. TrmB acts as a bifunctional sugar-sensing transcriptional regulator which controls two operons encoding maltose/trehalose and maltodextrin ABC transporters of Pyrococcus fruiosus. It functions as a dimer. Full length TrmB includes an N-terminal DNA-binding domain, a C-terminal sugar-binding domain and middle region that has been named as a PLD-like domain. The middle domain displays homology to PLD enzymes, which contain one or two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) per chain. The HKD motif characterizes the PLD superfamily. Due to the lack of key residues related to PLD activity in the PLD-like domain, members of this subfamily are unlikely to carry PLD activity.


Pssm-ID: 197223 [Multi-domain]  Cd Length: 126  Bit Score: 38.85  E-value: 1.08e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778  15 ALKARCQ-LIRQARHRILAQyySWEEDGsgKLLLAELVRAARRGVVVQLLIddlYGGENR-FLEAVAAEpgIEVRLFNPF 92
Cdd:cd09124    10 NILAKIReMINSAKEEIYIS--LPSEEL--EELLEELEKAAERGVKVVIII---FGDDDLdDLDSPAIE--VRVREGGGR 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2067386778  93 WLrgwrpltlllegvlsfrrinhrmhnkLLLVDGSQAVIGGRNIGD 138
Cdd:cd09124    81 PF--------------------------LLIVDSKEALIGPSSEEE 100
PLDc_unchar2_2 cd09130
Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins; ...
 13-138 1.24e-03

Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins; Putative catalytic domain, repeat 2, of uncharacterized phospholipase D (PLD, EC 3.1.4.4)-like proteins. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze transphosphatidylation of phospholipids to acceptor alcohols. Members of this subfamily contain two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the PLD superfamily. The two motifs may be part of the active site and may be involved in phosphatidyl group transfer.


Pssm-ID: 197228 [Multi-domain]  Cd Length: 157  Bit Score: 39.15  E-value: 1.24e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778  13 GAALKARCQLIRQAR---HRILAQYYSWEEDgsgklLLAELVRAARRGVVVQLLID---DLYGGENRFL--EAVAAE--- 81
Cdd:cd09130     4 GKIGEALLKEINSARagdKIWIGMFYLADRD-----VIKALIDAANRGVDVRLILDpnkDAFGREKNGIpnRPVAAElmk 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2067386778  82 ---PGIEVRLFNpfwlrgwrpltlllegvlsfrRINHRMHNKLLLVDGSQ--AVIGG------RNIGD 138
Cdd:cd09130    79 ktkGKIQIRWYN---------------------TGGEQFHTKLLLIKKKGqaIIIGGsanftrRNLRD 125
PRK13912 PRK13912
nuclease NucT; Provisional
 14-135 1.55e-03

nuclease NucT; Provisional


Pssm-ID: 184389 [Multi-domain]  Cd Length: 177  Bit Score: 39.37  E-value: 1.55e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778  14 AALKARCQLIRQARHRILAQYYSWeedgSGKLLLAELVRAARRGVVVQLLIDDLYGGENRF--LEAVAAEPGIEVrlfnp 91
Cdd:PRK13912   33 DALNKLVSLISNARSSIKIAIYSF----THKDIAKALKSAAKRGVKISIIYDYESNHNNDQstIGYLDKYPNIKV----- 103

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 2067386778  92 fwlrgwrpltLLLEGVLSFRRINH-RMHNKLLLVDGSQAVIGGRN 135
Cdd:PRK13912  104 ----------CLLKGLKAKNGKYYgIMHQKVAIIDDKIVVLGSAN 138
PLDc_ybhO_like_2 cd09159
Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; ...
 21-168 3.43e-03

Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; Catalytic domain, repeat 2, of Escherichia coli cardiolipin (CL) synthase ybhO and similar proteins. In Escherichia coli, there are two genes, f413 (ybhO) and o493 (ymdC), which are homologous to gene cls that encodes the Escherichia coli CL synthase. The prototype of this subfamily is Escherichia coli CL synthase ybhO specified by the f413 (ybhO) gene. ybhO is a membrane-bound protein that catalyzes the formation of cardiolipin (CL) by transferring phosphatidyl group between two phosphatidylglycerol molecules. It can also catalyze phosphatidyl group transfer to water to form phosphatidate. In contrast to the Escherichia coli CL synthase encoded by the cls gene (EcCLS), ybhO does not hydrolyze CL. Moreover, ybhO lacks an N-terminal segment encoded by Escherichia coli cls, which makes ybhO easy to denature. The monomer of ybhO consists of two catalytic domains. Each catalytic domain contains one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. Two HKD motifs from two domains form a single active site involved in phosphatidyl group transfer. ybhO can be stimulated by phosphate and inhibited by CL, the product of the reaction, and by phosphatidate. Phosphate stimulation may be unique to enzymes with CL synthase activity belonging to the PLD superfamily.


Pssm-ID: 197256 [Multi-domain]  Cd Length: 170  Bit Score: 38.29  E-value: 3.43e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778  21 QLIRQARHRIL--AQYYSweedgSGKLLLAELVRAARRGVVVQLLI----DD---------LYGgenRFLEAvaaepGIE 85
Cdd:cd09159    18 VAIAAARRRIWiaNAYFV-----PDRRLRRALIEAARRGVDVRLLLpgksDDpltvaasraLYG---KLLRA-----GVR 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778  86 VRLFNPfwlrgwrpltlllegvlsfrrinhRM-HNKLLLVDGSQAVIGGRNIGDRYFGLGMpphfiDLDLVCRGP-LCQQ 163
Cdd:cd09159    85 IFEYQP------------------------SMlHAKTAVIDGDWATVGSSNLDPRSLRLNL-----EANLVVEDPaFAAQ 135


                  ....*
gi 2067386778 164 AEQGF 168
Cdd:cd09159   136 LEELF 140
PLDc_vPLD3_4_5_like_1 cd09106
Putative catalytic domain, repeat 1, of vertebrate phospholipases, PLD3, PLD4 and PLD5, viral ...
 281-359 6.19e-03

Putative catalytic domain, repeat 1, of vertebrate phospholipases, PLD3, PLD4 and PLD5, viral envelope proteins K4 and p37, and similar proteins; Putative catalytic domain, repeat 1, of vertebrate phospholipases D, PLD3, PLD4, and PLD5 (EC 3.1.4.4), viral envelope proteins (vaccinia virus proteins K4 and p37), and similar proteins. Most family members contain two copies of the HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue), and have been classified into the phospholipase D (PLD) superfamily. Proteins in this subfamily are associated with Golgi membranes, altering their lipid content by the conversion of phospholipids into phosphatidic acid, which is thought to be involved in the regulation of lipid movement. ADP ribosylation factor (ARF), a small guanosine triphosphate binding protein, might be required activity. The vaccinia virus p37 protein, encoded by the F13L gene, is also associated with Golgi membranes and is required for the envelopment and spread of the extracellular enveloped virus (EEV). The vaccinia virus protein K4, encoded by the HindIII K4L gene, remains to be characterized. Sequence analysis indicates that the vaccinia virus proteins K4 and p37 might have evolved from one or more captured eukaryotic genes involved in cellular lipid metabolism. Up to date, no catalytic activity of PLD3 has been shown. Furthermore, due to the lack of functional important histidine and lysine residues in the HKD motif, mammalian PLD5 has been characterized as an inactive PLD. The poxvirus p37 proteins may also lack PLD enzymatic activity, since they contain only one partially conserved HKD motif (N-x-K-x(4)-D).


Pssm-ID: 197205 [Multi-domain]  Cd Length: 153  Bit Score: 37.23  E-value: 6.19e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2067386778 281 RLKGQRRQGVDIEILTNSlASTDVPLVYGAYRRHRPWLERQGVTLFELTTeAFSLHAKLILMGKEEALLGSFNLDPRSL 359
Cdd:cd09106    64 ALLEAAKRGVKIRILQDK-PSKDKPDEDDLELAALGGAEVRSLDFTKLIG-GGVLHTKFWIVDGKHFYLGSANLDWRSL 140
PLDc_yjhR_C_like cd09118
C-terminal domain of Escherichia coli uncharacterized protein yjhR and similar proteins; ...
 258-353 6.98e-03

C-terminal domain of Escherichia coli uncharacterized protein yjhR and similar proteins; C-terminal domain of Escherichia coli uncharacterized protein yjhR, encoded by the o338 gene, and similar proteins. Although the biological function of yjhR remains unknown, it shows sequence similarity to the C-terminal portions of superfamily I DNA and RNA helicases, which are ubiquitous enzymes mediating ATP-dependent unwinding of DNA and RNA duplexes, and play essential roles in gene replication and expression. Moreover, The C-termini of yjhR and similar proteins contain one HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. The PLDc-like domain of yjhR is similar to bacterial endonucleases, Nuc and BfiI, both of which have only one copy of the HKD motif per chain. They function as homodimers, with a single active site at the dimer interface containing the HKD motifs from both subunits. They utilize a two-step mechanism to cleave phosphodiester bonds. Upon substrate binding, the bond is first attacked by a histidine residue from one HKD motif to form a covalent phosphohistidine intermediate, which is then hydrolyzed by water with the aid of a second histidine residue from the other HKD motif in the opposite subunit.


Pssm-ID: 197217 [Multi-domain]  Cd Length: 144  Bit Score: 36.91  E-value: 6.98e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778 258 LASNQGALRLVSPYLILTR----GLRRRLKGQRRQGVDIEILTNS-LASTDVPLVYGAYRRHRPWLERQGVTLFELTtea 332
Cdd:cd09118    10 LATVRERIVIVSPWISLDAleadGLLEAIREAVSRGVDVTIYTDPhLNTGDANDTKANLEDAAEALAEAGIRIHEVN--- 86

                          90       100
                  ....*....|....*....|.
gi 2067386778 333 fSLHAKLILMGKEEALLGSFN 353
Cdd:cd09118    87 -GVHSKIVIVDNHLLAVGSFN 106
PLDc_vPLD1_2_yPLD_like_2 cd09141
Catalytic domain, repeat 2, of vertebrate phospholipases, PLD1 and PLD2, yeast PLDs, and ...
 16-139 7.27e-03

Catalytic domain, repeat 2, of vertebrate phospholipases, PLD1 and PLD2, yeast PLDs, and similar proteins; Catalytic domain, repeat 2, of vertebrate phospholipases D (PLD1 and PLD2), yeast phospholipase D (PLD SPO14/PLD1), and other similar eukaryotic proteins. These PLD enzymes play a pivotal role in transmembrane signaling and cellular regulation. They hydrolyze the terminal phosphodiester bond of phospholipids resulting in the formation of phosphatidic acid and alcohols. Phosphatidic acid is an essential compound involved in signal transduction. PLDs also catalyze the transphosphatidylation of phospholipids to acceptor alcohols, by which various phospholipids can be synthesized. The vertebrate PLD1 and PLD2 are membrane associated phosphatidylinositol 4,5-bisphosphate (PIP2)-dependent enzymes that selectively hydrolyze phosphatidylcholine (PC). Protein cofactors and calcium may be required for their activation. Yeast SPO14/PLD1 is a calcium-independent PLD, which needs PIP2 for its activity. Instead of the regulatory calcium-dependent phospholipid-binding C2 domain in plants, most mammalian and yeast PLDs have adjacent Phox (PX) and the Pleckstrin homology (PH) domains at the N-terminus, which have been shown to mediate membrane targeting of the protein and are closely linked to polyphosphoinositide signaling. The PX and PH domains are also present in zeta-type PLD from Arabidopsis, which is more closely related to vertebrate PLDs than to other plant PLD types. In addition, this subfamily also includes some related proteins which have either PX-like or PH domains in their N-termini. Like other members of the PLD superfamily, the monomer of mammalian and yeast PLDs consists of two catalytic domains, each containing one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue). Two HKD motifs from the two domains form a single active site. These PLDs utilize a common two-step ping-pong catalytic mechanism involving an enzyme-substrate intermediate to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine residue from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group.


Pssm-ID: 197239 [Multi-domain]  Cd Length: 183  Bit Score: 37.15  E-value: 7.27e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778  16 LKARCQLIRQARHRIL--AQYYSWEEDGS-------GKLLLAELVRAARRG------VVVQLL------IDD-------- 66
Cdd:cd09141    10 QNAYLDLIENAEHFIYieNQFFISSTGGEdpvknriGEALVDRIIRAHKEGekfrvyIVLPLLpgfegdLDDpggssira 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778  67 --------LYGGENRFLEAVAAEPGIE----VRLFNpfwLRGWRpltlLLEGVLSFRRINhrMHNKLLLVDGSQAVIGGR 134
Cdd:cd09141    90 imhwqyqsICRGEHSLLERLKKEEGVDpeqyISFLS---LRTHG----KLGGRPVTEQIY--VHSKLMIVDDRIVIIGSA 160


                  ....*
gi 2067386778 135 NIGDR 139
Cdd:cd09141   161 NINDR 165
PLDc_unchar1_1 cd09127
Putative catalytic domain, repeat 1, of uncharacterized phospholipase D-like proteins; ...
 267-383 7.83e-03

Putative catalytic domain, repeat 1, of uncharacterized phospholipase D-like proteins; Putative catalytic domain, repeat 1, of uncharacterized phospholipase D (PLD, EC 3.1.4.4)-like proteins. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze transphosphatidylation of phospholipids to acceptor alcohols. Members of this subfamily contain two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the PLD superfamily. The two motifs may be part of the active site and may be involved in phosphatidyl group transfer.


Pssm-ID: 197225 [Multi-domain]  Cd Length: 141  Bit Score: 36.47  E-value: 7.83e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067386778 267 LVSPYLILTRGLRRRLKGQRRQGVDIEILTNSLASTDVPLVYGAYRRhrpwLERQGVTLFELTTEA-FS-LHAKLILMGK 344
Cdd:cd09127    25 LLKMYEFTDPALEKALAAAAKRGVRVRVLLEGGPVGGISRAEKLLDY----LNEAGVEVRWTNGTArYRyTHAKYIVVDD 100

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 2067386778 345 EEALLGSFNLDPRSLMLNTELMLHLHSPTLCDELQQLID 383
Cdd:cd09127   101 ERALVLTENFKPSGFTGTRGFGVVTDDPAVVAEIADVFD 139
 
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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