NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2539731820|ref|WP_295942989|]
View 

phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase family protein [uncultured Acidovorax sp.]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 52-420 2.21e-133

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: 387.38  E-value: 2.21e-133
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820  52 GPGIVGGNAVTELINGDQIFPPMLAAIKSAQKSVTFETYIYWSGDIGKQFADALSERARAGVPVHVLLDWVGSAKMEESY 131
Cdd:COG1502     8 GLPLVGGNRVTLLVDGDEAFAALLEAIEAARRSIDLEYYIFDDDEVGRRLADALIAAARRGVKVRVLLDGIGSRALNRDF 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 132 LAEMKEAGVQIEKFHKPHWyNLARLNNRTHRKLLVVDGQVGFTGGVGIAPAWTGNAQDPEHWRDSHYLVRGPAVAQMQAT 211
Cdd:COG1502    88 LRRLRAAGVEVRLFNPVRL-LFRRLNGRNHRKIVVIDGRVAFVGGANITDEYLGRDPGFGPWRDTHVRIEGPAVADLQAV 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 212 FLDNWLKVTGKVLhgeayfPAIASAGGQKAQMFSSSPSSGSESMQLMYHLAITAAERSIDLSVAYFVPDDLTRKLLMDAL 291
Cdd:COG1502   167 FAEDWNFATGEAL------PFPEPAGDVRVQVVPSGPDSPRETIERALLAAIASARRRIYIETPYFVPDRSLLRALIAAA 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 292 ARGVRVRLVTPgEHTDTETVKAASRATWGELLQAGAEIYEYGPTMYHCKVMIVDQLLVSVGSTNFDNRSFRLNDEANLNV 371
Cdd:COG1502   241 RRGVDVRILLP-AKSDHPLVHWASRSYYEELLEAGVRIYEYEPGFLHAKVMVVDDEWALVGSANLDPRSLRLNFEVNLVI 319

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*....
gi 2539731820 372 YDATFAQRQTQVFEDDIKRSRRVTYEAWLERPWsEKLHEKMTGLLRSQL 420
Cdd:COG1502   320 YDPEFAAQLRARFEEDLAHSREVTLEEWRKRPL-RRLRERLARLLSPLL 367
 
Name Accession Description Interval E-value
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 52-420 2.21e-133

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: 387.38  E-value: 2.21e-133
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820  52 GPGIVGGNAVTELINGDQIFPPMLAAIKSAQKSVTFETYIYWSGDIGKQFADALSERARAGVPVHVLLDWVGSAKMEESY 131
Cdd:COG1502     8 GLPLVGGNRVTLLVDGDEAFAALLEAIEAARRSIDLEYYIFDDDEVGRRLADALIAAARRGVKVRVLLDGIGSRALNRDF 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 132 LAEMKEAGVQIEKFHKPHWyNLARLNNRTHRKLLVVDGQVGFTGGVGIAPAWTGNAQDPEHWRDSHYLVRGPAVAQMQAT 211
Cdd:COG1502    88 LRRLRAAGVEVRLFNPVRL-LFRRLNGRNHRKIVVIDGRVAFVGGANITDEYLGRDPGFGPWRDTHVRIEGPAVADLQAV 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 212 FLDNWLKVTGKVLhgeayfPAIASAGGQKAQMFSSSPSSGSESMQLMYHLAITAAERSIDLSVAYFVPDDLTRKLLMDAL 291
Cdd:COG1502   167 FAEDWNFATGEAL------PFPEPAGDVRVQVVPSGPDSPRETIERALLAAIASARRRIYIETPYFVPDRSLLRALIAAA 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 292 ARGVRVRLVTPgEHTDTETVKAASRATWGELLQAGAEIYEYGPTMYHCKVMIVDQLLVSVGSTNFDNRSFRLNDEANLNV 371
Cdd:COG1502   241 RRGVDVRILLP-AKSDHPLVHWASRSYYEELLEAGVRIYEYEPGFLHAKVMVVDDEWALVGSANLDPRSLRLNFEVNLVI 319

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*....
gi 2539731820 372 YDATFAQRQTQVFEDDIKRSRRVTYEAWLERPWsEKLHEKMTGLLRSQL 420
Cdd:COG1502   320 YDPEFAAQLRARFEEDLAHSREVTLEEWRKRPL-RRLRERLARLLSPLL 367
cls PRK01642
cardiolipin synthetase; Reviewed
 23-411 4.40e-99

cardiolipin synthetase; Reviewed


Pssm-ID: 234967 [Multi-domain]  Cd Length: 483  Bit Score: 304.01  E-value: 4.40e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820  23 AGEKKVQQQLPRLYSTAHPQFERALGSLLGPGIVGGNAVTELINGDQIFPPMLAAIKSAQKSVTFETYIYWSGDIGKQFA 102
Cdd:PRK01642   80 RDLKACKHIFAEENSEVAAPLFRLCERLQGIPGLKGNQLRLLTNGDETFQAIIRDIELARHYILMEFYIWRPDGLGDQVA 159

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 103 DALSERARAGVPVHVLLDWVGSAKMEES-YLAEMKEAGVQIEKFHKPH--WYNLARLNNRTHRKLLVVDGQVGFTGGVGI 179
Cdd:PRK01642  160 EALIAAAKRGVRVRLLYDSIGSFAFFRSpYPEELRNAGVEVVEFLKVNlgRVFRRRLDLRNHRKIVVIDGYIAYTGSMNV 239

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 180 A-PAWTGnaQDP--EHWRDSHYLVRGPAVAQMQATFLDNWLKVTGKVLHGEAYFPAIAS---AGGQKAQMFSSSPSSGSE 253
Cdd:PRK01642  240 VdPEYFK--QDPgvGQWRDTHVRIEGPVVTALQLIFAEDWEWETGERILPPPPDVLIMPfeeASGHTVQVIASGPGDPEE 317

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 254 SMQLMYHLAITAAERSIDLSVAYFVPDDLtrklLMDAL----ARGVRVRLVTPgEHTDTETVKAASRATWGELLQAGAEI 329
Cdd:PRK01642  318 TIHQFLLTAIYSARERLWITTPYFVPDED----LLAALktaaLRGVDVRIIIP-SKNDSLLVFWASRAFFTELLEAGVKI 392

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 330 YEYGPTMYHCKVMIVDQLLVSVGSTNFDNRSFRLNDEANLNVYDATFAQRQTQVFEDDIKRSRRVTYEAWLERPWSEKLH 409
Cdd:PRK01642  393 YRYEGGLLHTKSVLVDDELALVGTVNLDMRSFWLNFEITLVIDDTGFAADLAAMQEDYFARSRELDLEEWRKRPLWQRIA 472


                  ..
gi 2539731820 410 EK 411
Cdd:PRK01642  473 ER 474
bac_cardiolipin TIGR04265
cardiolipin synthase; This model is based on experimentally characterized bacterial ...
 22-416 1.41e-77

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: 248.55  E-value: 1.41e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820  22 TAGEKKVQQQLPRL----YSTAHPQFERA--LGSLLG--PGIVG--GNAVTELINGDQIFPPMLAAIKSAQKSVTFETYI 91
Cdd:TIGR04265  72 RAFWPITAQQLNDLkaenHIFANEQSQKAapLFKMLLrnQGIFLteGNQLKLMTDGDDVYDALIQDIKNARHYIHLEYYI 151

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820  92 YWSGDIGKQFADALSERARAGVPVHVLLDWVGSAKMEESYLAEMKEAGVQIEKFHKPHWYNLA-RLNNRTHRKLLVVDGQ 170
Cdd:TIGR04265 152 WQPDGLGDQILESLMAKAKQGVHVRILYDDVGSVALFKSWPELFRNAGGEVVAFFPVKLPLLNlRMNNRNHRKIIVIDGQ 231

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 171 VGFTGGVGIAPAWTGNAQDPEHWRDSHYLVRGPAVAQMQATFLDNWLKVTGK--VLHGEAYFPAI-ASAGGQKAQMFSSS 247
Cdd:TIGR04265 232 IGYVGGFNIGDEYLGKDAKFGYWRDTHLRIEGDAVTALQLIFILDWNSQTGRriIPYDPDYFPMPnEQAGGHGIQIIASG 311

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 248 PSSGSESMQLMYHLAITAAERSIDLSVAYFVPDDLTRKLLMDALARGVRVRLVTPGEhTDTETVKAASRATWGELLQAGA 327
Cdd:TIGR04265 312 PDFPWEQIKYGYLKMIYSAKKSIYIQSPYFIPDDDLLHAIKIAALSGVDVSIMIPNK-PDHPLVFWASRSNFTELLAAGV 390

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 328 EIYEYGPTMYHCKVMIVDQLLVSVGSTNFDNRSFRLNDEANLNVYDATFAQRQTQVFEDDIKRSRRVTYEAWLERPWSEK 407
Cdd:TIGR04265 391 KIYQYENGFLHSKSVLVDDEIASVGTANMDMRSFWLNFEVNAFIYDKGFAKDLAAAYDDDISRSRQLTKRLYAKRPLWQR 470


                  ....*....
gi 2539731820 408 LHEKMTGLL 416
Cdd:TIGR04265 471 FKESLSYLL 479
PLDc_CLS_1 cd09110
Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Catalytic ...
 65-216 1.35e-71

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: 221.97  E-value: 1.35e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820  65 INGDQIFPPMLAAIKSAQKSVTFETYIYWSGDIGKQFADALSERARAGVPVHVLLDWVGSAKMEESYLAEMKEAGVQIEK 144
Cdd:cd09110     1 TDGEEFFPALLEAIRAARHSIHLEYYIFRDDEIGRRFRDALIEKARRGVEVRLLYDGFGSLGLSRRFLRELREAGVEVRA 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2539731820 145 FHKPHWY-NLARLNNRTHRKLLVVDGQVGFTGGVGIAPAWTGNAQDPEHWRDSHYLVRGPAVAQMQATFLDNW 216
Cdd:cd09110    81 FNPLSFPlFLLRLNYRNHRKILVIDGKIAFVGGFNIGDEYLGKDPGFGPWRDTHVRIEGPAVADLQAAFLEDW 153
PLDc_2 pfam13091
PLD-like domain;
262-385 3.29e-32

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 118.55  E-value: 3.29e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 262 AITAAERSIDLSVAYFVPDDLTRKLLMDALARGVRVRLVTPGEHTDTETVKAASRATWGELLQAGAEIYEYGPT--MYHC 339
Cdd:pfam13091   4 LINSAKKSIDIATYYFVPDREIIDALIAAAKRGVDVRIILDSNKDDAGGPKKASLKELRSLLRAGVEIREYQSFlrSMHA 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2539731820 340 KVMIVDQLLVSVGSTNFDNRSFRLNDEANLNVYDATFAQRQTQVFE 385
Cdd:pfam13091  84 KFYIIDGKTVIVGSANLTRRALRLNLENNVVIKDPELAQELEKEFD 129
PLDc smart00155
Phospholipase D. Active site motifs; Phosphatidylcholine-hydrolyzing phospholipase D (PLD) ...
 337-360 7.35e-05

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


Pssm-ID: 197546 [Multi-domain]  Cd Length: 28  Bit Score: 39.30  E-value: 7.35e-05
                           10        20
                   ....*....|....*....|....
gi 2539731820  337 YHCKVMIVDQLLVSVGSTNFDNRS 360
Cdd:smart00155   5 LHTKLMIVDDEIAYIGSANLDGRS 28
 
Name Accession Description Interval E-value
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 52-420 2.21e-133

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: 387.38  E-value: 2.21e-133
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820  52 GPGIVGGNAVTELINGDQIFPPMLAAIKSAQKSVTFETYIYWSGDIGKQFADALSERARAGVPVHVLLDWVGSAKMEESY 131
Cdd:COG1502     8 GLPLVGGNRVTLLVDGDEAFAALLEAIEAARRSIDLEYYIFDDDEVGRRLADALIAAARRGVKVRVLLDGIGSRALNRDF 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 132 LAEMKEAGVQIEKFHKPHWyNLARLNNRTHRKLLVVDGQVGFTGGVGIAPAWTGNAQDPEHWRDSHYLVRGPAVAQMQAT 211
Cdd:COG1502    88 LRRLRAAGVEVRLFNPVRL-LFRRLNGRNHRKIVVIDGRVAFVGGANITDEYLGRDPGFGPWRDTHVRIEGPAVADLQAV 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 212 FLDNWLKVTGKVLhgeayfPAIASAGGQKAQMFSSSPSSGSESMQLMYHLAITAAERSIDLSVAYFVPDDLTRKLLMDAL 291
Cdd:COG1502   167 FAEDWNFATGEAL------PFPEPAGDVRVQVVPSGPDSPRETIERALLAAIASARRRIYIETPYFVPDRSLLRALIAAA 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 292 ARGVRVRLVTPgEHTDTETVKAASRATWGELLQAGAEIYEYGPTMYHCKVMIVDQLLVSVGSTNFDNRSFRLNDEANLNV 371
Cdd:COG1502   241 RRGVDVRILLP-AKSDHPLVHWASRSYYEELLEAGVRIYEYEPGFLHAKVMVVDDEWALVGSANLDPRSLRLNFEVNLVI 319

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*....
gi 2539731820 372 YDATFAQRQTQVFEDDIKRSRRVTYEAWLERPWsEKLHEKMTGLLRSQL 420
Cdd:COG1502   320 YDPEFAAQLRARFEEDLAHSREVTLEEWRKRPL-RRLRERLARLLSPLL 367
cls PRK01642
cardiolipin synthetase; Reviewed
 23-411 4.40e-99

cardiolipin synthetase; Reviewed


Pssm-ID: 234967 [Multi-domain]  Cd Length: 483  Bit Score: 304.01  E-value: 4.40e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820  23 AGEKKVQQQLPRLYSTAHPQFERALGSLLGPGIVGGNAVTELINGDQIFPPMLAAIKSAQKSVTFETYIYWSGDIGKQFA 102
Cdd:PRK01642   80 RDLKACKHIFAEENSEVAAPLFRLCERLQGIPGLKGNQLRLLTNGDETFQAIIRDIELARHYILMEFYIWRPDGLGDQVA 159

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 103 DALSERARAGVPVHVLLDWVGSAKMEES-YLAEMKEAGVQIEKFHKPH--WYNLARLNNRTHRKLLVVDGQVGFTGGVGI 179
Cdd:PRK01642  160 EALIAAAKRGVRVRLLYDSIGSFAFFRSpYPEELRNAGVEVVEFLKVNlgRVFRRRLDLRNHRKIVVIDGYIAYTGSMNV 239

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 180 A-PAWTGnaQDP--EHWRDSHYLVRGPAVAQMQATFLDNWLKVTGKVLHGEAYFPAIAS---AGGQKAQMFSSSPSSGSE 253
Cdd:PRK01642  240 VdPEYFK--QDPgvGQWRDTHVRIEGPVVTALQLIFAEDWEWETGERILPPPPDVLIMPfeeASGHTVQVIASGPGDPEE 317

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 254 SMQLMYHLAITAAERSIDLSVAYFVPDDLtrklLMDAL----ARGVRVRLVTPgEHTDTETVKAASRATWGELLQAGAEI 329
Cdd:PRK01642  318 TIHQFLLTAIYSARERLWITTPYFVPDED----LLAALktaaLRGVDVRIIIP-SKNDSLLVFWASRAFFTELLEAGVKI 392

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 330 YEYGPTMYHCKVMIVDQLLVSVGSTNFDNRSFRLNDEANLNVYDATFAQRQTQVFEDDIKRSRRVTYEAWLERPWSEKLH 409
Cdd:PRK01642  393 YRYEGGLLHTKSVLVDDELALVGTVNLDMRSFWLNFEITLVIDDTGFAADLAAMQEDYFARSRELDLEEWRKRPLWQRIA 472


                  ..
gi 2539731820 410 EK 411
Cdd:PRK01642  473 ER 474
bac_cardiolipin TIGR04265
cardiolipin synthase; This model is based on experimentally characterized bacterial ...
 22-416 1.41e-77

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: 248.55  E-value: 1.41e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820  22 TAGEKKVQQQLPRL----YSTAHPQFERA--LGSLLG--PGIVG--GNAVTELINGDQIFPPMLAAIKSAQKSVTFETYI 91
Cdd:TIGR04265  72 RAFWPITAQQLNDLkaenHIFANEQSQKAapLFKMLLrnQGIFLteGNQLKLMTDGDDVYDALIQDIKNARHYIHLEYYI 151

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820  92 YWSGDIGKQFADALSERARAGVPVHVLLDWVGSAKMEESYLAEMKEAGVQIEKFHKPHWYNLA-RLNNRTHRKLLVVDGQ 170
Cdd:TIGR04265 152 WQPDGLGDQILESLMAKAKQGVHVRILYDDVGSVALFKSWPELFRNAGGEVVAFFPVKLPLLNlRMNNRNHRKIIVIDGQ 231

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 171 VGFTGGVGIAPAWTGNAQDPEHWRDSHYLVRGPAVAQMQATFLDNWLKVTGK--VLHGEAYFPAI-ASAGGQKAQMFSSS 247
Cdd:TIGR04265 232 IGYVGGFNIGDEYLGKDAKFGYWRDTHLRIEGDAVTALQLIFILDWNSQTGRriIPYDPDYFPMPnEQAGGHGIQIIASG 311

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 248 PSSGSESMQLMYHLAITAAERSIDLSVAYFVPDDLTRKLLMDALARGVRVRLVTPGEhTDTETVKAASRATWGELLQAGA 327
Cdd:TIGR04265 312 PDFPWEQIKYGYLKMIYSAKKSIYIQSPYFIPDDDLLHAIKIAALSGVDVSIMIPNK-PDHPLVFWASRSNFTELLAAGV 390

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 328 EIYEYGPTMYHCKVMIVDQLLVSVGSTNFDNRSFRLNDEANLNVYDATFAQRQTQVFEDDIKRSRRVTYEAWLERPWSEK 407
Cdd:TIGR04265 391 KIYQYENGFLHSKSVLVDDEIASVGTANMDMRSFWLNFEVNAFIYDKGFAKDLAAAYDDDISRSRQLTKRLYAKRPLWQR 470


                  ....*....
gi 2539731820 408 LHEKMTGLL 416
Cdd:TIGR04265 471 FKESLSYLL 479
PLDc_CLS_1 cd09110
Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Catalytic ...
 65-216 1.35e-71

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: 221.97  E-value: 1.35e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820  65 INGDQIFPPMLAAIKSAQKSVTFETYIYWSGDIGKQFADALSERARAGVPVHVLLDWVGSAKMEESYLAEMKEAGVQIEK 144
Cdd:cd09110     1 TDGEEFFPALLEAIRAARHSIHLEYYIFRDDEIGRRFRDALIEKARRGVEVRLLYDGFGSLGLSRRFLRELREAGVEVRA 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2539731820 145 FHKPHWY-NLARLNNRTHRKLLVVDGQVGFTGGVGIAPAWTGNAQDPEHWRDSHYLVRGPAVAQMQATFLDNW 216
Cdd:cd09110    81 FNPLSFPlFLLRLNYRNHRKILVIDGKIAFVGGFNIGDEYLGKDPGFGPWRDTHVRIEGPAVADLQAAFLEDW 153
PLDc_ybhO_like_2 cd09159
Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; ...
 255-408 6.47e-71

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: 220.87  E-value: 6.47e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 255 MQLMYHLAITAAERSIDLSVAYFVPDDLTRKLLMDALARGVRVRLVTPGEHTDTETVkAASRATWGELLQAGAEIYEYGP 334
Cdd:cd09159    12 IRRAYLVAIAAARRRIWIANAYFVPDRRLRRALIEAARRGVDVRLLLPGKSDDPLTV-AASRALYGKLLRAGVRIFEYQP 90

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2539731820 335 TMYHCKVMIVDQLLVSVGSTNFDNRSFRLNDEANLNVYDATFAQRQTQVFEDDIKRSRRVTYEAWLERPWSEKL 408
Cdd:cd09159    91 SMLHAKTAVIDGDWATVGSSNLDPRSLRLNLEANLVVEDPAFAAQLEELFEEDLARSREITLEEWRRRPLWQRL 164
PRK12452 PRK12452
cardiolipin synthase;
64-416 5.51e-69

cardiolipin synthase;


Pssm-ID: 171510 [Multi-domain]  Cd Length: 509  Bit Score: 226.72  E-value: 5.51e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820  64 LINGDQIFPPMLAAIKSAQKSVTFETYIYWSGDIGKQFADALSERARAGVPVHVLLDWVGSAKMEESYLAEMKEAGVQIE 143
Cdd:PRK12452  145 LTNGDQTFSEILQAIEQAKHHIHIQYYIYKSDEIGTKVRDALIKKAKDGVIVRFLYDGLGSNTLRRRFLQPMKEAGIEIV 224

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 144 KFHK--PHWYnLARLNNRTHRKLLVVDGQVGFTGGVGIAPAWTGNAQDPEHWRDSHYLVRGPAVAQMQATFLDNWLKV-- 219
Cdd:PRK12452  225 EFDPifSAWL-LETVNYRNHRKIVIVDGEIGFTGGLNVGDEYLGRSKKFPVWRDSHLKVEGKALYKLQAIFLEDWLYAss 303

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 220 -----TGKVLHGEAYFPA--IASAGGqKAQMFSSSPSSGSESMQLMYHLAITAAERSIDLSVAYFVPDDLTRKLLMDALA 292
Cdd:PRK12452  304 glntySWDPFMNRQYFPGkeISNAEG-AVQIVASGPSSDDKSIRNTLLAVMGSAKKSIWIATPYFIPDQETLTLLRLSAI 382

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 293 RGVRVRLVTPGEhTDTETVKAASRATWGELLQAGAEIYEYGPTMYHCKVMIVDQLLVSVGSTNFDNRSFRLNDEANLNVY 372
Cdd:PRK12452  383 SGIDVRILYPGK-SDSIISDQASQSYFTPLLKAGASIYSYKDGFMHAKIVLVDDKIATIGTANMDVRSFELNYEIISVLY 461

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....
gi 2539731820 373 DATFAQRQTQVFEDDIKRSRRVTYEAWLERPWSEKLHEKMTGLL 416
Cdd:PRK12452  462 ESETVHDIKRDFEDDFKHSTEIKWNAFQKRSIKKRILESFMRLI 505
PLDc_CLS_2 cd09112
catalytic domain repeat 2 of bacterial cardiolipin synthase and similar proteins; This CD ...
 255-416 2.25e-54

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: 178.06  E-value: 2.25e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 255 MQLMYHlAITAAERSIDLSVAYFVPDDLTRKLLMDALARGVRVRLVTPGeHTDTETVKAASRATWGELLQAGAEIYEYGP 334
Cdd:cd09112    13 EQAYLK-AINSAKKSIYIQTPYFIPDESLLEALKTAALSGVDVRIMIPG-KPDHKLVYWASRSYFEELLKAGVKIYEYNK 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 335 TMYHCKVMIVDQLLVSVGSTNFDNRSFRLNDEANLNVYDATFAQRQTQVFEDDIKRSRRVTYEAWLERPWSEKLHEKMTG 414
Cdd:cd09112    91 GFLHSKTLIVDDEIASVGTANLDIRSFELNFEVNAVIYDKEVAKKLEEIFEEDLKDSELLTLEEWRKRSLWKRFKESLAR 170


                  ..
gi 2539731820 415 LL 416
Cdd:cd09112   171 LL 172
PRK11263 PRK11263
cardiolipin synthase ClsB;
56-404 2.38e-51

cardiolipin synthase ClsB;


Pssm-ID: 236888 [Multi-domain]  Cd Length: 411  Bit Score: 177.83  E-value: 2.38e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820  56 VGGNAVTELINGDQIFPPMLAAIKSAQKSVTFETYIYWSGDIGKQFADALSERARAGVPVHVLLDWVGSAKMEESYLAEM 135
Cdd:PRK11263    5 REGNRIQLLENGEQYYPRVFEAIAAAQEEILLETFILFEDKVGKQLHAALLAAAQRGVKVEVLVDGYGSPDLSDEFVNEL 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 136 KEAGVQIEKFhKPHWYNLA-RLN--NRTHRKLLVVDGQVGFTGGVGIAP---AWTGnaqdPEHWRDSHYLVRGPAVAQMQ 209
Cdd:PRK11263   85 TAAGVRFRYF-DPRPRLLGmRTNlfRRMHRKIVVIDGRIAFVGGINYSAdhlSDYG----PEAKQDYAVEVEGPVVADIH 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 210 ATFLDNWL--KVTGKVLHGEAYFPAIASAGGQKAQMFSSSPSSGSESMQLMYHLAITAAERSIDLSVAYFVPDDLTRKLL 287
Cdd:PRK11263  160 QFELEALPgqSAARRWWRRHHRAEENRQPGEAQALLVWRDNEEHRDDIERHYLKALRQARREVIIANAYFFPGYRLLRAL 239

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 288 MDALARGVRVRLVTPGEhTDTETVKAASRATWGELLQAGAEIYEYGPTMYHCKVMIVDQLLVSVGSTNFDNRSFRLNDEA 367
Cdd:PRK11263  240 RNAARRGVRVRLILQGE-PDMPIVRVGARLLYNYLLKGGVQIYEYCRRPLHGKVALMDDHWATVGSSNLDPLSLSLNLEA 318

                         330       340       350
                  ....*....|....*....|....*....|....*...
gi 2539731820 368 NLNVYDATFAQRQTQVFEDDIKRS-RRVTYEAWLERPW 404
Cdd:PRK11263  319 NLIIRDRAFNQTLRDNLNGLIAADcQQVDETMLPKRTW 356
PLDc_PaCLS_like_1 cd09155
Putative catalytic domain, repeat 1, of Pseudomonas aeruginosa cardiolipin synthase and ...
 65-217 4.57e-47

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: 158.56  E-value: 4.57e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820  65 INGDQIFPPMLAAIKSAQKSVTFETYIYWSGDIGKQFADALSERARAGVPVHVLLDWVGSAKMEESYLAEMKEAGVQIEK 144
Cdd:cd09155     1 IDGEATFAAIFEAIASAEEYILVQFYIIRDDDLGRELKDALIARAQAGVRVYLLYDEIGSHSLSRSYIERLRKAGVEVSA 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2539731820 145 FHK-PHWYNLARLNNRTHRKLLVVDGQVGFTGGVGIAPAWTGnaQDPE--HWRDSHYLVRGPAVAQMQATFLDNWL 217
Cdd:cd09155    81 FNTtRGWGNRFQLNFRNHRKIVVVDGQTAFVGGHNVGDEYLG--RDPRlgPWRDTHVKLEGPAVQQLQLSFAEDWY 154
PLDc_CLS_unchar2_1 cd09157
Putative catalytic domain, repeat 1, of uncharacterized proteins similar to bacterial ...
 65-216 1.33e-43

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: 149.64  E-value: 1.33e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820  65 INGDQIFPPMLAAIKSAQKSVTFETYIYWSGDIGKQFADALSERARAGVPVHVLLDWVGSAKMEESYLAEMKEAGVQIEK 144
Cdd:cd09157     1 VNGDEAYPAMLEAIDAARHSIALSSYIFDNDGVGREFVDALAEAVARGVDVRVLIDGVGARYSRPSIRRRLRRAGVPVAR 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2539731820 145 F-HKPHWYNLARLNNRTHRKLLVVDGQVGFTGGVGI-APAWTGNAQDPEHwRDSHYLVRGPAVAQMQATFLDNW 216
Cdd:cd09157    81 FlPPRLPPRLPFINLRNHRKILVVDGRTGFTGGMNIrDGHLVADDPKNPV-QDLHFRVEGPVVAQLQEVFAEDW 153
PLDc_EcCLS_like_2 cd09158
Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase and similar proteins; ...
 255-418 8.17e-42

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: 145.41  E-value: 8.17e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 255 MQLMYHLAITAAERSIDLSVAYFVPDDLTRKLLMDALARGVRVRLVTPgEHTDTETVKAASRATWGELLQAGAEIYEYGP 334
Cdd:cd09158    12 IPQLLLSAIHAARRRVVITTPYFVPDESLLQALCTAALRGVEVTLILP-AKNDSFLVGAASRSYYEELLEAGVKIYLYRG 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 335 TMYHCKVMIVDQLLVSVGSTNFDNRSFRLNDEANLNVYDATFAQRQTQVFEDDIKRSRRVTYEAWLERPWSEKLHEKMTG 414
Cdd:cd09158    91 GLLHAKTVTVDDEVALVGSSNFDIRSFALNFEISLILYDKEFTAQLRAIQERYLARSDPLTLEEWKKRPLWRRLLENLAR 170


                  ....
gi 2539731820 415 LLRS 418
Cdd:cd09158   171 LLSP 174
PLDc_PaCLS_like_2 cd09161
Putative catalytic domain, repeat 2, of Pseudomonas aeruginosa cardiolipin synthase and ...
 257-408 3.01e-36

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: 130.87  E-value: 3.01e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 257 LMYHLAITAAERSIDLSVAYFVPDDLTRKLLMDALARGVRVRLVTPgEHTDTETVKAASRATWGELLQAGAEIYEYGPTM 336
Cdd:cd09161    14 LFFVQAINAAQKRLWIASPYFVPDEGVLAALQLAALRGVDVRILIP-ERPDHLLVYLASFSYLPELIRAGVKVYRYQPGF 92

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2539731820 337 YHCKVMIVDQLLVSVGSTNFDNRSFRLNDEANLNVYDATFAQRQTQVFEDDIKRSRRVTYEAWLERPWSEKL 408
Cdd:cd09161    93 LHQKVVLVDDELAAVGTANLDNRSFRLNFEITALVADPGFAQEVEAMLEADFAASREVTAAELANRPLWFRL 164
PLDc_CLS_unchar2_2 cd09163
Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial ...
 262-408 1.79e-32

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: 120.74  E-value: 1.79e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 262 AITAAERSIDLSVAYFVPDDLTRKLLMDALARGVRVRLVTPgEHTDTETVKAASRATWGELLQAGAEIYEYGPTMYHCKV 341
Cdd:cd09163    19 AISAARHSIRIMTPYFLPDRTLITALQAAALRGVEVDIVLP-ERNNLPLVDWAMRANLWELLEHGVRIYLQPPPFDHSKL 97

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2539731820 342 MIVDQLLVSVGSTNFDNRSFRLNDEANLNVYDATFAQRQTQVFEDDIKRSRRVTYEAWLERPWSEKL 408
Cdd:cd09163    98 MVVDGAWALIGSANWDPRSLRLNFELNLEVYDTALAGQLDALFDSKIAKSREVTLEELDARPLPIRL 164
PLDc_2 pfam13091
PLD-like domain;
262-385 3.29e-32

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 118.55  E-value: 3.29e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 262 AITAAERSIDLSVAYFVPDDLTRKLLMDALARGVRVRLVTPGEHTDTETVKAASRATWGELLQAGAEIYEYGPT--MYHC 339
Cdd:pfam13091   4 LINSAKKSIDIATYYFVPDREIIDALIAAAKRGVDVRIILDSNKDDAGGPKKASLKELRSLLRAGVEIREYQSFlrSMHA 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2539731820 340 KVMIVDQLLVSVGSTNFDNRSFRLNDEANLNVYDATFAQRQTQVFE 385
Cdd:pfam13091  84 KFYIIDGKTVIVGSANLTRRALRLNLENNVVIKDPELAQELEKEFD 129
PLDc_CLS_unchar1_1 cd09156
Putative catalytic domain, repeat 1, of uncharacterized proteins similar to bacterial ...
 67-216 5.08e-32

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: 118.90  E-value: 5.08e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820  67 GDQIFPPMLAAIKSAQKSVTFETYIYWSGDIGKQFADALSERARAGVPVHVLLDWVGSAKMEESYLAEMKEAGVQIEKF- 145
Cdd:cd09156     3 GVEAYQALIQLIESAKHSIDVCTFILGDDATGRRVIDALARKAREGVEVRLLLDALGSFFLSRRALKKLRAAGGKVAFFm 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2539731820 146 ---HKPHwynLARLNNRTHRKLLVVDGQVGFTGGVGIAPAWTGNAQDPEHWRDSHYLVRGPAVAQMQATFLDNW 216
Cdd:cd09156    83 pvfRLPF---RGRTNLRNHRKIAIADGSTAISGGMNLANEYMGPEPDDGRWVDLSFLIEGPAVAQYQEVFRSDW 153
PLDc_EcCLS_like_1 cd09152
Catalytic domain, repeat 1, of Escherichia coli cardiolipin synthase and similar proteins; ...
 58-216 1.20e-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: 115.38  E-value: 1.20e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820  58 GNAVTELINGDQIFPPMLAAIKSAQKSVTFETYIYWSGDIGKQFADALSERARAGVPVHVLLDWVGSAKM-EESYLAEMK 136
Cdd:cd09152     1 GNRVELLTDYDAVIDRLIADIDAAKHHVHLLFYIWADDGTGDRVAEALERAAKRGVTCRLLLDAVGSRAFfRSSLWKRLR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 137 EAGVQI-EKFH-KPHWYNLARLNNRTHRKLLVVDGQVGFTGGVGIApawtgnaqDPEH--------WRDSHYLVRGPAVA 206
Cdd:cd09152    81 EAGVEVvEALPlRLFRRRLARFDLRNHRKIAVIDGRIAYTGSQNII--------DPEFfkkagggpWVDLMVRVEGPVVS 152

                         170
                  ....*....|
gi 2539731820 207 QMQATFLDNW 216
Cdd:cd09152   153 QLQAVFASDW 162
PLDc_SMU_988_like_1 cd09154
Putative catalytic domain, repeat 1, of Streptococcus mutans uncharacterized protein SMU_988 ...
 66-216 5.77e-28

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: 108.00  E-value: 5.77e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820  66 NGDQIFPPMLAAIKSAQKSVTFETYIYWSGDIGKQFADALSERARAGVPVHVLLDWVGS-AKMEESYLAEMKEAGVQIEK 144
Cdd:cd09154     3 LGEDMFEDMLEDLKKAEKFIFMEYFIIEEGYMWDSILEILKEKAKEGVEVRIMYDDFGSiTTLPKDYPKELEKIGIKCRV 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2539731820 145 FHKPHWYNLARLNNRTHRKLLVVDGQVGFTGGVGIAPAWTgNAQDPE-HWRDSHYLVRGPAVAQMQATFLDNW 216
Cdd:cd09154    83 FNPFKPILSLYMNNRDHRKITVIDGKVAFTGGINLADEYI-NKIERFgYWKDTGIRLEGEAVWSLTVMFLEMW 154
PLDc_SMU_988_like_2 cd09160
Putative catalytic domain, repeat 2, of Streptococcus mutans uncharacterized protein SMU_988 ...
 263-412 2.90e-27

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: 106.81  E-value: 2.90e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 263 ITAAERSIDLSVAYFVPDDLTRKLLMDALARGVRVRLVTPGEhTDTETVKAASRATWGELLQAGAEIYEYGPTMYHCKVM 342
Cdd:cd09160    20 INQAKDYVYITTPYLILDDEMLDALCLAAKRGVDVRIITPHI-PDKKYVFLVTRSNYPELLEAGVKIYEYTPGFIHAKTF 98

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 343 IVDQLLVSVGSTNFDNRSFRLNDEANLNVYDATFAQRQTQVFEDDIKRSRRVTYEAWLERPWSEKLHEKM 412
Cdd:cd09160    99 VSDDKAAVVGTINLDYRSLYLHFECGVYMYDTPVISDIKEDFEETLAQSQEITLEECRKRSLVTRLIGAI 168
PLDc_CLS_unchar1_2 cd09162
Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial ...
 262-392 8.59e-24

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: 96.95  E-value: 8.59e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 262 AITAAERSIDLSVAYFVPDDLTRKLLMDALARGVRVRLVTPgEHTDTETVKAASRATWGELLQAGAEIYEYGPTMYHCKV 341
Cdd:cd09162    19 AIFEAEHRIWIVTPYFVPDEVLLRALRLAARRGVDVRLIVP-KRSNHRIADLARGSYLRDLQEAGAEIYLYQPGMLHAKA 97

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2539731820 342 MIVDQLLVSVGSTNFDNRSFRLNDEANLNVYDATFAQRQTQVFEDDIKRSR 392
Cdd:cd09162    98 VVVDDKLALVGSANLDMRSLFLNYEVAVFFYSPADIKELSDWIESLISQCT 148
PLDc_ymdC_like_2 cd09113
Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and ...
 256-404 9.25e-20

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: 87.27  E-value: 9.25e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 256 QLMYHLA--ITAAERSIDLSVAYFVPDDLTRKLLMDALARGVRVRLVTPG-EHTDTETVKAASRATWGELLQAGAEIYEY 332
Cdd:cd09113    17 VLAYQLAelLKNAKREVLIVSPYFVPGDEGVALLAELARRGVRVRILTNSlAATDVPAVHSGYARYRKRLLKAGVELYEL 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 333 GPT----------------MYHCKVMIVDQLLVSVGSTNFDNRSFRLNDEANLNVYDATFAQRQTQVFEDDIKRSR-RVT 395
Cdd:cd09113    97 KPDaakrkrlrglfgssraSLHAKSFVIDDRLVFVGSFNLDPRSAYLNTEMGLVIDSPELAAQLRAAMEEDLAPSAyWVL 176


                  ....*....
gi 2539731820 396 YEAWLERPW 404
Cdd:cd09113   177 LLDDGGLVW 185
PLDc_ymdC_like_1 cd09111
Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and ...
 75-216 3.06e-19

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: 84.12  E-value: 3.06e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820  75 LAAIKSAQKSVTFETYIYWSGDIGKQFADALSERARAGVPVHVLLDWVGSAKMEESYLAEMKEAGVQIeKFHKP------ 148
Cdd:cd09111    12 LALIRSAERSIDLQYYIWHDDESGRLLLGELLEAADRGVRVRLLLDDLGTSGRDRLLAALDAHPNIEV-RLFNPfrnrgg 90

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2539731820 149 HWYNLA----RLNNRTHRKLLVVDGQVGFTGGVGIAPAWTGNaqDPEH-WRDSHYLVRGPAVAQMQATFLDNW 216
Cdd:cd09111    91 RLLEFLtdfsRLNRRMHNKLFIVDGAVAIVGGRNIGDEYFGA--SPEVnFRDLDVLAVGPVVRQLSESFDTYW 161
PLDc_unchar1_2 cd09128
Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins; ...
 263-387 5.59e-18

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: 80.01  E-value: 5.59e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 263 ITAAERSIDLSVAYFVPDDLTRKLLMDALARGVRVRLVTPGEHTDTETVKAASRAtwgeLLQAGAEIYEYGPTMY--HCK 340
Cdd:cd09128    19 IDSAEESLLIQNEEMGDDAPILDALVDAAKRGVDVRVLLPSAWSAEDERQARLRA----LEGAGVPVRLLKDKFLkiHAK 94

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2539731820 341 VMIVDQLLVSVGSTNFDNRSFRLNDEANLNVYDATFAQRQTQVFEDD 387
Cdd:cd09128    95 GIVVDGKTALVGSENWSANSLDRNREVGLIFDDPEVAAYLQAVFESD 141
PLDc_SF cd00138
Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D ...
 262-371 8.51e-14

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: 67.54  E-value: 8.51e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 262 AITAAERSIDLSVAYFVPDDLTR--KLLMDALARGVRVRLVTPGEHTDTETVKAASRAtwgELLQAGAEIYEY-----GP 334
Cdd:cd00138     6 LLKNAKESIFIATPNFSFNSADRllKALLAAAERGVDVRLIIDKPPNAAGSLSAALLE---ALLRAGVNVRSYvtpphFF 82

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2539731820 335 TMYHCKVMIVDQLLVSVGSTNFDNRSFRLNDEANLNV 371
Cdd:cd00138    83 ERLHAKVVVIDGEVAYVGSANLSTASAAQNREAGVLV 119
PLDc_vPLD1_2_like_2 cd09105
Catalytic domain, repeat 2, of vertebrate phospholipases, PLD1 and PLD2, and similar proteins; ...
 262-373 6.19e-12

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: 63.09  E-value: 6.19e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 262 AITAAERSIDLSVAYFVPDDLTrKLLMDALA--RGVRVRLVTPGEHTD----------------TETVKAASRATWGE-- 321
Cdd:cd09105    16 AIRNARRYIYIEDQYLWSPELL-DALAEALKanPGLRVVLVLPALPDAvafgaddgldalallaLLLLADAAPDRVAVfs 94

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2539731820 322 LLQAGAEIYEYGPTMYHCKVMIVDQLLVSVGSTNFDNRSFRLNDEANLNVYD 373
Cdd:cd09105    95 LATHRRGLLGGPPIYVHSKVVIVDDEWATVGSANLNRRSMTWDTELNLAVVD 146
PLDc_unchar1_2 cd09128
Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins; ...
 74-216 1.26e-11

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


Pssm-ID: 197226 [Multi-domain]  Cd Length: 142  Bit Score: 61.91  E-value: 1.26e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820  74 MLAAIKSAQKSVTFET-YIYWSGDIgkqfADALSERARAGVPVHVLL-DWVGSAKMEESYLAEMKEAGVQIEKFHKPHWY 151
Cdd:cd09128    15 LLALIDSAEESLLIQNeEMGDDAPI----LDALVDAAKRGVDVRVLLpSAWSAEDERQARLRALEGAGVPVRLLKDKFLK 90

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2539731820 152 NlarlnnrtHRKLLVVDGQVGFTGGVGiapaWTGNAQDPEhwRDSHYLVRGPAVAQM-QATFLDNW 216
Cdd:cd09128    91 I--------HAKGIVVDGKTALVGSEN----WSANSLDRN--REVGLIFDDPEVAAYlQAVFESDW 142
PLDc_unchar1_1 cd09127
Putative catalytic domain, repeat 1, of uncharacterized phospholipase D-like proteins; ...
 262-387 1.94e-11

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: 61.51  E-value: 1.94e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 262 AITAAERSIDLSVAYFVPDDLTRKLLmDALARGVRVR-LVTPGehtdTETVKAASRATWGELLQAGAEIYEYGPTM---- 336
Cdd:cd09127    16 AIASAKRSILLKMYEFTDPALEKALA-AAAKRGVRVRvLLEGG----PVGGISRAEKLLDYLNEAGVEVRWTNGTAryry 90

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2539731820 337 YHCKVMIVDQLLVSVGSTNFDNRSFRLNDEANLNVYDATFAQRQTQVFEDD 387
Cdd:cd09127    91 THAKYIVVDDERALVLTENFKPSGFTGTRGFGVVTDDPAVVAEIADVFDAD 141
PLDc_Nuc_like cd09116
Catalytic domain of EDTA-resistant nuclease Nuc, vertebrate phospholipase D6, and similar ...
 262-385 6.56e-11

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: 60.00  E-value: 6.56e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 262 AITAAERSIDLSVAyfvpdDLTRKLLMDALA----RGVRVRLVTpgehTDTETVKAASRATWGELLQAGAEIYEYG-PTM 336
Cdd:cd09116    17 LIANAKSSIDVAMY-----ALTDPEIAEALKraakRGVRVRIIL----DKDSLADNLSITLLALLSNLGIPVRTDSgSKL 87

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 2539731820 337 YHCKVMIVDQLLVSVGSTNFDNRSFRLNDEANLNVYDATFAQRQTQVFE 385
Cdd:cd09116    88 MHHKFIIIDGKIVITGSANWTKSGFHRNDENLLIIDDPKLAASFEEEFN 136
PLDc_2 pfam13091
PLD-like domain;
74-212 1.08e-10

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 59.23  E-value: 1.08e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820  74 MLAAIKSAQKSVTFETYIYWSGdigKQFADALSERARAGVPVHVLLD-----WVGSAKMEESYLAEMKEAGVQIekfhkp 148
Cdd:pfam13091   1 LIDLINSAKKSIDIATYYFVPD---REIIDALIAAAKRGVDVRIILDsnkddAGGPKKASLKELRSLLRAGVEI------ 71

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2539731820 149 HWYNlaRLNNRTHRKLLVVDGQVGFTGGVGiapaWTGNAQDpeHWRDSHYLVRGPAVA-QMQATF 212
Cdd:pfam13091  72 REYQ--SFLRSMHAKFYIIDGKTVIVGSAN----LTRRALR--LNLENNVVIKDPELAqELEKEF 128
PLDc_Nuc cd09170
Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar ...
 262-382 5.70e-10

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: 57.14  E-value: 5.70e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 262 AITAAERSIDLSVAYFVPDDLTRKLLmDALARGVRVRLVTpgehtDTETVKAaSRATWGELLQAGAEIYEYG--PTMyHC 339
Cdd:cd09170    19 VIDSARRSIDVAAYSFTSPPIARALI-AAKKRGVDVRVVL-----DKSQAGG-KYSALNYLANAGIPVRIDDnyAIM-HN 90

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2539731820 340 KVMIVDQLLVSVGSTNFDNRSFRLNDEaNLNV----------YDATFAQRQTQ 382
Cdd:cd09170    91 KVMVIDGKTVITGSFNFTASAEKRNAE-NLLVirnppelaqqYLQEWQRRWAQ 142
PLDc_SF cd00138
Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D ...
 74-175 1.60e-09

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: 55.22  E-value: 1.60e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820  74 MLAAIKSAQKSVTFETYiYWSGDIGKQFADALSERARAGVPVHVLLDWVGSAK--MEESYLAEMKEAGVQIekfhkpHWY 151
Cdd:cd00138     3 LLELLKNAKESIFIATP-NFSFNSADRLLKALLAAAERGVDVRLIIDKPPNAAgsLSAALLEALLRAGVNV------RSY 75

                          90       100
                  ....*....|....*....|....*
gi 2539731820 152 NLARLNNRT-HRKLLVVDGQVGFTG 175
Cdd:cd00138    76 VTPPHFFERlHAKVVVIDGEVAYVG 100
PLDc_vPLD1_2_like_bac_2 cd09143
Catalytic domain, repeat 2, of uncharacterized bacterial proteins with similarity to ...
 262-369 3.34e-09

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: 55.22  E-value: 3.34e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 262 AITAAERSIDLSVAYFvpddlTRKLLMDALAR------GVRVRLVTPGEHTD--TETVKAASRATWGELLQAGAE----- 328
Cdd:cd09143    16 AIAAARRFIYIENQYF-----TSRRIAEALAErlrepdGPEIVIVLPRTSDGwlEQLTMGVARARLLRRLREADRhgrlr 90

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 2539731820 329 IY-------EYGPTMYHCKVMIVDQLLVSVGSTNFDNRSFRLNDEANL 369
Cdd:cd09143    91 VYypvtaggGGRPIYVHSKLMIVDDRLLRVGSANLNNRSMGLDTECDL 138
PLDc_vPLD6_like cd09171
Catalytic domain of vertebrate phospholipase D6 and similar proteins; Catalytic domain of ...
 263-385 2.66e-08

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: 52.23  E-value: 2.66e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 263 ITAAERSIDLSVAYFVPDDLTRKLLmDALARGVRVRLVtpgehTDTETVKAAsRATWGELLQAGAEIYE-YGPTMYHCKV 341
Cdd:cd09171    17 LLSARKSLDVCVFTITCDDLADAIL-DLHRRGVRVRII-----TDDDQMEDK-GSDIGKLRKAGIPVRTdLSSGHMHHKF 89

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 2539731820 342 MIVDQLLVSVGSTNFDNRSFRLNDEANLNVYDATFAQRQTQVFE 385
Cdd:cd09171    90 AVIDGKILITGSFNWTRQAVTGNQENVLITNDPKLVKPFTEEFE 133
PLDc_unchar1_1 cd09127
Putative catalytic domain, repeat 1, of uncharacterized phospholipase D-like proteins; ...
 68-170 3.41e-08

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: 52.27  E-value: 3.41e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820  68 DQIFPPMLAAIKSAQKSVTFETYIYWSGDIgkqfADALSERARAGVPVHVLLDW--VGSAKMEESYLAEMKEAGVQIekf 145
Cdd:cd09127     7 DDGVAPVVDAIASAKRSILLKMYEFTDPAL----EKALAAAAKRGVRVRVLLEGgpVGGISRAEKLLDYLNEAGVEV--- 79

                          90       100
                  ....*....|....*....|....*.
gi 2539731820 146 hkpHWYN-LARLnNRTHRKLLVVDGQ 170
Cdd:cd09127    80 ---RWTNgTARY-RYTHAKYIVVDDE 101
PLDc_vPLD3_4_5_like_2 cd09107
Putative catalytic domain, repeat 2, of vertebrate phospholipases, PLD3, PLD4 and PLD5, viral ...
 262-387 5.71e-08

Putative catalytic domain, repeat 2, of vertebrate phospholipases, PLD3, PLD4 and PLD5, viral envelope proteins K4 and p37, and similar proteins; Putative catalytic domain, repeat 2, of vertebrate phospholipases D, PLD3, PLD4, and PLD5 (EC 3.1.4.4), viral envelope proteins (vaccinia virus proteins K4 and p37), and similar proteins. Most family members contain two copies of the HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue), and have been classified into the phospholipase D (PLD) superfamily. Proteins in this subfamily are associated with Golgi membranes, altering their lipid content by the conversion of phospholipids into phosphatidic acid, which is thought to be involved in the regulation of lipid movement. ADP ribosylation factor (ARF), a small guanosine triphosphate binding protein, might be required activity. The vaccinia virus p37 protein, encoded by the F13L gene, is also associated with Golgi membranes and is required for the envelopment and spread of the extracellular enveloped virus (EEV). The vaccinia virus protein K4, encoded by the HindIII K4L gene, remains to be characterized. Sequence analysis indicates that the vaccinia virus proteins K4 and p37 might have evolved from one or more captured eukaryotic genes involved in cellular lipid metabolism. Up to date, no catalytic activity of PLD3 has been shown. Furthermore, due to the lack of functional important histidine and lysine residues in the HKD motif, mammalian PLD5 has been characterized as an inactive PLD. The poxvirus p37 proteins may also lack PLD enzymatic activity, since they contain only one partially conserved HKD motif (N-x-K-x(4)-D).


Pssm-ID: 197206 [Multi-domain]  Cd Length: 175  Bit Score: 52.25  E-value: 5.71e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 262 AITAAERSIDLSVAYFVP-----------DDLTRKLLMDALARGVRVR-LVTPGEHTDTETVKAASRATWGELLQAGAEI 329
Cdd:cd09107    24 TIDSAKKFIDISVMDYVPlsryadprkywPVIDNALRRAAVDRGVKVRlLVSNWKHTDPSMDAFLKSLQLLKSGVGNGDI 103

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2539731820 330 Y-------EYGPTMY------HCKVMIVDQlLVSVGSTN-----FDNRSFrlndeANLNVYDATFAQRQTQVFEDD 387
Cdd:cd09107   104 EvkiftvpGDQSTKIpfarvnHAKYMVTDE-RAYIGTSNwsgdyFYNTAG-----VSLVINDPAIVQQLKDVFERD 173
PLDc_Nuc cd09170
Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar ...
 75-175 6.47e-08

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: 51.36  E-value: 6.47e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820  75 LAAIKSAQKSVTFETYIYWSGDIgkqfADALSERARAGVPVHVLLDWvGSAKMEESYLAEMKEAGVQIekfhkphwynla 154
Cdd:cd09170    17 LDVIDSARRSIDVAAYSFTSPPI----ARALIAAKKRGVDVRVVLDK-SQAGGKYSALNYLANAGIPV------------ 79

                          90       100
                  ....*....|....*....|....
gi 2539731820 155 RLNNRT---HRKLLVVDGQVGFTG 175
Cdd:cd09170    80 RIDDNYaimHNKVMVIDGKTVITG 103
PLDc_CLS_1 cd09110
Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Catalytic ...
 262-355 9.47e-08

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: 51.32  E-value: 9.47e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 262 AITAAERSIDLSVAYFVPDDLTRKL---LMDALARGVRVRLVTPGEHTdtetvKAASRATWGELLQAGAEIYEYGPT--- 335
Cdd:cd09110    13 AIRAARHSIHLEYYIFRDDEIGRRFrdaLIEKARRGVEVRLLYDGFGS-----LGLSRRFLRELREAGVEVRAFNPLsfp 87

                          90       100
                  ....*....|....*....|....*...
gi 2539731820 336 ------MY--HCKVMIVDQLLVSVGSTN 355
Cdd:cd09110    88 lfllrlNYrnHRKILVIDGKIAFVGGFN 115
PLDc_vPLD3_4_5_like_1 cd09106
Putative catalytic domain, repeat 1, of vertebrate phospholipases, PLD3, PLD4 and PLD5, viral ...
 263-361 7.06e-07

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


Pssm-ID: 197205 [Multi-domain]  Cd Length: 153  Bit Score: 48.78  E-value: 7.06e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 263 ITAAERSIDLSVAYF------VPDDLTRKL-------LMDALARGVRVRLVT--PGEHTDTETVKAASRAtwgellqAGA 327
Cdd:cd09106    28 ISSAKKSIDIASFYWnlrgtdTNPDSSAQEgedifnaLLEAAKRGVKIRILQdkPSKDKPDEDDLELAAL-------GGA 100

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 2539731820 328 EIYE------YGPTMYHCKVMIVDQLLVSVGSTNFDNRSF 361
Cdd:cd09106   101 EVRSldftklIGGGVLHTKFWIVDGKHFYLGSANLDWRSL 140
PLDc_unchar3 cd09131
Putative catalytic domain of uncharacterized phospholipase D-like proteins; Putative catalytic ...
 71-175 1.09e-06

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


Pssm-ID: 197229 [Multi-domain]  Cd Length: 143  Bit Score: 47.72  E-value: 1.09e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820  71 FPPMLAAIKSAQKSVTFETYIY-WSGDIG---KQFADALSERARAGVPVHVLLD-----WVGSAKMEESYlAEMKEAGVQ 141
Cdd:cd09131     5 YPALLDLINNAKRSIYIAMYMFkYYENPGngvNTLLEALIDAHKRGVDVKVVLEdsiddDEVTEENDNTY-RYLKDNGVE 83

                          90       100       110
                  ....*....|....*....|....*....|....
gi 2539731820 142 IeKFHKPhwynlarlNNRTHRKLLVVDGQVGFTG 175
Cdd:cd09131    84 V-RFDSP--------SVTTHTKLVVIDGRTVYVG 108
PLDc_unchar3 cd09131
Putative catalytic domain of uncharacterized phospholipase D-like proteins; Putative catalytic ...
 262-384 4.18e-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: 46.18  E-value: 4.18e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 262 AITAAERSIDLSV----AYFVPDDLTRKL---LMDALARGVRVRLVTPGeHTDTETVKAASRATWGELLQAGAEIyEYGP 334
Cdd:cd09131    11 LINNAKRSIYIAMymfkYYENPGNGVNTLleaLIDAHKRGVDVKVVLED-SIDDDEVTEENDNTYRYLKDNGVEV-RFDS 88

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2539731820 335 --TMYHCKVMIVDQLLVSVGSTNFDNRSFRLNDEANLNVYDATFAQRQTQVF 384
Cdd:cd09131    89 psVTTHTKLVVIDGRTVYVGSHNWTYSALDYNHEASVLIESPEVADFAINYF 140
PLDc_unchar4 cd09132
Putative catalytic domain of uncharacterized phospholipase D-like proteins; Putative catalytic ...
 263-371 9.16e-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: 197230 [Multi-domain]  Cd Length: 122  Bit Score: 44.57  E-value: 9.16e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 263 ITAAERSIdLSVAY-FVPDDLTRKLLMDALARGVRVRLV--TPGEHTDTETVKAAsRATWGELlqAGAEIYEYGPTMY-- 337
Cdd:cd09132     8 IEGAERSL-LIVGYsAYKVSELLQALAAALERGVQVRVVveSSEKAGSVLSLDED-ELMWPKL--AGATLYVWPEKKRpg 83

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 2539731820 338 -----HCKVMIVDQLLVSVGSTNFDNRSFRLNDEANLNV 371
Cdd:cd09132    84 kraslHAKVIVADRRRLLVTSANLTGAGMERNIEAGVLV 122
PLDc_ymdC_like_1 cd09111
Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and ...
 261-299 7.24e-05

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: 42.91  E-value: 7.24e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 2539731820 261 LAITAAERSIDLSvaYF-VPDDLTRKLLMDAL--A--RGVRVRL 299
Cdd:cd09111    13 ALIRSAERSIDLQ--YYiWHDDESGRLLLGELleAadRGVRVRL 54
PLDc smart00155
Phospholipase D. Active site motifs; Phosphatidylcholine-hydrolyzing phospholipase D (PLD) ...
 337-360 7.35e-05

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


Pssm-ID: 197546 [Multi-domain]  Cd Length: 28  Bit Score: 39.30  E-value: 7.35e-05
                           10        20
                   ....*....|....*....|....
gi 2539731820  337 YHCKVMIVDQLLVSVGSTNFDNRS 360
Cdd:smart00155   5 LHTKLMIVDDEIAYIGSANLDGRS 28
PRK13912 PRK13912
nuclease NucT; Provisional
 263-385 1.45e-04

nuclease NucT; Provisional


Pssm-ID: 184389 [Multi-domain]  Cd Length: 177  Bit Score: 42.46  E-value: 1.45e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 263 ITAAERSIDLSVAYFVPDDLTrKLLMDALARGVRVRLVTpgehtDTETVKAASRATWGEL-------------LQAGAEI 329
Cdd:PRK13912   42 ISNARSSIKIAIYSFTHKDIA-KALKSAAKRGVKISIIY-----DYESNHNNDQSTIGYLdkypnikvcllkgLKAKNGK 115

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2539731820 330 YeYGptMYHCKVMIVDQLLVSVGSTNFDNRSFRLNDEANLNVYDATFAQRQTQVFE 385
Cdd:PRK13912  116 Y-YG--IMHQKVAIIDDKIVVLGSANWSKNAFENNYEVLLITDDTETILKAKEYFQ 168
PLDc_Nuc_like_unchar1_1 cd09172
Putative catalytic domain, repeat 1, of uncharacterized hypothetical proteins similar to Nuc, ...
 262-385 2.07e-04

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


Pssm-ID: 197269 [Multi-domain]  Cd Length: 144  Bit Score: 41.19  E-value: 2.07e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 262 AITAAERSIDLsVAYfvpdDLTRKLLMDALA----RGVRVRLVT--PGEHTDTETVKAASRATWGELLQAGaeiYEYGPT 335
Cdd:cd09172    17 EARSAGSSIRL-AIY----ELDDPEIIDALKaakdRGVRVRIILddSSVTGDPTEESAAATLSKGPGALVK---RRHSSG 88

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2539731820 336 MYHCKVMIVD--QLLVSV--GSTNFDNRSfrLNDEAN--LNVYDATFAQRQTQVFE 385
Cdd:cd09172    89 LMHNKFLVVDrkDGPNRVltGSTNFTTSG--LYGQSNnvLIFRNPAFAAAYLAYWN 142
PLDc_vPLD3_4_5_like_1 cd09106
Putative catalytic domain, repeat 1, of vertebrate phospholipases, PLD3, PLD4 and PLD5, viral ...
 78-175 3.19e-04

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


Pssm-ID: 197205 [Multi-domain]  Cd Length: 153  Bit Score: 41.08  E-value: 3.19e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820  78 IKSAQKSVTFETYiYWS---GDI--------GKQFADALSERARAGVPVHVLLDWVGSAKMEESYLAEMKEAGVQIEKFH 146
Cdd:cd09106    28 ISSAKKSIDIASF-YWNlrgTDTnpdssaqeGEDIFNALLEAAKRGVKIRILQDKPSKDKPDEDDLELAALGGAEVRSLD 106

                          90       100
                  ....*....|....*....|....*....
gi 2539731820 147 KPHWYNLARLnnrtHRKLLVVDGQVGFTG 175
Cdd:cd09106   107 FTKLIGGGVL----HTKFWIVDGKHFYLG 131
PLDc_Nuc_like_unchar1_2 cd09173
Putative catalytic domain, repeat 2, of uncharacterized hypothetical proteins similar to Nuc, ...
 262-378 3.54e-04

Putative catalytic domain, repeat 2, of uncharacterized hypothetical proteins similar to Nuc, an endonuclease from Salmonella typhimurium; Putative catalytic domain, repeat 2, of uncharacterized hypothetical proteins, which show high sequence homology to the endonuclease from Salmonella typhimurium and vertebrate phospholipase D6. Nuc and PLD6 belong to the phospholipase D (PLD) superfamily. They contain a short conserved sequence motif, the HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue), which characterizes the PLD superfamily and is essential for catalysis. Nuc and PLD6 utilize a two-step mechanism to cleave phosphodiester bonds: Upon substrate binding, the bond is first attacked by a histidine residue from one HKD motif to form a covalent phosphohistidine intermediate, which is then hydrolyzed by water with the aid of a second histidine residue from the other HKD motif in the opposite subunit. However, proteins in this subfamily have two HKD motifs in a single polypeptide chain.


Pssm-ID: 197270 [Multi-domain]  Cd Length: 159  Bit Score: 40.80  E-value: 3.54e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 262 AITAAERSIDLSVAYFVPDDL--TRKLLMDA--LARGVRVRLVTPGEHTDTETVKAASRATWGELLQAGAE------IYE 331
Cdd:cd09173    17 LVAKAKSSVLFALFDFSDGALldALLAAADAglFVRGLVDKRFGGRYYSAAADMGGIDPVYPAALAPDEPEkfvgepLLG 96

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2539731820 332 YGPTMYHcKVMIVDQL----LVSVGSTNFDNRSFRLNDEANLNVYDATFAQ 378
Cdd:cd09173    97 VGDKLHH-KFMVIDPFgddpVVITGSHNFSGAANDNNDENLLVIRDPAIAD 146
PLDc_Nuc_like cd09116
Catalytic domain of EDTA-resistant nuclease Nuc, vertebrate phospholipase D6, and similar ...
 74-187 5.05e-04

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: 39.97  E-value: 5.05e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820  74 MLAAIKSAQKSVTFETYIYWSGDIGKqfadALSERARAGVPVHVLLDwvgsaKMEESYLAEMKEAGvqIEKFHKPHWYNL 153
Cdd:cd09116    14 IVALIANAKSSIDVAMYALTDPEIAE----ALKRAAKRGVRVRIILD-----KDSLADNLSITLLA--LLSNLGIPVRTD 82

                          90       100       110
                  ....*....|....*....|....*....|....
gi 2539731820 154 ARlNNRTHRKLLVVDGQVGFTGgvgiAPAWTGNA 187
Cdd:cd09116    83 SG-SKLMHHKFIIIDGKIVITG----SANWTKSG 111
YrhO COG1378
Sugar-specific transcriptional regulator TrmB [Transcription];
263-392 5.95e-04

Sugar-specific transcriptional regulator TrmB [Transcription];


Pssm-ID: 440988 [Multi-domain]  Cd Length: 238  Bit Score: 41.16  E-value: 5.95e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 263 ITAAERSIDLSV--AYFVPDDLtRKLLMDALARGVRVRLVTPGEHTDTEtvkaasratwGELLQAGAEIYeYGPTMYHcK 340
Cdd:COG1378   126 IASAEEEILIVLspPELLLEEL-EEALEEALERGVKVRVLVSPEVLEVP----------ERLEEEGEEVR-VLPGLPG-R 192

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2539731820 341 VMIVD--QLLVSVGSTNfdnrsfrlNDEANLNVYDATFAQRQTQVFEDDIKRSR 392
Cdd:COG1378   193 LLIVDdkEALISVSEPD--------GEETAIWIEDPELAALLRELFETLWEKAE 238
COG3886 COG3886
HKD family nuclease [Replication, recombination and repair];
269-411 8.28e-04

HKD family nuclease [Replication, recombination and repair];


Pssm-ID: 443094 [Multi-domain]  Cd Length: 941  Bit Score: 41.89  E-value: 8.28e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 269 SIDLSVAYFVPDDLtrKLLMDAL----ARGVRVRLVTpGE---HTDTETVKaasratwgELLQ-AGAE--IYEYGPTMYH 338
Cdd:COG3886    44 SFDISVAFITWSGL--RLLLDALkellERGVKGRILT-STylgFTEPKALR--------ELLDlPNIEvrVSYDRKTRFH 112

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2539731820 339 CKVMIVDQLLVS---VGSTNFDNRSFRLNDEANLNV---YDATFAQRQTQVFEDDIKRSRRVTYEAWLERPWSEKLHEK 411
Cdd:COG3886   113 AKAYIFERTGYGtaiIGSSNLTRSALTDNLEWNVKLssaEDPDLIEKFRAEFESLWEDSEFVTLDPWIDKEEERYRRAL 191
PLDc_vPLD1_2_like_2 cd09105
Catalytic domain, repeat 2, of vertebrate phospholipases, PLD1 and PLD2, and similar proteins; ...
 69-175 9.63e-04

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: 39.21  E-value: 9.63e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820  69 QIFPPMLAAIKSAQKSVTFETYIYWSGDIGKQFADALSERARAGV----PVHVLLDWVGSAKMEESYLAEM--KEAGVQI 142
Cdd:cd09105     8 EIADAYLKAIRNARRYIYIEDQYLWSPELLDALAEALKANPGLRVvlvlPALPDAVAFGADDGLDALALLAllLLADAAP 87

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 2539731820 143 EKFHKPHWYNLARLNNR-----THRKLLVVDGQVGFTG 175
Cdd:cd09105    88 DRVAVFSLATHRRGLLGgppiyVHSKVVIVDDEWATVG 125
PLDc_CLS_unchar1_2 cd09162
Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial ...
 65-177 1.51e-03

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: 39.17  E-value: 1.51e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820  65 INGDQIFPPMLAAIKSAQKSVTFETYIYWSGDigkQFADALSERARAGVPV---------HVLLDWVGSakmeeSYLAEM 135
Cdd:cd09162     7 VPGDPLYEALLSAIFEAEHRIWIVTPYFVPDE---VLLRALRLAARRGVDVrlivpkrsnHRIADLARG-----SYLRDL 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 2539731820 136 KEAGVQIekfhkpHWYNLARLnnrtHRKLLVVDGQVGFTGGV 177
Cdd:cd09162    79 QEAGAEI------YLYQPGML----HAKAVVVDDKLALVGSA 110
PLDc_Bfil_DEXD_like cd09117
Catalytic domain of type II restriction endonucleases BfiI and NgoFVII, and uncharacterized ...
 259-369 2.92e-03

Catalytic domain of type II restriction endonucleases BfiI and NgoFVII, and uncharacterized proteins with a DEAD domain; Catalytic domain of type II restriction endonucleases BfiI and NgoFVII, uncharacterized type III restriction endonuclease Res subunit, and uncharacterized DNA/RNA helicase superfamily II members. Proteins in this family are found mainly in prokaryotes. They contain one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) in a single polypeptide chain, and have been classified as members of the phospholipase D (PLD, EC 3.1.4.4) superfamily. BfiI consists of two discrete domains with distinct functions: an N-terminal catalytic domain with non-specific nuclease activity and dimerization function that is more closely related to Nuc, an EDTA-resistant nuclease from the phospholipase D (PLD) superfamily; and a C-terminal domain that specifically recognizes its target sequences, 5'-ACTGGG-3'. BfiI forms a functionally active homodimer which has two DNA-binding surfaces located at the C-terminal domains but only one active site, located at the dimer interface between the two N-terminal catalytic domains that contain the two HKD motifs from both subunits. BfiI utilizes a single active site to cut both DNA strands, which represents a novel mechanism for the scission of double-stranded DNA. It uses a histidine residue from the HKD motif in one subunit as the nucleophile for the cleavage of the target phosphodiester bond in both of the anti-parallel DNA strands, while the symmetrically-related histidine residue from the HKD motif of the opposite subunit acts as the proton donor/acceptor during both strand-scission events.


Pssm-ID: 197216 [Multi-domain]  Cd Length: 117  Bit Score: 37.37  E-value: 2.92e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 259 YHLAITAAER---SIDLSVAYFVPDDLTRKLlmDALARGVRVRLVTpGEHTDTETVKAASRATWGELLQAGAEIYEYGPt 335
Cdd:cd09117     3 LEELLTRLIEradTIRIAVAFASAGGAIKLL--DKFREGKKIRLIV-GLDFGGTSPADFALKLLLALGNLNVRIFDAGP- 78

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2539731820 336 MYHCKVMI---VDQLLVSVGSTNFDNRSFRLNDEANL 369
Cdd:cd09117    79 LLHAKLYLfenDDPTRAIVGSANLTQGGLSGNIEAAV 115
PLDc pfam00614
Phospholipase D Active site motif; Phosphatidylcholine-hydrolysing phospholipase D (PLD) ...
 337-360 5.11e-03

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


Pssm-ID: 395489 [Multi-domain]  Cd Length: 28  Bit Score: 34.32  E-value: 5.11e-03
                          10        20
                  ....*....|....*....|....
gi 2539731820 337 YHCKVMIVDQLLVSVGSTNFDNRS 360
Cdd:pfam00614   5 LHRKIVVVDDELAYIGGANLDGRS 28
PLDc_EcCLS_like_1 cd09152
Catalytic domain, repeat 1, of Escherichia coli cardiolipin synthase and similar proteins; ...
 262-362 7.66e-03

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: 37.19  E-value: 7.66e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539731820 262 AITAAERSIDLSVAYFVPDDLTRKL---LMDALARGVRVRLVtpgehTDTETVKAASRATWGELLQ-AGAEIYEYGP--- 334
Cdd:cd09152    20 DIDAAKHHVHLLFYIWADDGTGDRVaeaLERAAKRGVTCRLL-----LDAVGSRAFFRSSLWKRLReAGVEVVEALPlrl 94

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2539731820 335 -----TMY----HCKVMIVDQLLVSVGSTNFDNRSFR 362
Cdd:cd09152    95 frrrlARFdlrnHRKIAVIDGRIAYTGSQNIIDPEFF 131
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH