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Conserved domains on  [gi|497594290|ref|WP_009908474|]
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cardiolipin synthase ClsB [Burkholderia thailandensis]

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 ...
 23-408 2.67e-91

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: 280.29  E-value: 2.67e-91
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290  23 ASRLAFTSGNAVRLCDGGAAFFPALIERIDAARERVGLETYIFCDDAVGRAVSDALVRAAARGVHVRVITDGIGTERLP- 101
Cdd:COG1502    6 AAGLPLVGGNRVTLLVDGDEAFAALLEAIEAARRSIDLEYYIFDDDEVGRRLADALIAAARRGVKVRVLLDGIGSRALNr 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 102 -LFGAWPDAGVEHRIYNP-YLFGRFGFSRTHRKLAVIDDAYAFCGGINIVDDFEQNGERLPYpRWDFALELQGPAVADVR 179
Cdd:COG1502   86 dFLRRLRAAGVEVRLFNPvRLLFRRLNGRNHRKIVVIDGRVAFVGGANITDEYLGRDPGFGP-WRDTHVRIEGPAVADLQ 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 180 AAFEVQWHRIAAGHKRYAEYVPHGAdgtafagrfrrwmrshrwvkagalrvvtepsVAFVARDNVVNRRAIEKAYLAAIG 259
Cdd:COG1502  165 AVFAEDWNFATGEALPFPEPAGDVR-------------------------------VQVVPSGPDSPRETIERALLAAIA 213

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 260 RARQSILLANPYFMPGRKLRRALAGAARRGVDVRILL-GRNEFASLDMAVPFLYHALLRSGVRVAEYDKTILHGKVAVID 338
Cdd:COG1502  214 SARRRIYIETPYFVPDRSLLRALIAAARRGVDVRILLpAKSDHPLVHWASRSYYEELLEAGVRIYEYEPGFLHAKVMVVD 293

                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 339 DHWATVGSSNLDALSLMLNNEANVVlVRHREETAALRDAIAVAFADGREIDPALYAARPaVERFLNWFAY 408
Cdd:COG1502  294 DEWALVGSANLDPRSLRLNFEVNLV-IYDPEFAAQLRARFEEDLAHSREVTLEEWRKRP-LRRLRERLAR 361
 
Name Accession Description Interval E-value
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 23-408 2.67e-91

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: 280.29  E-value: 2.67e-91
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290  23 ASRLAFTSGNAVRLCDGGAAFFPALIERIDAARERVGLETYIFCDDAVGRAVSDALVRAAARGVHVRVITDGIGTERLP- 101
Cdd:COG1502    6 AAGLPLVGGNRVTLLVDGDEAFAALLEAIEAARRSIDLEYYIFDDDEVGRRLADALIAAARRGVKVRVLLDGIGSRALNr 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 102 -LFGAWPDAGVEHRIYNP-YLFGRFGFSRTHRKLAVIDDAYAFCGGINIVDDFEQNGERLPYpRWDFALELQGPAVADVR 179
Cdd:COG1502   86 dFLRRLRAAGVEVRLFNPvRLLFRRLNGRNHRKIVVIDGRVAFVGGANITDEYLGRDPGFGP-WRDTHVRIEGPAVADLQ 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 180 AAFEVQWHRIAAGHKRYAEYVPHGAdgtafagrfrrwmrshrwvkagalrvvtepsVAFVARDNVVNRRAIEKAYLAAIG 259
Cdd:COG1502  165 AVFAEDWNFATGEALPFPEPAGDVR-------------------------------VQVVPSGPDSPRETIERALLAAIA 213

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 260 RARQSILLANPYFMPGRKLRRALAGAARRGVDVRILL-GRNEFASLDMAVPFLYHALLRSGVRVAEYDKTILHGKVAVID 338
Cdd:COG1502  214 SARRRIYIETPYFVPDRSLLRALIAAARRGVDVRILLpAKSDHPLVHWASRSYYEELLEAGVRIYEYEPGFLHAKVMVVD 293

                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 339 DHWATVGSSNLDALSLMLNNEANVVlVRHREETAALRDAIAVAFADGREIDPALYAARPaVERFLNWFAY 408
Cdd:COG1502  294 DEWALVGSANLDPRSLRLNFEVNLV-IYDPEFAAQLRARFEEDLAHSREVTLEEWRKRP-LRRLRERLAR 361
PRK11263 PRK11263
cardiolipin synthase ClsB;
30-376 1.59e-77

cardiolipin synthase ClsB;


Pssm-ID: 236888 [Multi-domain]  Cd Length: 411  Bit Score: 246.40  E-value: 1.59e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290  30 SGNAVRLCDGGAAFFPALIERIDAARERVGLETYIFCDDAVGRAVSDALVRAAARGVHVRVITDGIGTERLP--LFGAWP 107
Cdd:PRK11263   6 EGNRIQLLENGEQYYPRVFEAIAAAQEEILLETFILFEDKVGKQLHAALLAAAQRGVKVEVLVDGYGSPDLSdeFVNELT 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 108 DAGVEHRIYNPY--LFGRFG--FSRTHRKLAVIDDAYAFCGGINIVDDfeQNGERLPYPRWDFALELQGPAVADVRAaFE 183
Cdd:PRK11263  86 AAGVRFRYFDPRprLLGMRTnlFRRMHRKIVVIDGRIAFVGGINYSAD--HLSDYGPEAKQDYAVEVEGPVVADIHQ-FE 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 184 VQwhriAAGHkryaeyvphgadgtafAGRFRRWMRSHRwvKAGALRVVTEPSVAFVARDNVVNRRAIEKAYLAAIGRARQ 263
Cdd:PRK11263 163 LE----ALPG----------------QSAARRWWRRHH--RAEENRQPGEAQALLVWRDNEEHRDDIERHYLKALRQARR 220

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 264 SILLANPYFMPGRKLRRALAGAARRGVDVR-ILLGRNEFASLDMAVPFLYHALLRSGVRVAEYDKTILHGKVAVIDDHWA 342
Cdd:PRK11263 221 EVIIANAYFFPGYRLLRALRNAARRGVRVRlILQGEPDMPIVRVGARLLYNYLLKGGVQIYEYCRRPLHGKVALMDDHWA 300

                        330       340       350
                 ....*....|....*....|....*....|....
gi 497594290 343 TVGSSNLDALSLMLNNEANVVlVRHREETAALRD 376
Cdd:PRK11263 301 TVGSSNLDPLSLSLNLEANLI-IRDRAFNQTLRD 333
PLDc_ybhO_like_2 cd09159
Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; ...
 239-408 7.49e-49

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: 163.86  E-value: 7.49e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 239 VARDNVVNRRAIEKAYLAAIGRARQSILLANPYFMPGRKLRRALAGAARRGVDVRILLGRNEFASLD-MAVPFLYHALLR 317
Cdd:cd09159    1 VVSDPRRRRSSIRRAYLVAIAAARRRIWIANAYFVPDRRLRRALIEAARRGVDVRLLLPGKSDDPLTvAASRALYGKLLR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 318 SGVRVAEYDKTILHGKVAVIDDHWATVGSSNLDALSLMLNNEANVVlVRHREETAALRDAIAVAFADGREIDPALYAARP 397
Cdd:cd09159   81 AGVRIFEYQPSMLHAKTAVIDGDWATVGSSNLDPRSLRLNLEANLV-VEDPAFAAQLEELFEEDLARSREITLEEWRRRP 159

                        170
                 ....*....|.
gi 497594290 398 AVERFLNWFAY 408
Cdd:cd09159  160 LWQRLLEWLAY 170
bac_cardiolipin TIGR04265
cardiolipin synthase; This model is based on experimentally characterized bacterial ...
 2-402 1.22e-46

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: 166.89  E-value: 1.22e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290    2 SGKARHRLAQLRQMFLQERGSASrlafTSGNAVRLCDGGAAFFPALIERIDAARERVGLETYIFCDDAVGRAVSDALVRA 81
Cdd:TIGR04265  93 ANEQSQKAAPLFKMLLRNQGIFL----TEGNQLKLMTDGDDVYDALIQDIKNARHYIHLEYYIWQPDGLGDQILESLMAK 168

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290   82 AARGVHVRVITDGIGTERLplFGAWP----DAGVEHRIYN----PYLFGRFGFsRTHRKLAVIDDAYAFCGGINIVDDFE 153
Cdd:TIGR04265 169 AKQGVHVRILYDDVGSVAL--FKSWPelfrNAGGEVVAFFpvklPLLNLRMNN-RNHRKIIVIDGQIGYVGGFNIGDEYL 245

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290  154 QNGERLPYPRwDFALELQGPAVADVRAAFEVQWHRIAagHKRYAEYVPH--------GADG---TAFAGRFRRWmrshrw 222
Cdd:TIGR04265 246 GKDAKFGYWR-DTHLRIEGDAVTALQLIFILDWNSQT--GRRIIPYDPDyfpmpneqAGGHgiqIIASGPDFPW------ 316

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290  223 vkagalrvvtepsvafvardnvvnrRAIEKAYLAAIGRARQSILLANPYFMPGRKLRRALAGAARRGVDVRILLGRNEFA 302
Cdd:TIGR04265 317 -------------------------EQIKYGYLKMIYSAKKSIYIQSPYFIPDDDLLHAIKIAALSGVDVSIMIPNKPDH 371

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290  303 sldmavPFLYHA-------LLRSGVRVAEYDKTILHGKVAVIDDHWATVGSSNLDALSLMLNNEANVVLvrHREETAA-L 374
Cdd:TIGR04265 372 ------PLVFWAsrsnfteLLAAGVKIYQYENGFLHSKSVLVDDEIASVGTANMDMRSFWLNFEVNAFI--YDKGFAKdL 443

                         410       420
                  ....*....|....*....|....*...
gi 497594290  375 RDAIAVAFADGREIDPALYAARPAVERF 402
Cdd:TIGR04265 444 AAAYDDDISRSRQLTKRLYAKRPLWQRF 471
PLDc_2 pfam13091
PLD-like domain;
254-376 4.06e-21

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 88.50  E-value: 4.06e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290  254 YLAAIGRARQSILLANPYFMPGRKLRRALAGAARRGVDVRILLGRN--EFASLDMAVPFLYHALLRSGVRVAEYDKT--I 329
Cdd:pfam13091   1 LIDLINSAKKSIDIATYYFVPDREIIDALIAAAKRGVDVRIILDSNkdDAGGPKKASLKELRSLLRAGVEIREYQSFlrS 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 497594290  330 LHGKVAVIDDHWATVGSSNLDALSLMLNNEANVVlVRHREETAALRD 376
Cdd:pfam13091  81 MHAKFYIIDGKTVIVGSANLTRRALRLNLENNVV-IKDPELAQELEK 126
 
Name Accession Description Interval E-value
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 23-408 2.67e-91

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: 280.29  E-value: 2.67e-91
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290  23 ASRLAFTSGNAVRLCDGGAAFFPALIERIDAARERVGLETYIFCDDAVGRAVSDALVRAAARGVHVRVITDGIGTERLP- 101
Cdd:COG1502    6 AAGLPLVGGNRVTLLVDGDEAFAALLEAIEAARRSIDLEYYIFDDDEVGRRLADALIAAARRGVKVRVLLDGIGSRALNr 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 102 -LFGAWPDAGVEHRIYNP-YLFGRFGFSRTHRKLAVIDDAYAFCGGINIVDDFEQNGERLPYpRWDFALELQGPAVADVR 179
Cdd:COG1502   86 dFLRRLRAAGVEVRLFNPvRLLFRRLNGRNHRKIVVIDGRVAFVGGANITDEYLGRDPGFGP-WRDTHVRIEGPAVADLQ 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 180 AAFEVQWHRIAAGHKRYAEYVPHGAdgtafagrfrrwmrshrwvkagalrvvtepsVAFVARDNVVNRRAIEKAYLAAIG 259
Cdd:COG1502  165 AVFAEDWNFATGEALPFPEPAGDVR-------------------------------VQVVPSGPDSPRETIERALLAAIA 213

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 260 RARQSILLANPYFMPGRKLRRALAGAARRGVDVRILL-GRNEFASLDMAVPFLYHALLRSGVRVAEYDKTILHGKVAVID 338
Cdd:COG1502  214 SARRRIYIETPYFVPDRSLLRALIAAARRGVDVRILLpAKSDHPLVHWASRSYYEELLEAGVRIYEYEPGFLHAKVMVVD 293

                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 339 DHWATVGSSNLDALSLMLNNEANVVlVRHREETAALRDAIAVAFADGREIDPALYAARPaVERFLNWFAY 408
Cdd:COG1502  294 DEWALVGSANLDPRSLRLNFEVNLV-IYDPEFAAQLRARFEEDLAHSREVTLEEWRKRP-LRRLRERLAR 361
PRK11263 PRK11263
cardiolipin synthase ClsB;
30-376 1.59e-77

cardiolipin synthase ClsB;


Pssm-ID: 236888 [Multi-domain]  Cd Length: 411  Bit Score: 246.40  E-value: 1.59e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290  30 SGNAVRLCDGGAAFFPALIERIDAARERVGLETYIFCDDAVGRAVSDALVRAAARGVHVRVITDGIGTERLP--LFGAWP 107
Cdd:PRK11263   6 EGNRIQLLENGEQYYPRVFEAIAAAQEEILLETFILFEDKVGKQLHAALLAAAQRGVKVEVLVDGYGSPDLSdeFVNELT 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 108 DAGVEHRIYNPY--LFGRFG--FSRTHRKLAVIDDAYAFCGGINIVDDfeQNGERLPYPRWDFALELQGPAVADVRAaFE 183
Cdd:PRK11263  86 AAGVRFRYFDPRprLLGMRTnlFRRMHRKIVVIDGRIAFVGGINYSAD--HLSDYGPEAKQDYAVEVEGPVVADIHQ-FE 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 184 VQwhriAAGHkryaeyvphgadgtafAGRFRRWMRSHRwvKAGALRVVTEPSVAFVARDNVVNRRAIEKAYLAAIGRARQ 263
Cdd:PRK11263 163 LE----ALPG----------------QSAARRWWRRHH--RAEENRQPGEAQALLVWRDNEEHRDDIERHYLKALRQARR 220

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 264 SILLANPYFMPGRKLRRALAGAARRGVDVR-ILLGRNEFASLDMAVPFLYHALLRSGVRVAEYDKTILHGKVAVIDDHWA 342
Cdd:PRK11263 221 EVIIANAYFFPGYRLLRALRNAARRGVRVRlILQGEPDMPIVRVGARLLYNYLLKGGVQIYEYCRRPLHGKVALMDDHWA 300

                        330       340       350
                 ....*....|....*....|....*....|....
gi 497594290 343 TVGSSNLDALSLMLNNEANVVlVRHREETAALRD 376
Cdd:PRK11263 301 TVGSSNLDPLSLSLNLEANLI-IRDRAFNQTLRD 333
cls PRK01642
cardiolipin synthetase; Reviewed
 25-408 5.22e-52

cardiolipin synthetase; Reviewed


Pssm-ID: 234967 [Multi-domain]  Cd Length: 483  Bit Score: 181.52  E-value: 5.22e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290  25 RLAFTSGNAVRLCDGGAAFFPALIERIDAARERVGLETYIFCDDAVGRAVSDALVRAAARGVHVRVITDGIGTERLPLfG 104
Cdd:PRK01642 109 GIPGLKGNQLRLLTNGDETFQAIIRDIELARHYILMEFYIWRPDGLGDQVAEALIAAAKRGVRVRLLYDSIGSFAFFR-S 187

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 105 AWP----DAGVE-HRIYNPYLFgRFGFSRT----HRKLAVIDDAYAFCGGINIVDD--FEQNGerlPYPRW-DFALELQG 172
Cdd:PRK01642 188 PYPeelrNAGVEvVEFLKVNLG-RVFRRRLdlrnHRKIVVIDGYIAYTGSMNVVDPeyFKQDP---GVGQWrDTHVRIEG 263

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 173 PAVADVRAAFEVQWHrIAAGHKRYAEyVPHGAdgtafagrfrrWMRSHRWVKAGALRVVTEPSVAfvardnvvnRRAIEK 252
Cdd:PRK01642 264 PVVTALQLIFAEDWE-WETGERILPP-PPDVL-----------IMPFEEASGHTVQVIASGPGDP---------EETIHQ 321

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 253 AYLAAIGRARQSILLANPYFMPGRKLRRALAGAARRGVDVRILL-GRNefaslDMAVPFL-----YHALLRSGVRVAEYD 326
Cdd:PRK01642 322 FLLTAIYSARERLWITTPYFVPDEDLLAALKTAALRGVDVRIIIpSKN-----DSLLVFWasrafFTELLEAGVKIYRYE 396

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 327 KTILHGKVAVIDDHWATVGSSNLDALSLMLNNEANVVLVrHREETAALRDAIAVAFADGREIDPALYAARPAVERFLNWF 406
Cdd:PRK01642 397 GGLLHTKSVLVDDELALVGTVNLDMRSFWLNFEITLVID-DTGFAADLAAMQEDYFARSRELDLEEWRKRPLWQRIAERV 475


                 ..
gi 497594290 407 AY 408
Cdd:PRK01642 476 AR 477
PLDc_ybhO_like_2 cd09159
Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; ...
 239-408 7.49e-49

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: 163.86  E-value: 7.49e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 239 VARDNVVNRRAIEKAYLAAIGRARQSILLANPYFMPGRKLRRALAGAARRGVDVRILLGRNEFASLD-MAVPFLYHALLR 317
Cdd:cd09159    1 VVSDPRRRRSSIRRAYLVAIAAARRRIWIANAYFVPDRRLRRALIEAARRGVDVRLLLPGKSDDPLTvAASRALYGKLLR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 318 SGVRVAEYDKTILHGKVAVIDDHWATVGSSNLDALSLMLNNEANVVlVRHREETAALRDAIAVAFADGREIDPALYAARP 397
Cdd:cd09159   81 AGVRIFEYQPSMLHAKTAVIDGDWATVGSSNLDPRSLRLNLEANLV-VEDPAFAAQLEELFEEDLARSREITLEEWRRRP 159

                        170
                 ....*....|.
gi 497594290 398 AVERFLNWFAY 408
Cdd:cd09159  160 LWQRLLEWLAY 170
PLDc_CLS_1 cd09110
Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Catalytic ...
 40-187 1.17e-47

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: 160.33  E-value: 1.17e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290  40 GAAFFPALIERIDAARERVGLETYIFCDDAVGRAVSDALVRAAARGVHVRVITDGIGTERLP--LFGAWPDAGVEHRIYN 117
Cdd:cd09110    3 GEEFFPALLEAIRAARHSIHLEYYIFRDDEIGRRFRDALIEKARRGVEVRLLYDGFGSLGLSrrFLRELREAGVEVRAFN 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 497594290 118 PYLFGRFGFS---RTHRKLAVIDDAYAFCGGINIVDDFEQNGERLPyPRWDFALELQGPAVADVRAAFEVQWH 187
Cdd:cd09110   83 PLSFPLFLLRlnyRNHRKILVIDGKIAFVGGFNIGDEYLGKDPGFG-PWRDTHVRIEGPAVADLQAAFLEDWY 154
bac_cardiolipin TIGR04265
cardiolipin synthase; This model is based on experimentally characterized bacterial ...
 2-402 1.22e-46

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: 166.89  E-value: 1.22e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290    2 SGKARHRLAQLRQMFLQERGSASrlafTSGNAVRLCDGGAAFFPALIERIDAARERVGLETYIFCDDAVGRAVSDALVRA 81
Cdd:TIGR04265  93 ANEQSQKAAPLFKMLLRNQGIFL----TEGNQLKLMTDGDDVYDALIQDIKNARHYIHLEYYIWQPDGLGDQILESLMAK 168

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290   82 AARGVHVRVITDGIGTERLplFGAWP----DAGVEHRIYN----PYLFGRFGFsRTHRKLAVIDDAYAFCGGINIVDDFE 153
Cdd:TIGR04265 169 AKQGVHVRILYDDVGSVAL--FKSWPelfrNAGGEVVAFFpvklPLLNLRMNN-RNHRKIIVIDGQIGYVGGFNIGDEYL 245

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290  154 QNGERLPYPRwDFALELQGPAVADVRAAFEVQWHRIAagHKRYAEYVPH--------GADG---TAFAGRFRRWmrshrw 222
Cdd:TIGR04265 246 GKDAKFGYWR-DTHLRIEGDAVTALQLIFILDWNSQT--GRRIIPYDPDyfpmpneqAGGHgiqIIASGPDFPW------ 316

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290  223 vkagalrvvtepsvafvardnvvnrRAIEKAYLAAIGRARQSILLANPYFMPGRKLRRALAGAARRGVDVRILLGRNEFA 302
Cdd:TIGR04265 317 -------------------------EQIKYGYLKMIYSAKKSIYIQSPYFIPDDDLLHAIKIAALSGVDVSIMIPNKPDH 371

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290  303 sldmavPFLYHA-------LLRSGVRVAEYDKTILHGKVAVIDDHWATVGSSNLDALSLMLNNEANVVLvrHREETAA-L 374
Cdd:TIGR04265 372 ------PLVFWAsrsnfteLLAAGVKIYQYENGFLHSKSVLVDDEIASVGTANMDMRSFWLNFEVNAFI--YDKGFAKdL 443

                         410       420
                  ....*....|....*....|....*...
gi 497594290  375 RDAIAVAFADGREIDPALYAARPAVERF 402
Cdd:TIGR04265 444 AAAYDDDISRSRQLTKRLYAKRPLWQRF 471
PRK12452 PRK12452
cardiolipin synthase;
33-406 1.40e-39

cardiolipin synthase;


Pssm-ID: 171510 [Multi-domain]  Cd Length: 509  Bit Score: 148.14  E-value: 1.40e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290  33 AVRLCDGGAAFFPALIERIDAARERVGLETYIFCDDAVGRAVSDALVRAAARGVHVRVITDGIGTERLPLFGAWP--DAG 110
Cdd:PRK12452 141 TTKLLTNGDQTFSEILQAIEQAKHHIHIQYYIYKSDEIGTKVRDALIKKAKDGVIVRFLYDGLGSNTLRRRFLQPmkEAG 220

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 111 VEHRIYNPYLFGRFGFS---RTHRKLAVIDDAYAFCGGINIVDDFEQNGERLPYPRwDFALELQGPAVADVRAAFEVQWH 187
Cdd:PRK12452 221 IEIVEFDPIFSAWLLETvnyRNHRKIVIVDGEIGFTGGLNVGDEYLGRSKKFPVWR-DSHLKVEGKALYKLQAIFLEDWL 299

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 188 RIAAGHKRYAeyvphgadGTAFAGRfrRWMRSHRWVKagalrvvTEPSVAFVARDNVVNRRAIEKAYLAAIGRARQSILL 267
Cdd:PRK12452 300 YASSGLNTYS--------WDPFMNR--QYFPGKEISN-------AEGAVQIVASGPSSDDKSIRNTLLAVMGSAKKSIWI 362

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 268 ANPYFMPGRKLRRALAGAARRGVDVRILL-GRNEFASLDMAVPFLYHALLRSGVRVAEYDKTILHGKVAVIDDHWATVGS 346
Cdd:PRK12452 363 ATPYFIPDQETLTLLRLSAISGIDVRILYpGKSDSIISDQASQSYFTPLLKAGASIYSYKDGFMHAKIVLVDDKIATIGT 442

                        330       340       350       360       370       380
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 497594290 347 SNLDALSLMLNNEanVVLVRHREETAA--LRDAIAvAFADGREIDPALYAARPAVERFLNWF 406
Cdd:PRK12452 443 ANMDVRSFELNYE--IISVLYESETVHdiKRDFED-DFKHSTEIKWNAFQKRSIKKRILESF 501
PLDc_CLS_2 cd09112
catalytic domain repeat 2 of bacterial cardiolipin synthase and similar proteins; This CD ...
 239-407 7.57e-34

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: 124.51  E-value: 7.57e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 239 VARDNVVNRRAIEKAYLAAIGRARQSILLANPYFMPGRKLRRALAGAARRGVDVRILL-GRNefaslDMavPFLYHA--- 314
Cdd:cd09112    1 VSSGPDSDWSSIEQAYLKAINSAKKSIYIQTPYFIPDESLLEALKTAALSGVDVRIMIpGKP-----DH--KLVYWAsrs 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 315 ----LLRSGVRVAEYDKTILHGKVAVIDDHWATVGSSNLDALSLMLNNEANVVlVRHREETAALRDAIAVAFADGREIDP 390
Cdd:cd09112   74 yfeeLLKAGVKIYEYNKGFLHSKTLIVDDEIASVGTANLDIRSFELNFEVNAV-IYDKEVAKKLEEIFEEDLKDSELLTL 152

                        170
                 ....*....|....*..
gi 497594290 391 ALYAARPAVERFLNWFA 407
Cdd:cd09112  153 EEWRKRSLWKRFKESLA 169
PLDc_EcCLS_like_1 cd09152
Catalytic domain, repeat 1, of Escherichia coli cardiolipin synthase and similar proteins; ...
 31-187 1.87e-30

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: 115.00  E-value: 1.87e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290  31 GNAVRLCDGGAAFFPALIERIDAARERVGLETYIFCDDAVGRAVSDALVRAAARGVHVRVITDGIGTERLPLFGAWP--- 107
Cdd:cd09152    1 GNRVELLTDYDAVIDRLIADIDAAKHHVHLLFYIWADDGTGDRVAEALERAAKRGVTCRLLLDAVGSRAFFRSSLWKrlr 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 108 DAGVEHRIYNPYLFGRFGFS----RTHRKLAVIDDAYAFCGGINIVD-DFEQngeRLPYPRW-DFALELQGPAVADVRAA 181
Cdd:cd09152   81 EAGVEVVEALPLRLFRRRLArfdlRNHRKIAVIDGRIAYTGSQNIIDpEFFK---KAGGGPWvDLMVRVEGPVVSQLQAV 157


                 ....*.
gi 497594290 182 FEVQWH 187
Cdd:cd09152  158 FASDWY 163
PLDc_CLS_unchar2_1 cd09157
Putative catalytic domain, repeat 1, of uncharacterized proteins similar to bacterial ...
 39-187 2.65e-30

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: 114.20  E-value: 2.65e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290  39 GGAAFFPALIERIDAARERVGLETYIFCDDAVGRAVSDALVRAAARGVHVRVITDGIGT--ERLPLFGAWPDAGVEHRIY 116
Cdd:cd09157    2 NGDEAYPAMLEAIDAARHSIALSSYIFDNDGVGREFVDALAEAVARGVDVRVLIDGVGArySRPSIRRRLRRAGVPVARF 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 497594290 117 NPYLFGRFGFS---RTHRKLAVIDDAYAFCGGINIVDDFeQNGERLPYPRWDFALELQGPAVADVRAAFEVQWH 187
Cdd:cd09157   82 LPPRLPPRLPFinlRNHRKILVVDGRTGFTGGMNIRDGH-LVADDPKNPVQDLHFRVEGPVVAQLQEVFAEDWY 154
PLDc_PaCLS_like_1 cd09155
Putative catalytic domain, repeat 1, of Pseudomonas aeruginosa cardiolipin synthase and ...
 40-187 1.62e-26

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: 104.25  E-value: 1.62e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290  40 GAAFFPALIERIDAARERVGLETYIFCDDAVGRAVSDALVRAAARGVHVRVITDGIGTERLP--LFGAWPDAGVEHRIYN 117
Cdd:cd09155    3 GEATFAAIFEAIASAEEYILVQFYIIRDDDLGRELKDALIARAQAGVRVYLLYDEIGSHSLSrsYIERLRKAGVEVSAFN 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 497594290 118 --PYLFGRFGFS-RTHRKLAVIDDAYAFCGGINIVDdfEQNGERLPYPRW-DFALELQGPAVADVRAAFEVQWH 187
Cdd:cd09155   83 ttRGWGNRFQLNfRNHRKIVVVDGQTAFVGGHNVGD--EYLGRDPRLGPWrDTHVKLEGPAVQQLQLSFAEDWY 154
PLDc_CLS_unchar1_1 cd09156
Putative catalytic domain, repeat 1, of uncharacterized proteins similar to bacterial ...
 38-187 3.83e-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: 103.11  E-value: 3.83e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290  38 DGGAAFfPALIERIDAARERVGLETYIFCDDAVGRAVSDALVRAAARGVHVRVITDGIGTERLP--LFGAWPDAGVEHRI 115
Cdd:cd09156    2 DGVEAY-QALIQLIESAKHSIDVCTFILGDDATGRRVIDALARKAREGVEVRLLLDALGSFFLSrrALKKLRAAGGKVAF 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 497594290 116 YNPYL-FGRFGFS--RTHRKLAVIDDAYAFCGGINIVDDFEQNGerlPYP-RW-DFALELQGPAVADVRAAFEVQWH 187
Cdd:cd09156   81 FMPVFrLPFRGRTnlRNHRKIAIADGSTAISGGMNLANEYMGPE---PDDgRWvDLSFLIEGPAVAQYQEVFRSDWA 154
PLDc_EcCLS_like_2 cd09158
Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase and similar proteins; ...
 249-408 6.02e-22

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: 92.25  E-value: 6.02e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 249 AIEKAYLAAIGRARQSILLANPYFMPGRKLRRALAGAARRGVDVRILL-GRNEFASLDMAVPFLYHALLRSGVRVAEYDK 327
Cdd:cd09158   11 NIPQLLLSAIHAARRRVVITTPYFVPDESLLQALCTAALRGVEVTLILpAKNDSFLVGAASRSYYEELLEAGVKIYLYRG 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 328 TILHGKVAVIDDHWATVGSSNLDALSLMLNNEANvVLVRHREETAALRDAIAVAFADGREIDPALYAARPAVERFLNWFA 407
Cdd:cd09158   91 GLLHAKTVTVDDEVALVGSSNFDIRSFALNFEIS-LILYDKEFTAQLRAIQERYLARSDPLTLEEWKKRPLWRRLLENLA 169


                 .
gi 497594290 408 Y 408
Cdd:cd09158  170 R 170
PLDc_2 pfam13091
PLD-like domain;
254-376 4.06e-21

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 88.50  E-value: 4.06e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290  254 YLAAIGRARQSILLANPYFMPGRKLRRALAGAARRGVDVRILLGRN--EFASLDMAVPFLYHALLRSGVRVAEYDKT--I 329
Cdd:pfam13091   1 LIDLINSAKKSIDIATYYFVPDREIIDALIAAAKRGVDVRIILDSNkdDAGGPKKASLKELRSLLRAGVEIREYQSFlrS 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 497594290  330 LHGKVAVIDDHWATVGSSNLDALSLMLNNEANVVlVRHREETAALRD 376
Cdd:pfam13091  81 MHAKFYIIDGKTVIVGSANLTRRALRLNLENNVV-IKDPELAQELEK 126
PLDc_ymdC_like_1 cd09111
Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and ...
 46-187 2.10e-20

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: 87.59  E-value: 2.10e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290  46 ALIER---IDAARERVGLETYIFCDDAVGRAVSDALVRAAARGVHVRVITDGIGTERLPLFGAWPDA--GVEHRIYNPYL 120
Cdd:cd09111    7 ALAARlalIRSAERSIDLQYYIWHDDESGRLLLGELLEAADRGVRVRLLLDDLGTSGRDRLLAALDAhpNIEVRLFNPFR 86

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 497594290 121 FGRFGFS-----------RTHRKLAVIDDAYAFCGGINIVDD-FEQNGErlpYPRWDFALELQGPAVADVRAAFEVQWH 187
Cdd:cd09111   87 NRGGRLLefltdfsrlnrRMHNKLFIVDGAVAIVGGRNIGDEyFGASPE---VNFRDLDVLAVGPVVRQLSESFDTYWN 162
PLDc_CLS_unchar2_2 cd09163
Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial ...
 250-407 2.84e-19

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: 84.53  E-value: 2.84e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 250 IEKAYLAAIGRARQSILLANPYFMPGRKLRRALAGAARRGVDVRILL-GRNEFASLDMAVPFLYHALLRSGVRVAEYDKT 328
Cdd:cd09163   12 LRWTLLGAISAARHSIRIMTPYFLPDRTLITALQAAALRGVEVDIVLpERNNLPLVDWAMRANLWELLEHGVRIYLQPPP 91

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 497594290 329 ILHGKVAVIDDHWATVGSSNLDALSLMLNNEANVVLVrHREETAALRDAIAVAFADGREIDPALYAARPAVERFLNWFA 407
Cdd:cd09163   92 FDHSKLMVVDGAWALIGSANWDPRSLRLNFELNLEVY-DTALAGQLDALFDSKIAKSREVTLEELDARPLPIRLRDAAA 169
PLDc_PaCLS_like_2 cd09161
Putative catalytic domain, repeat 2, of Pseudomonas aeruginosa cardiolipin synthase and ...
 254-401 8.63e-17

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: 77.71  E-value: 8.63e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 254 YLAAIGRARQSILLANPYFMPGRKLRRALAGAARRGVDVRILLGRNEFASLDMAVPFLY-HALLRSGVRVAEYDKTILHG 332
Cdd:cd09161   16 FVQAINAAQKRLWIASPYFVPDEGVLAALQLAALRGVDVRILIPERPDHLLVYLASFSYlPELIRAGVKVYRYQPGFLHQ 95

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 497594290 333 KVAVIDDHWATVGSSNLDALSLMLNNEANVVLVRHR--EETAALRDAiavAFADGREIDPALYAARPAVER 401
Cdd:cd09161   96 KVVLVDDELAAVGTANLDNRSFRLNFEITALVADPGfaQEVEAMLEA---DFAASREVTAAELANRPLWFR 163
PLDc_2 pfam13091
PLD-like domain;
47-186 5.11e-16

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 74.25  E-value: 5.11e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290   47 LIERIDAARERVGLETYIFCDDavgRAVSDALVRAAARGVHVRVITDG----IGTERLPLFGAWP---DAGVEHRIYNPY 119
Cdd:pfam13091   1 LIDLINSAKKSIDIATYYFVPD---REIIDALIAAAKRGVDVRIILDSnkddAGGPKKASLKELRsllRAGVEIREYQSF 77

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 497594290  120 lfgrfgFSRTHRKLAVIDDAYAFCGGINIVDD-FEQNGErlpyprwdFALELQGPAVAD-VRAAFEVQW 186
Cdd:pfam13091  78 ------LRSMHAKFYIIDGKTVIVGSANLTRRaLRLNLE--------NNVVIKDPELAQeLEKEFDRLW 132
PLDc_ymdC_like_2 cd09113
Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and ...
 255-384 1.07e-15

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: 75.72  E-value: 1.07e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 255 LAAIGRARQSILLANPYFMPGRKLRRALAGAARRGVDVRILLgrNEFASLDmaVPFLyHA--------LLRSGVRVAEYD 326
Cdd:cd09113   23 AELLKNAKREVLIVSPYFVPGDEGVALLAELARRGVRVRILT--NSLAATD--VPAV-HSgyaryrkrLLKAGVELYELK 97

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 497594290 327 KTI----------------LHGKVAVIDDHWATVGSSNLDALSLMLNNEAnVVLVRHREETAALRDAIAVAFAD 384
Cdd:cd09113   98 PDAakrkrlrglfgssrasLHAKSFVIDDRLVFVGSFNLDPRSAYLNTEM-GLVIDSPELAAQLRAAMEEDLAP 170
PLDc_SMU_988_like_2 cd09160
Putative catalytic domain, repeat 2, of Streptococcus mutans uncharacterized protein SMU_988 ...
 251-405 3.18e-14

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: 70.22  E-value: 3.18e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 251 EKAYLAAIGRARQSILLANPYFMPGRKLRRALAGAARRGVDVRILLGrnefASLDMAVPFL-----YHALLRSGVRVAEY 325
Cdd:cd09160   13 ENVYLDLINQAKDYVYITTPYLILDDEMLDALCLAAKRGVDVRIITP----HIPDKKYVFLvtrsnYPELLEAGVKIYEY 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 326 DKTILHGKVAVIDDHWATVGSSNLDALSLMLNNEANVVLVRHrEETAALRDAIAVAFADGREIDPALYAARPAVERFLNW 405
Cdd:cd09160   89 TPGFIHAKTFVSDDKAAVVGTINLDYRSLYLHFECGVYMYDT-PVISDIKEDFEETLAQSQEITLEECRKRSLVTRLIGA 167
PLDc_CLS_unchar1_2 cd09162
Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial ...
 245-407 2.97e-13

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: 67.67  E-value: 2.97e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 245 VNRRAIEKAYLAAIGRARQSILLANPYFMPGRKLRRALAGAARRGVDVRILLGRNEFASL-DMAVPFLYHALLRSGVRVA 323
Cdd:cd09162    7 VPGDPLYEALLSAIFEAEHRIWIVTPYFVPDEVLLRALRLAARRGVDVRLIVPKRSNHRIaDLARGSYLRDLQEAGAEIY 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 324 EYDKTILHGKVAVIDDHWATVGSSNLDALSLMLNNEANVVlVRHREETAALRDAIAVAFADGREIDPALYAARPAVERFL 403
Cdd:cd09162   87 LYQPGMLHAKAVVVDDKLALVGSANLDMRSLFLNYEVAVF-FYSPADIKELSDWIESLISQCTEGAPPPSALRDIAEGLM 165


                 ....
gi 497594290 404 NWFA 407
Cdd:cd09162  166 RLLA 169
PLDc_SMU_988_like_1 cd09154
Putative catalytic domain, repeat 1, of Streptococcus mutans uncharacterized protein SMU_988 ...
 40-175 3.57e-13

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: 66.78  E-value: 3.57e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290  40 GAAFFPALIERIDAARERVGLETYIFCDDAVGRAVSDALVRAAARGVHVRVITDGIGTerlplFGAWP--------DAGV 111
Cdd:cd09154    4 GEDMFEDMLEDLKKAEKFIFMEYFIIEEGYMWDSILEILKEKAKEGVEVRIMYDDFGS-----ITTLPkdypkeleKIGI 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 497594290 112 EHRIYNPY--LFGRFGFSRTHRKLAVIDDAYAFCGGINIVDDFEQNGERlpYPRW-DFALELQGPAV 175
Cdd:cd09154   79 KCRVFNPFkpILSLYMNNRDHRKITVIDGKVAFTGGINLADEYINKIER--FGYWkDTGIRLEGEAV 143
PLDc_SF cd00138
Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D ...
 252-364 1.99e-11

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: 60.99  E-value: 1.99e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 252 KAYLAAIGRARQSILLANPYFMPG--RKLRRALAGAARRGVDVRILLGRNEFASLDMaVPFLYHALLRSGVRVAEYDKTI 329
Cdd:cd00138    1 EALLELLKNAKESIFIATPNFSFNsaDRLLKALLAAAERGVDVRLIIDKPPNAAGSL-SAALLEALLRAGVNVRSYVTPP 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 497594290 330 -----LHGKVAVIDDHWATVGSSNLDALSLMLNNEANVVL 364
Cdd:cd00138   80 hfferLHAKVVVIDGEVAYVGSANLSTASAAQNREAGVLV 119
PLDc_SF cd00138
Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D ...
 46-158 9.43e-11

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: 59.07  E-value: 9.43e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290  46 ALIERIDAARERVGLETYIFcDDAVGRAVSDALVRAAARGVHVRVITDGI----GTERLPLFGAWPDAGVEHRIYNpylF 121
Cdd:cd00138    2 ALLELLKNAKESIFIATPNF-SFNSADRLLKALLAAAERGVDVRLIIDKPpnaaGSLSAALLEALLRAGVNVRSYV---T 77

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 497594290 122 GRFGFSRTHRKLAVIDDAYAFCGGINIVD-DFEQNGER 158
Cdd:cd00138   78 PPHFFERLHAKVVVIDGEVAYVGSANLSTaSAAQNREA 115
PLDc_unchar1_2 cd09128
Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins; ...
 251-369 7.53e-10

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: 56.90  E-value: 7.53e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 251 EKAYLAAIGRARQSILLANPYFMPGRKLRRALAGAARRGVDVRILLGRNEFASLDMAVPFLYHALLRSGVRVAEYDKTIL 330
Cdd:cd09128   12 REALLALIDSAEESLLIQNEEMGDDAPILDALVDAAKRGVDVRVLLPSAWSAEDERQARLRALEGAGVPVRLLKDKFLKI 91

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 497594290 331 HGKVAVIDDHWATVGSSNLDALSLMLNNEAnVVLVRHRE 369
Cdd:cd09128   92 HAKGIVVDGKTALVGSENWSANSLDRNREV-GLIFDDPE 129
PLDc_Nuc_like cd09116
Catalytic domain of EDTA-resistant nuclease Nuc, vertebrate phospholipase D6, and similar ...
 47-189 2.19e-09

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: 55.38  E-value: 2.19e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290  47 LIERIDAARERVGLETYIFCDDAVGRAvsdaLVRAAARGVHVRVITDGIgterlplFGAWPDAGVEHRIYN----PYLFG 122
Cdd:cd09116   14 IVALIANAKSSIDVAMYALTDPEIAEA----LKRAAKRGVRVRIILDKD-------SLADNLSITLLALLSnlgiPVRTD 82

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 497594290 123 RfGFSRTHRKLAVIDDAYAFCGGINI-VDDFEQNGERLpyprwdfaLELQGPAVAdvrAAFEVQWHRI 189
Cdd:cd09116   83 S-GSKLMHHKFIIIDGKIVITGSANWtKSGFHRNDENL--------LIIDDPKLA---ASFEEEFNRL 138
PLDc_unchar1_2 cd09128
Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins; ...
 46-186 8.31e-09

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: 53.82  E-value: 8.31e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290  46 ALIERIDAARERVGLETYIFCDDAvgrAVSDALVRAAARGVHVRVITD---GIGTERLPLFGAWPDAGVEHRIYnpylfg 122
Cdd:cd09128   14 ALLALIDSAEESLLIQNEEMGDDA---PILDALVDAAKRGVDVRVLLPsawSAEDERQARLRALEGAGVPVRLL------ 84

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 497594290 123 RFGFSRTHRKLAVIDDAYAFCGGINIVDD-FEQNGErlpyprwdFALELQGPAVAD-VRAAFEVQW 186
Cdd:cd09128   85 KDKFLKIHAKGIVVDGKTALVGSENWSANsLDRNRE--------VGLIFDDPEVAAyLQAVFESDW 142
PLDc_vPLD1_2_like_2 cd09105
Catalytic domain, repeat 2, of vertebrate phospholipases, PLD1 and PLD2, and similar proteins; ...
 247-365 9.42e-08

Catalytic domain, repeat 2, of vertebrate phospholipases, PLD1 and PLD2, and similar proteins; Catalytic domain, repeat 2, of phospholipase D (PLD, EC 3.1.4.4) found in yeast, plants, and vertebrates, and their bacterial homologs. PLDs are involved in signal transduction, vesicle formation, protein transport, and mitosis by participating in phospholipid metabolism. 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. Both prokaryotic and eukaryotic PLDs have two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. PLDs are active as bi-lobed monomers. Each monomer contains two domains, each of which carries one copy of the HKD motif. Two HKD motifs from two domains form a single active site. 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: 197204 [Multi-domain]  Cd Length: 146  Bit Score: 51.15  E-value: 9.42e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 247 RRAIEKAYLAAIGRARQSILLANPYFMPgRKLRRALAGAARRGVDVRILL---GRNEFASLDMAVPFLYHALLR------ 317
Cdd:cd09105    6 EFEIADAYLKAIRNARRYIYIEDQYLWS-PELLDALAEALKANPGLRVVLvlpALPDAVAFGADDGLDALALLAllllad 84

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 497594290 318 -SGVRVAEYDKT------------ILHGKVAVIDDHWATVGSSNLDALSLMLNNEANVVLV 365
Cdd:cd09105   85 aAPDRVAVFSLAthrrgllggppiYVHSKVVIVDDEWATVGSANLNRRSMTWDTELNLAVV 145
PLDc_unchar1_1 cd09127
Putative catalytic domain, repeat 1, of uncharacterized phospholipase D-like proteins; ...
 47-177 1.45e-07

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: 50.34  E-value: 1.45e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290  47 LIERIDAARERVGLETYIFCDdavgRAVSDALVRAAARGVHVRVITD-----GIGTERlPLFGAWPDAGVEHRIYNPylf 121
Cdd:cd09127   13 VVDAIASAKRSILLKMYEFTD----PALEKALAAAAKRGVRVRVLLEggpvgGISRAE-KLLDYLNEAGVEVRWTNG--- 84

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 497594290 122 gRFGFSRTHRKLAVIDDAYAFCGGINIVDdfeqngERLPYPRwDFALELQGPAVAD 177
Cdd:cd09127   85 -TARYRYTHAKYIVVDDERALVLTENFKP------SGFTGTR-GFGVVTDDPAVVA 132
PLDc_CLS_2 cd09112
catalytic domain repeat 2 of bacterial cardiolipin synthase and similar proteins; This CD ...
 46-155 2.47e-07

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: 50.55  E-value: 2.47e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290  46 ALIERIDAARERVGLET-YIFCDDAVgravSDALVRAAARGVHVRVITDGIGTERLPLFGA---WPD---AGVEHRIYNP 118
Cdd:cd09112   15 AYLKAINSAKKSIYIQTpYFIPDESL----LEALKTAALSGVDVRIMIPGKPDHKLVYWASrsyFEEllkAGVKIYEYNK 90

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 497594290 119 ylfgrfGFSrtHRKLAVIDDAYAFCGGINIvD------DFEQN 155
Cdd:cd09112   91 ------GFL--HSKTLIVDDEIASVGTANL-DirsfelNFEVN 124
PLDc_vPLD6_like cd09171
Catalytic domain of vertebrate phospholipase D6 and similar proteins; Catalytic domain of ...
 41-147 2.12e-06

Catalytic domain of vertebrate phospholipase D6 and similar proteins; Catalytic domain of vertebrate phospholipase D6 (PLD6, EC 3.1.4.4), a homolog of the EDTA-resistant nuclease Nuc from Salmonella typhimurium, and similar proteins. PLD6 can selectively hydrolyze 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. It also catalyzes the transphosphatidylation of phospholipids to acceptor alcohols, by which various phospholipids can be synthesized. PLD6 belongs to the phospholipase D (PLD) superfamily. Its monomer contains a short conserved sequence motif, H-x-K-x(4)-D (where x represents any amino acid residue), termed the HKD motif, which is essential in catalysis. PLD6 is more closely related to the nuclease Nuc than to other vertebrate phospholipases, which have two copies of the HKD motif in a single polypeptide chain. Like Nuc, PLD6 may utilize a two-step mechanism to cleave phosphodiester bonds: Upon substrate binding, the bond is first attacked by a histidine residue from the HKD motif of one subunit 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: 197268 [Multi-domain]  Cd Length: 136  Bit Score: 46.83  E-value: 2.12e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290  41 AAFFP------ALIERIDAARERVGLETYIFCDDAVgravSDALVRAAARGVHVRVITDGIGTER----LPLFGawpDAG 110
Cdd:cd09171    1 CLFFPgetslsKLLRYLLSARKSLDVCVFTITCDDL----ADAILDLHRRGVRVRIITDDDQMEDkgsdIGKLR---KAG 73

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 497594290 111 VEHRI-YNPYLFgrfgfsrtHRKLAVIDDAYAFCGGIN 147
Cdd:cd09171   74 IPVRTdLSSGHM--------HHKFAVIDGKILITGSFN 103
PLDc_Nuc cd09170
Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar ...
 38-147 2.57e-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: 2.57e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290  38 DGGAAffPALIERIDAARERVGLETYIFCDdavgRAVSDALVRAAARGVHVRVITD-----GIGTERLPLFgawpDAGVE 112
Cdd:cd09170    9 EGGAR--ELILDVIDSARRSIDVAAYSFTS----PPIARALIAAKKRGVDVRVVLDksqagGKYSALNYLA----NAGIP 78

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 497594290 113 HRI-YNPYLFgrfgfsrtHRKLAVIDDAYAFCGGIN 147
Cdd:cd09170   79 VRIdDNYAIM--------HNKVMVIDGKTVITGSFN 106
PLDc_SMU_988_like_2 cd09160
Putative catalytic domain, repeat 2, of Streptococcus mutans uncharacterized protein SMU_988 ...
 51-147 6.92e-06

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: 46.34  E-value: 6.92e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290  51 IDAARERVGLET-YIFCDDAVgravSDALVRAAARGVHVRVITDGIGTERLPL------FGAWPDAGVehRI--YNPylf 121
Cdd:cd09160   20 INQAKDYVYITTpYLILDDEM----LDALCLAAKRGVDVRIITPHIPDKKYVFlvtrsnYPELLEAGV--KIyeYTP--- 90

                         90       100
                 ....*....|....*....|....*.
gi 497594290 122 grfGFsrTHRKLAVIDDAYAFCGGIN 147
Cdd:cd09160   91 ---GF--IHAKTFVSDDKAAVVGTIN 111
PLDc_unchar3 cd09131
Putative catalytic domain of uncharacterized phospholipase D-like proteins; Putative catalytic ...
 290-365 9.29e-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: 45.02  E-value: 9.29e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 497594290 290 VDVRILL-GRNEFASLDMAVPFLYHALLRSGVRVaEYD--KTILHGKVAVIDDHWATVGSSNLDALSLMLNNEANVVLV 365
Cdd:cd09131   51 VDVKVVLeDSIDDDEVTEENDNTYRYLKDNGVEV-RFDspSVTTHTKLVVIDGRTVYVGSHNWTYSALDYNHEASVLIE 128
PLDc_unchar3 cd09131
Putative catalytic domain of uncharacterized phospholipase D-like proteins; Putative catalytic ...
 43-147 1.43e-05

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: 44.64  E-value: 1.43e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290  43 FFPALIERIDAARERVGLETYIF-CDDAVGRAVS---DALVRAAARGVHVRVITD-GIGTERLPlfgAWPDAGVEhRIYN 117
Cdd:cd09131    4 YYPALLDLINNAKRSIYIAMYMFkYYENPGNGVNtllEALIDAHKRGVDVKVVLEdSIDDDEVT---EENDNTYR-YLKD 79

                         90       100       110
                 ....*....|....*....|....*....|..
gi 497594290 118 PYLFGRFGFS--RTHRKLAVIDDAYAFCGGIN 147
Cdd:cd09131   80 NGVEVRFDSPsvTTHTKLVVIDGRTVYVGSHN 111
PLDc_unchar1_1 cd09127
Putative catalytic domain, repeat 1, of uncharacterized phospholipase D-like proteins; ...
 255-376 3.29e-05

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: 43.41  E-value: 3.29e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 255 LAAIGRARQSILLaNPYFMPGRKLRRALAGAARRGVDVRILLGRNEFASLDMAVPfLYHALLRSGVRVAEY----DKTIL 330
Cdd:cd09127   14 VDAIASAKRSILL-KMYEFTDPALEKALAAAAKRGVRVRVLLEGGPVGGISRAEK-LLDYLNEAGVEVRWTngtaRYRYT 91

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 497594290 331 HGKVAVIDDHWATVGSSNLDALSLMlNNEANVVLVRHREETAALRD 376
Cdd:cd09127   92 HAKYIVVDDERALVLTENFKPSGFT-GTRGFGVVTDDPAVVAEIAD 136
YrhO COG1378
Sugar-specific transcriptional regulator TrmB [Transcription];
47-188 1.46e-04

Sugar-specific transcriptional regulator TrmB [Transcription];


Pssm-ID: 440988 [Multi-domain]  Cd Length: 238  Bit Score: 43.09  E-value: 1.46e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290  47 LIERIDAARERVgletYIFC--DDAVGRAVSDALVRAAARGVHVRVITDGigtERLPLFGAWPDAGVEHRIYNPyLFGRF 124
Cdd:COG1378  122 LRELIASAEEEI----LIVLspPELLLEELEEALEEALERGVKVRVLVSP---EVLEVPERLEEEGEEVRVLPG-LPGRL 193

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 497594290 125 gfsrthrklAVIDDAYAFCGGINIVDDfeqngerlpyprwDFALELQGPAVADV-RAAFEVQWHR 188
Cdd:COG1378  194 ---------LIVDDKEALISVSEPDGE-------------ETAIWIEDPELAALlRELFETLWEK 236
PLDc_ymdC_like_2 cd09113
Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and ...
 44-144 2.53e-04

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: 42.21  E-value: 2.53e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290  44 FPALIERIDAARERVGLET-YIFCddavGRAVSDALVRAAARGVHVRVITDGIG-TERLPLFGAWP-------DAGVEhr 114
Cdd:cd09113   19 AYQLAELLKNAKREVLIVSpYFVP----GDEGVALLAELARRGVRVRILTNSLAaTDVPAVHSGYAryrkrllKAGVE-- 92

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 497594290 115 IY--------NPYLFGRFGFSRT--HRKLAVIDDAYAFCG 144
Cdd:cd09113   93 LYelkpdaakRKRLRGLFGSSRAslHAKSFVIDDRLVFVG 132
PLDc_vPLD1_2_like_bac_2 cd09143
Catalytic domain, repeat 2, of uncharacterized bacterial proteins with similarity to ...
 247-364 7.77e-04

Catalytic domain, repeat 2, of uncharacterized bacterial proteins with similarity to vertebrate phospholipases, PLD1 and PLD2; Catalytic domain, repeat 2, of uncharacterized bacterial counterparts of vertebrate, yeast and plant phospholipase D (PLD, EC 3.1.4.4). PLDs hydrolyze the terminal phosphodiester bond of phospholipids with the formation of phosphatidic acid and alcohols. They also catalyze the transphosphatidylation of phospholipids to acceptor alcohols, by which various phospholipids can be synthesized. Instead of the regulatory C2 (calcium-activated lipid binding) domain in plants and the adjacent Phox (PX) and the Pleckstrin homology (PH) N-terminal domains in most mammalian and yeast PLDs, many members in this subfamily contain a SNARE associated C-terminal domain, whose functional role is unclear. Like other PLD enzymes, members in this subfamily contain two copies of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue), that may play an important role in the catalysis.


Pssm-ID: 197241 [Multi-domain]  Cd Length: 142  Bit Score: 39.43  E-value: 7.77e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 247 RRAIEKAYLAAIGRARQSILLANPYFMpGRKLRRALAGAARRGVDVRILL-------GRNEFASLDMAvpflYHALLRSG 319
Cdd:cd09143    6 VREIEALYLDAIAAARRFIYIENQYFT-SRRIAEALAERLREPDGPEIVIvlprtsdGWLEQLTMGVA----RARLLRRL 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 320 VRVAEYDK---------------TILHGKVAVIDDHWATVGSSNLDALSLMLNNEANVVL 364
Cdd:cd09143   81 READRHGRlrvyypvtaggggrpIYVHSKLMIVDDRLLRVGSANLNNRSMGLDTECDLAI 140
PLDc_Nuc cd09170
Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar ...
 250-374 1.33e-03

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: 39.04  E-value: 1.33e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 250 IEKAYLAAIGRARQSILLAnPYFMPGRKLRRALAGAARRGVDVRILLGRNEFASLDMAVPFLYHAllrsGVRVAEYDKT- 328
Cdd:cd09170   12 ARELILDVIDSARRSIDVA-AYSFTSPPIARALIAAKKRGVDVRVVLDKSQAGGKYSALNYLANA----GIPVRIDDNYa 86

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 497594290 329 ILHGKVAVIDDHWATVGSSNLDALSLMLNNEaNVVLVRHREETAAL 374
Cdd:cd09170   87 IMHNKVMVIDGKTVITGSFNFTASAEKRNAE-NLLVIRNPPELAQQ 131
PLDc_PMFPLD_like_1 cd09108
Catalytic domain, repeat 1, of phospholipase D from Streptomyces Sp. Strain PMF and similar ...
 123-186 2.76e-03

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: 38.95  E-value: 2.76e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 497594290 123 RFGFSRTHRKLAVIDDAYAFCGGINIVDDFEQNGERlpyPRWDFALELQGPAVADVRAAFEVQW 186
Cdd:cd09108  150 TYFLPWNHAKLLVVDGEELLTGGYNLWDDHYLDGGN---PVHDLSLVVRGPAARSGVRFFDDLW 210
PLDc_unchar4 cd09132
Putative catalytic domain of uncharacterized phospholipase D-like proteins; Putative catalytic ...
 44-142 3.25e-03

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: 197230 [Multi-domain]  Cd Length: 122  Bit Score: 37.25  E-value: 3.25e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290  44 FPALIERIDAARERVGLETYIFCDDAvgrAVSDALVRAAARGVHVRVITDGI----GTERLPLFGAWPDAGVEHRIYN-P 118
Cdd:cd09132    1 EQVLLELIEGAERSLLIVGYSAYKVS---ELLQALAAALERGVQVRVVVESSekagSVLSLDEDELMWPKLAGATLYVwP 77

                         90       100
                 ....*....|....*....|....
gi 497594290 119 YLFGRFGFSRTHRKLAVIDDAYAF 142
Cdd:cd09132   78 EKKRPGKRASLHAKVIVADRRRLL 101
PLDc_N_Snf2_like cd09178
N-terminal putative catalytic domain of uncharacterized HKD family nucleases fused to putative ...
 292-375 4.10e-03

N-terminal putative catalytic domain of uncharacterized HKD family nucleases fused to putative helicases from the Snf2-like family; N-terminal putative catalytic domain of uncharacterized archaeal and prokaryotic HKD family nucleases fused to putative helicases from the Snf2-like family, which belong to the DNA/RNA helicase superfamily II (SF2). Although Snf2-like family enzymes do not possess helicase activity, they contain a helicase-like region, where seven helicase-related sequence motifs are found, similar to those in DEAD/DEAH box helicases, which represent the biggest family within the SF2 superfamily. In addition to the helicase-like region, members of this family also contain an N-terminal putative catalytic domain with one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue), and have been classified as members of the phospholipase D (PLD, EC 3.1.4.4) superfamily.


Pssm-ID: 197275 [Multi-domain]  Cd Length: 134  Bit Score: 37.15  E-value: 4.10e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290 292 VRILLGRNefasldmavpflyhaLLRSG---VRVaeYDKTILHGKVAVID-------DHWATVGSSNLDALSLMLNNEAN 361
Cdd:cd09178   49 LRILIGIE---------------LIKEGkveIRV--YTKGFLHAKAYLFDgpdndngPGTAIVGSSNFTKAGLTGNLELN 111

                         90
                 ....*....|....
gi 497594290 362 VVLVRHREETAALR 375
Cdd:cd09178  112 VEVKDRDDVEELKE 125
PLDc_vPLD1_2_like_bac_1 cd09140
Catalytic domain, repeat 1, of uncharacterized bacterial proteins with similarity to ...
 40-165 8.04e-03

Catalytic domain, repeat 1, of uncharacterized bacterial proteins with similarity to vertebrate phospholipases, PLD1 and PLD2; Catalytic domain, repeat 1, of uncharacterized bacterial counterparts of vertebrate, yeast and plant phospholipase D (PLD, EC 3.1.4.4). PLDs hydrolyze the terminal phosphodiester bond of phospholipids with the formation of phosphatidic acid and alcohols. They also catalyze the transphosphatidylation of phospholipids to acceptor alcohols, by which various phospholipids can be synthesized. Instead of the regulatory C2 (calcium-activated lipid binding) domain in plants and the adjacent Phox (PX) and the Pleckstrin homology (PH) N-terminal domains in most mammalian and yeast PLDs, many members in this subfamily contain a SNARE associated C-terminal domain, whose functional role is unclear. Like other PLD enzymes, members in this subfamily contain two copies of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue), that may play an important role in the catalysis.


Pssm-ID: 197238 [Multi-domain]  Cd Length: 146  Bit Score: 36.76  E-value: 8.04e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497594290  40 GAAFFPALIERIDAARERVGLETYIF----------CDDAVGRAVSDALVRAAAR--GVHVRVIT-D-----GIGTERLP 101
Cdd:cd09140    7 AADYFRALREALLRARRSILIVGWDFdsrirlrrggDDDGGPERLGDFLNWLAERrpDLDIRILKwDfamlyALERELLP 86

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 497594290 102 LFG-AWPDAgveHRIynpylfgRFGFSRT-------HRKLAVIDDAYAFCGGINIVDDfeqngerlpypRWD 165
Cdd:cd09140   87 LFLlRWKTH---PRI-------HFRLDGHhplgashHQKIVVIDDALAFCGGIDLTVD-----------RWD 137
 
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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