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Conserved domains on  [gi|736049347|ref|WP_034194997|]
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MULTISPECIES: phospholipase D family protein [Burkholderia]

Protein Classification

phospholipase D family protein( domain architecture ID 11445371)

phospholipase D family protein similar to Escherichia coli cardiolipin synthase C and Neisseria gonorrhoeae phospholipase D; hydrolyzes phospholipid phosphodiester bonds

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PLDc_ymdC_like_2 cd09113
Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and ...
 289-512 1.20e-99

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: 299.13  E-value: 1.20e-99
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 289 LYDDPAKIARAPnDSEGHLLPQLRALALRPEHELLIVSPYLVPGAAMIERLRALTARGVRVTILTNSLASTDVAAVHAGY 368
Cdd:cd09113    1 LSDPPEKALKEA-GPEPVLAYQLAELLKNAKREVLIVSPYFVPGDEGVALLAELARRGVRVRILTNSLAATDVPAVHSGY 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 369 RRYRRELVEAGVRLYERRPSGDKSISKRLIIGSSRASLHAKTYVFDRKSVFIGSMNLDPRSLRLNTEIGVYCESPALAAQ 448
Cdd:cd09113   80 ARYRKRLLKAGVELYELKPDAAKRKRLRGLFGSSRASLHAKSFVIDDRLVFVGSFNLDPRSAYLNTEMGLVIDSPELAAQ 159

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 736049347 449 VAADLEPRLDRIAWRVEATTDpsgtrRLEWIQTDEDGKVTEFDHEPEVSTARRVEVWFLGLFPI 512
Cdd:cd09113  160 LRAAMEEDLAPSAYWVLLLDD-----GGLVWETEEDGKEKEYDSEPETSFWRRLGAWLLSLLPI 218
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 46-479 9.25e-92

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: 284.53  E-value: 9.25e-92
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347  46 FRAQAAAHPGQ--DAFHLLSDPVDALDARVLLADRADRSLDLQYYIWHDDLTGHALADAIIRAADRGVRVRVLLDDLGTN 123
Cdd:COG1502    2 AAPLAAGLPLVggNRVTLLVDGDEAFAALLEAIEAARRSIDLEYYIFDDDEVGRRLADALIAAARRGVKVRVLLDGIGSR 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 124 ADDRKLLEISSHPHIEIRLFNPVATRefkkigtvleFSRVNRRMHNKAMIADNQAAIIGGRNIGDEYFGASSMLE-FGDL 202
Cdd:COG1502   82 ALNRDFLRRLRAAGVEVRLFNPVRLL----------FRRLNGRNHRKIVVIDGRVAFVGGANITDEYLGRDPGFGpWRDT 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 203 DVVVHGRVVNDISTEFDTFWNSpyaysvgalvghdatpgsldrererlrdylramednpyvlEARERLDRIvhgegTELS 282
Cdd:COG1502  152 HVRIEGPAVADLQAVFAEDWNF----------------------------------------ATGEALPFP-----EPAG 186

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 283 WGRATVLYDDPakiARAPNDSEGHLLPQLRAlalrPEHELLIVSPYLVPGAAMIERLRALTARGVRVTILTNslASTDVA 362
Cdd:COG1502  187 DVRVQVVPSGP---DSPRETIERALLAAIAS----ARRRIYIETPYFVPDRSLLRALIAAARRGVDVRILLP--AKSDHP 257

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 363 AVHAGYRRYRRELVEAGVRLYERRPSgdksiskrliigssraSLHAKTYVFDRKSVFIGSMNLDPRSLRLNTEIGVYCES 442
Cdd:COG1502  258 LVHWASRSYYEELLEAGVRIYEYEPG----------------FLHAKVMVVDDEWALVGSANLDPRSLRLNFEVNLVIYD 321

                        410       420       430
                 ....*....|....*....|....*....|....*....
gi 736049347 443 PALAAQVAADLEPRLDRiAWRV--EATTDPSGTRRLEWI 479
Cdd:COG1502  322 PEFAAQLRARFEEDLAH-SREVtlEEWRKRPLRRLRERL 359
 
Name Accession Description Interval E-value
PLDc_ymdC_like_2 cd09113
Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and ...
 289-512 1.20e-99

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: 299.13  E-value: 1.20e-99
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 289 LYDDPAKIARAPnDSEGHLLPQLRALALRPEHELLIVSPYLVPGAAMIERLRALTARGVRVTILTNSLASTDVAAVHAGY 368
Cdd:cd09113    1 LSDPPEKALKEA-GPEPVLAYQLAELLKNAKREVLIVSPYFVPGDEGVALLAELARRGVRVRILTNSLAATDVPAVHSGY 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 369 RRYRRELVEAGVRLYERRPSGDKSISKRLIIGSSRASLHAKTYVFDRKSVFIGSMNLDPRSLRLNTEIGVYCESPALAAQ 448
Cdd:cd09113   80 ARYRKRLLKAGVELYELKPDAAKRKRLRGLFGSSRASLHAKSFVIDDRLVFVGSFNLDPRSAYLNTEMGLVIDSPELAAQ 159

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 736049347 449 VAADLEPRLDRIAWRVEATTDpsgtrRLEWIQTDEDGKVTEFDHEPEVSTARRVEVWFLGLFPI 512
Cdd:cd09113  160 LRAAMEEDLAPSAYWVLLLDD-----GGLVWETEEDGKEKEYDSEPETSFWRRLGAWLLSLLPI 218
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 46-479 9.25e-92

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: 284.53  E-value: 9.25e-92
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347  46 FRAQAAAHPGQ--DAFHLLSDPVDALDARVLLADRADRSLDLQYYIWHDDLTGHALADAIIRAADRGVRVRVLLDDLGTN 123
Cdd:COG1502    2 AAPLAAGLPLVggNRVTLLVDGDEAFAALLEAIEAARRSIDLEYYIFDDDEVGRRLADALIAAARRGVKVRVLLDGIGSR 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 124 ADDRKLLEISSHPHIEIRLFNPVATRefkkigtvleFSRVNRRMHNKAMIADNQAAIIGGRNIGDEYFGASSMLE-FGDL 202
Cdd:COG1502   82 ALNRDFLRRLRAAGVEVRLFNPVRLL----------FRRLNGRNHRKIVVIDGRVAFVGGANITDEYLGRDPGFGpWRDT 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 203 DVVVHGRVVNDISTEFDTFWNSpyaysvgalvghdatpgsldrererlrdylramednpyvlEARERLDRIvhgegTELS 282
Cdd:COG1502  152 HVRIEGPAVADLQAVFAEDWNF----------------------------------------ATGEALPFP-----EPAG 186

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 283 WGRATVLYDDPakiARAPNDSEGHLLPQLRAlalrPEHELLIVSPYLVPGAAMIERLRALTARGVRVTILTNslASTDVA 362
Cdd:COG1502  187 DVRVQVVPSGP---DSPRETIERALLAAIAS----ARRRIYIETPYFVPDRSLLRALIAAARRGVDVRILLP--AKSDHP 257

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 363 AVHAGYRRYRRELVEAGVRLYERRPSgdksiskrliigssraSLHAKTYVFDRKSVFIGSMNLDPRSLRLNTEIGVYCES 442
Cdd:COG1502  258 LVHWASRSYYEELLEAGVRIYEYEPG----------------FLHAKVMVVDDEWALVGSANLDPRSLRLNFEVNLVIYD 321

                        410       420       430
                 ....*....|....*....|....*....|....*....
gi 736049347 443 PALAAQVAADLEPRLDRiAWRV--EATTDPSGTRRLEWI 479
Cdd:COG1502  322 PEFAAQLRARFEEDLAH-SREVtlEEWRKRPLRRLRERL 359
PLDc_ymdC_like_1 cd09111
Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and ...
 62-223 7.96e-84

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: 256.69  E-value: 7.96e-84
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347  62 LSDPVDALDARVLLADRADRSLDLQYYIWHDDLTGHALADAIIRAADRGVRVRVLLDDLGTNADDRKLLEISSHPHIEIR 141
Cdd:cd09111    1 LEDGLDALAARLALIRSAERSIDLQYYIWHDDESGRLLLGELLEAADRGVRVRLLLDDLGTSGRDRLLAALDAHPNIEVR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 142 LFNPVATREFKKIGTVLEFSRVNRRMHNKAMIADNQAAIIGGRNIGDEYFGASSMLEFGDLDVVVHGRVVNDISTEFDTF 221
Cdd:cd09111   81 LFNPFRNRGGRLLEFLTDFSRLNRRMHNKLFIVDGAVAIVGGRNIGDEYFGASPEVNFRDLDVLAVGPVVRQLSESFDTY 160


                 ..
gi 736049347 222 WN 223
Cdd:cd09111  161 WN 162
cls PRK01642
cardiolipin synthetase; Reviewed
 60-463 1.34e-37

cardiolipin synthetase; Reviewed


Pssm-ID: 234967 [Multi-domain]  Cd Length: 483  Bit Score: 144.15  E-value: 1.34e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347  60 HLLSDPVDALDArvLLAD--RADRSLDLQYYIWHDDLTGHALADAIIRAADRGVRVRVLLDDLGTNADDRklleiSSHPH 137
Cdd:PRK01642 119 RLLTNGDETFQA--IIRDieLARHYILMEFYIWRPDGLGDQVAEALIAAAKRGVRVRLLYDSIGSFAFFR-----SPYPE 191

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 138 ------IEIRLFNPVatrefkKIGTVLeFSRVNRRMHNKAMIADNQAAIIGGRNIGD-EYFGASSMLEFG-DLDVVVHGR 209
Cdd:PRK01642 192 elrnagVEVVEFLKV------NLGRVF-RRRLDLRNHRKIVVIDGYIAYTGSMNVVDpEYFKQDPGVGQWrDTHVRIEGP 264

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 210 VVNDISTEF--DTFWnspyaysvgalvghdATpgsldreRERLRDYLRAMEDNPYVLEarerldrivhgegtelswGRAT 287
Cdd:PRK01642 265 VVTALQLIFaeDWEW---------------ET-------GERILPPPPDVLIMPFEEA------------------SGHT 304

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 288 VLYddpakIARAPNDSEgHLLPQLRALAL-RPEHELLIVSPYLVPGAAMIERLRALTARGVRVTILTNSLAstDVAAVHA 366
Cdd:PRK01642 305 VQV-----IASGPGDPE-ETIHQFLLTAIySARERLWITTPYFVPDEDLLAALKTAALRGVDVRIIIPSKN--DSLLVFW 376

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 367 GYRRYRRELVEAGVRLYERRPsgdksiskrliigssrASLHAKTYVFDRKSVFIGSMNLDPRSLRLNTEIGVYCESPALA 446
Cdd:PRK01642 377 ASRAFFTELLEAGVKIYRYEG----------------GLLHTKSVLVDDELALVGTVNLDMRSFWLNFEITLVIDDTGFA 440

                        410       420
                 ....*....|....*....|...
gi 736049347 447 AQVAADLEP------RLDRIAWR 463
Cdd:PRK01642 441 ADLAAMQEDyfarsrELDLEEWR 463
bac_cardiolipin TIGR04265
cardiolipin synthase; This model is based on experimentally characterized bacterial ...
 47-459 4.19e-28

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: 117.20  E-value: 4.19e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347   47 RAQAAAHPGQDAFHLLSDPVDALDARVLLADRADRSLDLQYYIWHDDLTGHALADAIIRAADRGVRVRVLLDDLGTNADD 126
Cdd:TIGR04265 109 RNQGIFLTEGNQLKLMTDGDDVYDALIQDIKNARHYIHLEYYIWQPDGLGDQILESLMAKAKQGVHVRILYDDVGSVALF 188

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347  127 RKLLEISSHPHIEIRLFNPVATrefkkigtVLEFSRVNRRMHNKAMIADNQAAIIGGRNIGDEYFGASSmlEFG---DLD 203
Cdd:TIGR04265 189 KSWPELFRNAGGEVVAFFPVKL--------PLLNLRMNNRNHRKIIVIDGQIGYVGGFNIGDEYLGKDA--KFGywrDTH 258

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347  204 VVVHGRVVNDISTEFDTFWNSpyaysvgalvghdatpgsldrererlrdylramEDNPYVLEARERLDRIVHGEGTelsw 283
Cdd:TIGR04265 259 LRIEGDAVTALQLIFILDWNS---------------------------------QTGRRIIPYDPDYFPMPNEQAG---- 301

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347  284 gratvlyDDPAKIARAPNDSEGHLLPQ-LRALALRPEHELLIVSPYLVPGAAMIERLRALTARGVRVTILTNSlaSTDVA 362
Cdd:TIGR04265 302 -------GHGIQIIASGPDFPWEQIKYgYLKMIYSAKKSIYIQSPYFIPDDDLLHAIKIAALSGVDVSIMIPN--KPDHP 372

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347  363 AVHAGYRRYRRELVEAGVRLYErrpsgdksiskrliigSSRASLHAKTYVFDRKSVFIGSMNLDPRSLRLNTEIGVYCES 442
Cdd:TIGR04265 373 LVFWASRSNFTELLAAGVKIYQ----------------YENGFLHSKSVLVDDEIASVGTANMDMRSFWLNFEVNAFIYD 436

                         410
                  ....*....|....*..
gi 736049347  443 PALAAQVAADLEPRLDR 459
Cdd:TIGR04265 437 KGFAKDLAAAYDDDISR 453
PLDc_2 pfam13091
PLD-like domain;
311-454 1.63e-27

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 106.99  E-value: 1.63e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347  311 LRALALRPEHELLIVSPYLVPGAAMIERLRALTARGVRVTILTNSLASTDVAAVHAGYRRYRrELVEAGVRLYERRPSGD 390
Cdd:pfam13091   1 LIDLINSAKKSIDIATYYFVPDREIIDALIAAAKRGVDVRIILDSNKDDAGGPKKASLKELR-SLLRAGVEIREYQSFLR 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 736049347  391 ksiskrliigssraSLHAKTYVFDRKSVFIGSMNLDPRSLRLNTEIGVYCESPALAAQVAADLE 454
Cdd:pfam13091  80 --------------SMHAKFYIIDGKTVIVGSANLTRRALRLNLENNVVIKDPELAQELEKEFD 129
PLDc_2 pfam13091
PLD-like domain;
75-222 8.24e-14

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 68.47  E-value: 8.24e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347   75 LADRADRSLDLQYYIWHDDLtghALADAIIRAADRGVRVRVLLDDlgTNADDRKLLEISSHphieirlfnpvATREFKKI 154
Cdd:pfam13091   4 LINSAKKSIDIATYYFVPDR---EIIDALIAAAKRGVDVRIILDS--NKDDAGGPKKASLK-----------ELRSLLRA 67

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347  155 GT-VLEFSRVNRRMHNKAMIADNQAAIIGGRNigdeyFGASSMLEFGDLDVVVHGRVVND-ISTEFDTFW 222
Cdd:pfam13091  68 GVeIREYQSFLRSMHAKFYIIDGKTVIVGSAN-----LTRRALRLNLENNVVIKDPELAQeLEKEFDRLW 132
PLDc smart00155
Phospholipase D. Active site motifs; Phosphatidylcholine-hydrolyzing phospholipase D (PLD) ...
 406-429 2.28e-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: 41.22  E-value: 2.28e-05
                           10        20
                   ....*....|....*....|....
gi 736049347   406 LHAKTYVFDRKSVFIGSMNLDPRS 429
Cdd:smart00155   5 LHTKLMIVDDEIAYIGSANLDGRS 28
COG3886 COG3886
HKD family nuclease [Replication, recombination and repair];
336-425 2.64e-04

HKD family nuclease [Replication, recombination and repair];


Pssm-ID: 443094 [Multi-domain]  Cd Length: 941  Bit Score: 43.82  E-value: 2.64e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 336 IERLRALTARGVRVTILTNS-LASTDVAAVhagyrRYRRELVEAGVRLYERRpsgdksiskrliigssRASLHAKTYVFD 414
Cdd:COG3886   61 LDALKELLERGVKGRILTSTyLGFTEPKAL-----RELLDLPNIEVRVSYDR----------------KTRFHAKAYIFE 119

                         90
                 ....*....|....
gi 736049347 415 RK---SVFIGSMNL 425
Cdd:COG3886  120 RTgygTAIIGSSNL 133
PLDc smart00155
Phospholipase D. Active site motifs; Phosphatidylcholine-hydrolyzing phospholipase D (PLD) ...
 163-190 3.91e-04

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


Pssm-ID: 197546 [Multi-domain]  Cd Length: 28  Bit Score: 37.75  E-value: 3.91e-04
                           10        20
                   ....*....|....*....|....*...
gi 736049347   163 VNRRMHNKAMIADNQAAIIGGRNIGDEY 190
Cdd:smart00155   1 YDGVLHTKLMIVDDEIAYIGSANLDGRS 28
PHA03003 PHA03003
palmytilated EEV membrane glycoprotein; Provisional
 332-458 5.43e-04

palmytilated EEV membrane glycoprotein; Provisional


Pssm-ID: 177506 [Multi-domain]  Cd Length: 369  Bit Score: 42.34  E-value: 5.43e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 332 GAAMIERLRALTARGVRVTILtnslasTDVAAVHAGYrryrRELVEAGVRLYERRpsgdksISKRLIIGSSRASLhaktY 411
Cdd:PHA03003  62 GRLILDKLKEAAESGVKVTIL------VDEQSGDKDE----EELQSSNINYIKVD------IGKLNNVGVLLGSF----W 121

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 736049347 412 VFDRKSVFIGSMNLDPRSLRLNTEIGVYCESPALaaqvAADLEPRLD 458
Cdd:PHA03003 122 VSDDRRCYIGNASLTGGSISTIKTLGVYSTYPPL----ATDLRRRFD 164
 
Name Accession Description Interval E-value
PLDc_ymdC_like_2 cd09113
Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and ...
 289-512 1.20e-99

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: 299.13  E-value: 1.20e-99
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 289 LYDDPAKIARAPnDSEGHLLPQLRALALRPEHELLIVSPYLVPGAAMIERLRALTARGVRVTILTNSLASTDVAAVHAGY 368
Cdd:cd09113    1 LSDPPEKALKEA-GPEPVLAYQLAELLKNAKREVLIVSPYFVPGDEGVALLAELARRGVRVRILTNSLAATDVPAVHSGY 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 369 RRYRRELVEAGVRLYERRPSGDKSISKRLIIGSSRASLHAKTYVFDRKSVFIGSMNLDPRSLRLNTEIGVYCESPALAAQ 448
Cdd:cd09113   80 ARYRKRLLKAGVELYELKPDAAKRKRLRGLFGSSRASLHAKSFVIDDRLVFVGSFNLDPRSAYLNTEMGLVIDSPELAAQ 159

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 736049347 449 VAADLEPRLDRIAWRVEATTDpsgtrRLEWIQTDEDGKVTEFDHEPEVSTARRVEVWFLGLFPI 512
Cdd:cd09113  160 LRAAMEEDLAPSAYWVLLLDD-----GGLVWETEEDGKEKEYDSEPETSFWRRLGAWLLSLLPI 218
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 46-479 9.25e-92

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: 284.53  E-value: 9.25e-92
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347  46 FRAQAAAHPGQ--DAFHLLSDPVDALDARVLLADRADRSLDLQYYIWHDDLTGHALADAIIRAADRGVRVRVLLDDLGTN 123
Cdd:COG1502    2 AAPLAAGLPLVggNRVTLLVDGDEAFAALLEAIEAARRSIDLEYYIFDDDEVGRRLADALIAAARRGVKVRVLLDGIGSR 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 124 ADDRKLLEISSHPHIEIRLFNPVATRefkkigtvleFSRVNRRMHNKAMIADNQAAIIGGRNIGDEYFGASSMLE-FGDL 202
Cdd:COG1502   82 ALNRDFLRRLRAAGVEVRLFNPVRLL----------FRRLNGRNHRKIVVIDGRVAFVGGANITDEYLGRDPGFGpWRDT 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 203 DVVVHGRVVNDISTEFDTFWNSpyaysvgalvghdatpgsldrererlrdylramednpyvlEARERLDRIvhgegTELS 282
Cdd:COG1502  152 HVRIEGPAVADLQAVFAEDWNF----------------------------------------ATGEALPFP-----EPAG 186

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 283 WGRATVLYDDPakiARAPNDSEGHLLPQLRAlalrPEHELLIVSPYLVPGAAMIERLRALTARGVRVTILTNslASTDVA 362
Cdd:COG1502  187 DVRVQVVPSGP---DSPRETIERALLAAIAS----ARRRIYIETPYFVPDRSLLRALIAAARRGVDVRILLP--AKSDHP 257

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 363 AVHAGYRRYRRELVEAGVRLYERRPSgdksiskrliigssraSLHAKTYVFDRKSVFIGSMNLDPRSLRLNTEIGVYCES 442
Cdd:COG1502  258 LVHWASRSYYEELLEAGVRIYEYEPG----------------FLHAKVMVVDDEWALVGSANLDPRSLRLNFEVNLVIYD 321

                        410       420       430
                 ....*....|....*....|....*....|....*....
gi 736049347 443 PALAAQVAADLEPRLDRiAWRV--EATTDPSGTRRLEWI 479
Cdd:COG1502  322 PEFAAQLRARFEEDLAH-SREVtlEEWRKRPLRRLRERL 359
PLDc_ymdC_like_1 cd09111
Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and ...
 62-223 7.96e-84

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: 256.69  E-value: 7.96e-84
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347  62 LSDPVDALDARVLLADRADRSLDLQYYIWHDDLTGHALADAIIRAADRGVRVRVLLDDLGTNADDRKLLEISSHPHIEIR 141
Cdd:cd09111    1 LEDGLDALAARLALIRSAERSIDLQYYIWHDDESGRLLLGELLEAADRGVRVRLLLDDLGTSGRDRLLAALDAHPNIEVR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 142 LFNPVATREFKKIGTVLEFSRVNRRMHNKAMIADNQAAIIGGRNIGDEYFGASSMLEFGDLDVVVHGRVVNDISTEFDTF 221
Cdd:cd09111   81 LFNPFRNRGGRLLEFLTDFSRLNRRMHNKLFIVDGAVAIVGGRNIGDEYFGASPEVNFRDLDVLAVGPVVRQLSESFDTY 160


                 ..
gi 736049347 222 WN 223
Cdd:cd09111  161 WN 162
cls PRK01642
cardiolipin synthetase; Reviewed
 60-463 1.34e-37

cardiolipin synthetase; Reviewed


Pssm-ID: 234967 [Multi-domain]  Cd Length: 483  Bit Score: 144.15  E-value: 1.34e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347  60 HLLSDPVDALDArvLLAD--RADRSLDLQYYIWHDDLTGHALADAIIRAADRGVRVRVLLDDLGTNADDRklleiSSHPH 137
Cdd:PRK01642 119 RLLTNGDETFQA--IIRDieLARHYILMEFYIWRPDGLGDQVAEALIAAAKRGVRVRLLYDSIGSFAFFR-----SPYPE 191

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 138 ------IEIRLFNPVatrefkKIGTVLeFSRVNRRMHNKAMIADNQAAIIGGRNIGD-EYFGASSMLEFG-DLDVVVHGR 209
Cdd:PRK01642 192 elrnagVEVVEFLKV------NLGRVF-RRRLDLRNHRKIVVIDGYIAYTGSMNVVDpEYFKQDPGVGQWrDTHVRIEGP 264

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 210 VVNDISTEF--DTFWnspyaysvgalvghdATpgsldreRERLRDYLRAMEDNPYVLEarerldrivhgegtelswGRAT 287
Cdd:PRK01642 265 VVTALQLIFaeDWEW---------------ET-------GERILPPPPDVLIMPFEEA------------------SGHT 304

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 288 VLYddpakIARAPNDSEgHLLPQLRALAL-RPEHELLIVSPYLVPGAAMIERLRALTARGVRVTILTNSLAstDVAAVHA 366
Cdd:PRK01642 305 VQV-----IASGPGDPE-ETIHQFLLTAIySARERLWITTPYFVPDEDLLAALKTAALRGVDVRIIIPSKN--DSLLVFW 376

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 367 GYRRYRRELVEAGVRLYERRPsgdksiskrliigssrASLHAKTYVFDRKSVFIGSMNLDPRSLRLNTEIGVYCESPALA 446
Cdd:PRK01642 377 ASRAFFTELLEAGVKIYRYEG----------------GLLHTKSVLVDDELALVGTVNLDMRSFWLNFEITLVIDDTGFA 440

                        410       420
                 ....*....|....*....|...
gi 736049347 447 AQVAADLEP------RLDRIAWR 463
Cdd:PRK01642 441 ADLAAMQEDyfarsrELDLEEWR 463
PLDc_CLS_1 cd09110
Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Catalytic ...
 67-223 5.00e-32

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: 120.27  E-value: 5.00e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347  67 DALDARVLLADRADRSLDLQYYIWHDDLTGHALADAIIRAADRGVRVRVLLDDLGTNADDRKLLEISSHPHIEIRLFNPV 146
Cdd:cd09110    5 EFFPALLEAIRAARHSIHLEYYIFRDDEIGRRFRDALIEKARRGVEVRLLYDGFGSLGLSRRFLRELREAGVEVRAFNPL 84

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 736049347 147 ATREFkkigtvleFSRVNRRMHNKAMIADNQAAIIGGRNIGDEYFGASSMLE-FGDLDVVVHGRVVNDISTEFDTFWN 223
Cdd:cd09110   85 SFPLF--------LLRLNYRNHRKILVIDGKIAFVGGFNIGDEYLGKDPGFGpWRDTHVRIEGPAVADLQAAFLEDWY 154
bac_cardiolipin TIGR04265
cardiolipin synthase; This model is based on experimentally characterized bacterial ...
 47-459 4.19e-28

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: 117.20  E-value: 4.19e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347   47 RAQAAAHPGQDAFHLLSDPVDALDARVLLADRADRSLDLQYYIWHDDLTGHALADAIIRAADRGVRVRVLLDDLGTNADD 126
Cdd:TIGR04265 109 RNQGIFLTEGNQLKLMTDGDDVYDALIQDIKNARHYIHLEYYIWQPDGLGDQILESLMAKAKQGVHVRILYDDVGSVALF 188

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347  127 RKLLEISSHPHIEIRLFNPVATrefkkigtVLEFSRVNRRMHNKAMIADNQAAIIGGRNIGDEYFGASSmlEFG---DLD 203
Cdd:TIGR04265 189 KSWPELFRNAGGEVVAFFPVKL--------PLLNLRMNNRNHRKIIVIDGQIGYVGGFNIGDEYLGKDA--KFGywrDTH 258

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347  204 VVVHGRVVNDISTEFDTFWNSpyaysvgalvghdatpgsldrererlrdylramEDNPYVLEARERLDRIVHGEGTelsw 283
Cdd:TIGR04265 259 LRIEGDAVTALQLIFILDWNS---------------------------------QTGRRIIPYDPDYFPMPNEQAG---- 301

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347  284 gratvlyDDPAKIARAPNDSEGHLLPQ-LRALALRPEHELLIVSPYLVPGAAMIERLRALTARGVRVTILTNSlaSTDVA 362
Cdd:TIGR04265 302 -------GHGIQIIASGPDFPWEQIKYgYLKMIYSAKKSIYIQSPYFIPDDDLLHAIKIAALSGVDVSIMIPN--KPDHP 372

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347  363 AVHAGYRRYRRELVEAGVRLYErrpsgdksiskrliigSSRASLHAKTYVFDRKSVFIGSMNLDPRSLRLNTEIGVYCES 442
Cdd:TIGR04265 373 LVFWASRSNFTELLAAGVKIYQ----------------YENGFLHSKSVLVDDEIASVGTANMDMRSFWLNFEVNAFIYD 436

                         410
                  ....*....|....*..
gi 736049347  443 PALAAQVAADLEPRLDR 459
Cdd:TIGR04265 437 KGFAKDLAAAYDDDISR 453
PLDc_2 pfam13091
PLD-like domain;
311-454 1.63e-27

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 106.99  E-value: 1.63e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347  311 LRALALRPEHELLIVSPYLVPGAAMIERLRALTARGVRVTILTNSLASTDVAAVHAGYRRYRrELVEAGVRLYERRPSGD 390
Cdd:pfam13091   1 LIDLINSAKKSIDIATYYFVPDREIIDALIAAAKRGVDVRIILDSNKDDAGGPKKASLKELR-SLLRAGVEIREYQSFLR 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 736049347  391 ksiskrliigssraSLHAKTYVFDRKSVFIGSMNLDPRSLRLNTEIGVYCESPALAAQVAADLE 454
Cdd:pfam13091  80 --------------SMHAKFYIIDGKTVIVGSANLTRRALRLNLENNVVIKDPELAQELEKEFD 129
PLDc_ybhO_like_2 cd09159
Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; ...
 310-479 1.96e-26

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: 105.31  E-value: 1.96e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 310 QLRALAlRPEHELLIVSPYLVPGAAMIERLRALTARGVRVTILTNSlASTDVAAVHAGYRRYRReLVEAGVRLYERRPSg 389
Cdd:cd09159   16 YLVAIA-AARRRIWIANAYFVPDRRLRRALIEAARRGVDVRLLLPG-KSDDPLTVAASRALYGK-LLRAGVRIFEYQPS- 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 390 dksiskrliigssraSLHAKTYVFDRKSVFIGSMNLDPRSLRLNTEIGVYCESPALAAQVAADLEprlDRIAWRVEATTD 469
Cdd:cd09159   92 ---------------MLHAKTAVIDGDWATVGSSNLDPRSLRLNLEANLVVEDPAFAAQLEELFE---EDLARSREITLE 153

                        170
                 ....*....|....*
gi 736049347 470 -----PSGTRRLEWI 479
Cdd:cd09159  154 ewrrrPLWQRLLEWL 168
PLDc_CLS_unchar1_1 cd09156
Putative catalytic domain, repeat 1, of uncharacterized proteins similar to bacterial ...
 63-223 6.52e-25

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: 100.41  E-value: 6.52e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347  63 SDPVDALDARVLLADRADRSLDLQYYIWHDDLTGHALADAIIRAADRGVRVRVLLDDLGTNADDRKLLEISSHPHIEIRL 142
Cdd:cd09156    1 ADGVEAYQALIQLIESAKHSIDVCTFILGDDATGRRVIDALARKAREGVEVRLLLDALGSFFLSRRALKKLRAAGGKVAF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 143 FNPVATREFkkigtvleFSRVNRRMHNKAMIADNQAAIIGGRNIGDEYFGASSMLE-FGDLDVVVHGRVVNDISTEFDTF 221
Cdd:cd09156   81 FMPVFRLPF--------RGRTNLRNHRKIAIADGSTAISGGMNLANEYMGPEPDDGrWVDLSFLIEGPAVAQYQEVFRSD 152


                 ..
gi 736049347 222 WN 223
Cdd:cd09156  153 WA 154
PRK11263 PRK11263
cardiolipin synthase ClsB;
72-461 9.32e-25

cardiolipin synthase ClsB;


Pssm-ID: 236888 [Multi-domain]  Cd Length: 411  Bit Score: 106.18  E-value: 9.32e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347  72 RVLLA-DRADRSLDLQYYIWHDDLTGHALADAIIRAADRGVRVRVLLDDLGTNADDRKLLEISSHPHIEIRLFNPvATRE 150
Cdd:PRK11263  22 RVFEAiAAAQEEILLETFILFEDKVGKQLHAALLAAAQRGVKVEVLVDGYGSPDLSDEFVNELTAAGVRFRYFDP-RPRL 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 151 FKKigtvlefsRVN--RRMHNKAMIADNQAAIIGGRNigdeyFGASSMLEFG-----DLDVVVHGRVVNDIstefdtfwn 223
Cdd:PRK11263 101 LGM--------RTNlfRRMHRKIVVIDGRIAFVGGIN-----YSADHLSDYGpeakqDYAVEVEGPVVADI--------- 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 224 spYAYSVGALVGHDATPGSLDRERERlrdylramEDNPYVLEARERLdrivhgegtelswgratVLYDDpakiARAPNDS 303
Cdd:PRK11263 159 --HQFELEALPGQSAARRWWRRHHRA--------EENRQPGEAQALL-----------------VWRDN----EEHRDDI 207

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 304 EGHLLPQLRAlalrPEHELLIVSPYLVPGAAMIERLRALTARGVRVT-ILTnslASTDVAAVHAGYRRYRRELVEAGVRL 382
Cdd:PRK11263 208 ERHYLKALRQ----ARREVIIANAYFFPGYRLLRALRNAARRGVRVRlILQ---GEPDMPIVRVGARLLYNYLLKGGVQI 280

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 383 YE--RRPsgdksiskrliigssrasLHAKTYVFDRKSVFIGSMNLDPRSLRLNTEIGVYCESPALAAQvaadLEPRLDRI 460
Cdd:PRK11263 281 YEycRRP------------------LHGKVALMDDHWATVGSSNLDPLSLSLNLEANLIIRDRAFNQT----LRDNLNGL 338


                 .
gi 736049347 461 A 461
Cdd:PRK11263 339 I 339
PLDc_CLS_2 cd09112
catalytic domain repeat 2 of bacterial cardiolipin synthase and similar proteins; This CD ...
 296-454 2.86e-24

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: 99.47  E-value: 2.86e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 296 IARAPNDSEGHLLPQLRALALRPEHELLIVSPYLVPGAAMIERLRALTARGVRVTILTNSLAstDVAAVHAGYRRYRREL 375
Cdd:cd09112    1 VSSGPDSDWSSIEQAYLKAINSAKKSIYIQTPYFIPDESLLEALKTAALSGVDVRIMIPGKP--DHKLVYWASRSYFEEL 78

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 736049347 376 VEAGVRLYERRPsgdksiskrliigssrASLHAKTYVFDRKSVFIGSMNLDPRSLRLNTEIGVYCESPALAAQVAADLE 454
Cdd:cd09112   79 LKAGVKIYEYNK----------------GFLHSKTLIVDDEIASVGTANLDIRSFELNFEVNAVIYDKEVAKKLEEIFE 141
PRK12452 PRK12452
cardiolipin synthase;
77-458 3.03e-23

cardiolipin synthase;


Pssm-ID: 171510 [Multi-domain]  Cd Length: 509  Bit Score: 102.69  E-value: 3.03e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347  77 DRADRSLDLQYYIWHDDLTGHALADAIIRAADRGVRVRVLLDDLGTNADDRKLLEISSHPHIEIRLFNPVATREFkkigt 156
Cdd:PRK12452 160 EQAKHHIHIQYYIYKSDEIGTKVRDALIKKAKDGVIVRFLYDGLGSNTLRRRFLQPMKEAGIEIVEFDPIFSAWL----- 234

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 157 vleFSRVNRRMHNKAMIADNQAAIIGGRNIGDEYFGASSMLEF-GDLDVVVHGRVVNDISTEFDTFWnsPYAYSvgalvg 235
Cdd:PRK12452 235 ---LETVNYRNHRKIVIVDGEIGFTGGLNVGDEYLGRSKKFPVwRDSHLKVEGKALYKLQAIFLEDW--LYASS------ 303

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 236 hdaTPGSLDRERERLRDYLRAMEdnpyVLEARERLDRIVHGEGTelswgratvlyDDPAkiarapndseghLLPQLRALA 315
Cdd:PRK12452 304 ---GLNTYSWDPFMNRQYFPGKE----ISNAEGAVQIVASGPSS-----------DDKS------------IRNTLLAVM 353

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 316 LRPEHELLIVSPYLVPGAAMIERLRALTARGVRVTILTNslASTDVAAVHAGYRRYRRELVEAGVRLYERRpsgdksisk 395
Cdd:PRK12452 354 GSAKKSIWIATPYFIPDQETLTLLRLSAISGIDVRILYP--GKSDSIISDQASQSYFTPLLKAGASIYSYK--------- 422

                        330       340       350       360       370       380
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 736049347 396 rliigssRASLHAKTYVFDRKSVFIGSMNLDPRSLRLNTEIGVYCESPALAAQVAADLEPRLD 458
Cdd:PRK12452 423 -------DGFMHAKIVLVDDKIATIGTANMDVRSFELNYEIISVLYESETVHDIKRDFEDDFK 478
PLDc_EcCLS_like_2 cd09158
Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase and similar proteins; ...
 319-451 3.33e-21

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: 90.71  E-value: 3.33e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 319 EHELLIVSPYLVPGAAMIERLRALTARGVRVTILTNslASTDVAAVHAGYRRYRRELVEAGVRLYERRPsgdksiskrli 398
Cdd:cd09158   24 RRRVVITTPYFVPDESLLQALCTAALRGVEVTLILP--AKNDSFLVGAASRSYYEELLEAGVKIYLYRG----------- 90

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 736049347 399 igssrASLHAKTYVFDRKSVFIGSMNLDPRSLRLNTEIGVYCESPALAAQVAA 451
Cdd:cd09158   91 -----GLLHAKTVTVDDEVALVGSSNFDIRSFALNFEISLILYDKEFTAQLRA 138
PLDc_CLS_unchar2_2 cd09163
Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial ...
 319-454 1.35e-20

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: 89.15  E-value: 1.35e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 319 EHELLIVSPYLVPGAAMIERLRALTARGVRVTILTNslASTDVAAVHAGYRRYRRELVEAGVRLYERRPSGDksiskrli 398
Cdd:cd09163   24 RHSIRIMTPYFLPDRTLITALQAAALRGVEVDIVLP--ERNNLPLVDWAMRANLWELLEHGVRIYLQPPPFD-------- 93

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 736049347 399 igssraslHAKTYVFDRKSVFIGSMNLDPRSLRLNTEIGVYCESPALAAQVAADLE 454
Cdd:cd09163   94 --------HSKLMVVDGAWALIGSANWDPRSLRLNFELNLEVYDTALAGQLDALFD 141
PLDc_EcCLS_like_1 cd09152
Catalytic domain, repeat 1, of Escherichia coli cardiolipin synthase and similar proteins; ...
 60-218 4.46e-20

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


Pssm-ID: 197250 [Multi-domain]  Cd Length: 163  Bit Score: 87.26  E-value: 4.46e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347  60 HLLSDPVDALDARVLLADRADRSLDLQYYIWHDDLTGHALADAIIRAADRGVRVRVLLDDLGTNADDR-KLLEISSHPHI 138
Cdd:cd09152    5 ELLTDYDAVIDRLIADIDAAKHHVHLLFYIWADDGTGDRVAEALERAAKRGVTCRLLLDAVGSRAFFRsSLWKRLREAGV 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 139 EIRLFNPVATREFKkigtvleFSRVNRRMHNKAMIADNQAAIIGGRNIGD-EYFGASSMLEFGDLDVVVHGRVVNDISTE 217
Cdd:cd09152   85 EVVEALPLRLFRRR-------LARFDLRNHRKIAVIDGRIAYTGSQNIIDpEFFKKAGGGPWVDLMVRVEGPVVSQLQAV 157


                 .
gi 736049347 218 F 218
Cdd:cd09152  158 F 158
PLDc_PaCLS_like_1 cd09155
Putative catalytic domain, repeat 1, of Pseudomonas aeruginosa cardiolipin synthase and ...
 77-192 1.18e-17

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: 79.98  E-value: 1.18e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347  77 DRADRSLDLQYYIWHDDLTGHALADAIIRAADRGVRVRVLLDDLGTNADDRKLLEISSHPHIEIRLFNpvATREFKKIgt 156
Cdd:cd09155   15 ASAEEYILVQFYIIRDDDLGRELKDALIARAQAGVRVYLLYDEIGSHSLSRSYIERLRKAGVEVSAFN--TTRGWGNR-- 90

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 736049347 157 vlefSRVNRRMHNKAMIADNQAAIIGGRNIGDEYFG 192
Cdd:cd09155   91 ----FQLNFRNHRKIVVVDGQTAFVGGHNVGDEYLG 122
PLDc_SMU_988_like_2 cd09160
Putative catalytic domain, repeat 2, of Streptococcus mutans uncharacterized protein SMU_988 ...
 324-454 1.28e-16

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: 77.54  E-value: 1.28e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 324 IVSPYLVPGAAMIERLRALTARGVRVTILTNSLAstDVAAVHAGYRRYRRELVEAGVRLYERRPsgdksiskrliigssr 403
Cdd:cd09160   29 ITTPYLILDDEMLDALCLAAKRGVDVRIITPHIP--DKKYVFLVTRSNYPELLEAGVKIYEYTP---------------- 90

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 736049347 404 ASLHAKTYVFDRKSVFIGSMNLDPRSLRLNTEIGVY-CESPALAAqVAADLE 454
Cdd:cd09160   91 GFIHAKTFVSDDKAAVVGTINLDYRSLYLHFECGVYmYDTPVISD-IKEDFE 141
PLDc_PaCLS_like_2 cd09161
Putative catalytic domain, repeat 2, of Pseudomonas aeruginosa cardiolipin synthase and ...
 319-454 1.04e-15

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: 75.02  E-value: 1.04e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 319 EHELLIVSPYLVPGAAMIERLRALTARGVRVTILTNSLAstDVAAVHAGYRRYRRELVEAGVRLYERRPsgdksiskrli 398
Cdd:cd09161   24 QKRLWIASPYFVPDEGVLAALQLAALRGVDVRILIPERP--DHLLVYLASFSYLPELIRAGVKVYRYQP----------- 90

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 736049347 399 igssrASLHAKTYVFDRKSVFIGSMNLDPRSLRLNTEIGVYCESPALAAQVAADLE 454
Cdd:cd09161   91 -----GFLHQKVVLVDDELAAVGTANLDNRSFRLNFEITALVADPGFAQEVEAMLE 141
PLDc_CLS_unchar2_1 cd09157
Putative catalytic domain, repeat 1, of uncharacterized proteins similar to bacterial ...
 77-223 1.35e-15

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: 74.14  E-value: 1.35e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347  77 DRADRSLDLQYYIWHDDLTGHALADAIIRAADRGVRVRVLLDDLGTNADDRKLLEISSHPHIEIRLFNPVatrefkKIGT 156
Cdd:cd09157   15 DAARHSIALSSYIFDNDGVGREFVDALAEAVARGVDVRVLIDGVGARYSRPSIRRRLRRAGVPVARFLPP------RLPP 88

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 736049347 157 VLEFsrVNRRMHNKAMIADNQAAIIGGRNIGDEYfgassMLEFG------DLDVVVHGRVVNDISTEFDTFWN 223
Cdd:cd09157   89 RLPF--INLRNHRKILVVDGRTGFTGGMNIRDGH-----LVADDpknpvqDLHFRVEGPVVAQLQEVFAEDWY 154
PLDc_CLS_unchar1_2 cd09162
Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial ...
 296-444 3.74e-15

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: 73.45  E-value: 3.74e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 296 IARAPNDSEGHLLPQLRALALRPEHELLIVSPYLVPGAAMIERLRALTARGVRVTILTNslASTDVAAVHAGYRRYRREL 375
Cdd:cd09162    1 VPSGPDVPGDPLYEALLSAIFEAEHRIWIVTPYFVPDEVLLRALRLAARRGVDVRLIVP--KRSNHRIADLARGSYLRDL 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 736049347 376 VEAGVRLYERRPsgdksiskrliigssrASLHAKTYVFDRKSVFIGSMNLDPRSLRLNTEIGVYCESPA 444
Cdd:cd09162   79 QEAGAEIYLYQP----------------GMLHAKAVVVDDKLALVGSANLDMRSLFLNYEVAVFFYSPA 131
PLDc_2 pfam13091
PLD-like domain;
75-222 8.24e-14

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 68.47  E-value: 8.24e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347   75 LADRADRSLDLQYYIWHDDLtghALADAIIRAADRGVRVRVLLDDlgTNADDRKLLEISSHphieirlfnpvATREFKKI 154
Cdd:pfam13091   4 LINSAKKSIDIATYYFVPDR---EIIDALIAAAKRGVDVRIILDS--NKDDAGGPKKASLK-----------ELRSLLRA 67

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347  155 GT-VLEFSRVNRRMHNKAMIADNQAAIIGGRNigdeyFGASSMLEFGDLDVVVHGRVVND-ISTEFDTFW 222
Cdd:pfam13091  68 GVeIREYQSFLRSMHAKFYIIDGKTVIVGSAN-----LTRRALRLNLENNVVIKDPELAQeLEKEFDRLW 132
PLDc_unchar1_2 cd09128
Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins; ...
 60-222 2.64e-13

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: 67.30  E-value: 2.64e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347  60 HLLSDPVDALDARVLLADRADRSLDLQY-YIWHDDltghALADAIIRAADRGVRVRVLLDDLGTNADDRKLLEISSHphi 138
Cdd:cd09128    3 QLLLSPDNAREALLALIDSAEESLLIQNeEMGDDA----PILDALVDAAKRGVDVRVLLPSAWSAEDERQARLRALE--- 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 139 eiRLFNPVATREFKKIgtvlefsrvnrRMHNKAMIADNQAAIIGGRNigdeyFGASSMLEFGDLDVVVHGR-VVNDISTE 217
Cdd:cd09128   76 --GAGVPVRLLKDKFL-----------KIHAKGIVVDGKTALVGSEN-----WSANSLDRNREVGLIFDDPeVAAYLQAV 137


                 ....*
gi 736049347 218 FDTFW 222
Cdd:cd09128  138 FESDW 142
PLDc_SF cd00138
Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D ...
 310-438 3.68e-13

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: 66.00  E-value: 3.68e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 310 QLRALALRPEHELLIVSPYLVPGAA--MIERLRALTARGVRVTILTNSLASTDVAAVHAGYRRYRRELVEagVRLYERRP 387
Cdd:cd00138    2 ALLELLKNAKESIFIATPNFSFNSAdrLLKALLAAAERGVDVRLIIDKPPNAAGSLSAALLEALLRAGVN--VRSYVTPP 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 736049347 388 SGDKSiskrliigssrasLHAKTYVFDRKSVFIGSMNLDPRSLRLNTEIGV 438
Cdd:cd00138   80 HFFER-------------LHAKVVVIDGEVAYVGSANLSTASAAQNREAGV 117
PLDc_unchar1_2 cd09128
Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins; ...
 299-451 1.05e-12

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: 65.37  E-value: 1.05e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 299 APNDSEGHLLPQLRAlalrPEHELLIVSPYLVPGAAMIERLRALTARGVRVTILTNSLASTDvaavhAGYRRYRRELVEA 378
Cdd:cd09128    7 SPDNAREALLALIDS----AEESLLIQNEEMGDDAPILDALVDAAKRGVDVRVLLPSAWSAE-----DERQARLRALEGA 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 736049347 379 GVRLYERRPSGDKsiskrliigssrasLHAKTYVFDRKSVFIGSMNLDPRSLRLNTEIGVYCESPALAAQVAA 451
Cdd:cd09128   78 GVPVRLLKDKFLK--------------IHAKGIVVDGKTALVGSENWSANSLDRNREVGLIFDDPEVAAYLQA 136
PLDc_vPLD3_4_5_like_2 cd09107
Putative catalytic domain, repeat 2, of vertebrate phospholipases, PLD3, PLD4 and PLD5, viral ...
 101-223 8.32e-12

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: 63.81  E-value: 8.32e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 101 DAIIRAA-DRGVRVRVLLDDLGTN-------ADDRKLLEISS-HPHIEIRLFN-PVATREFKKigtvleFSRVNrrmHNK 170
Cdd:cd09107   57 NALRRAAvDRGVKVRLLVSNWKHTdpsmdafLKSLQLLKSGVgNGDIEVKIFTvPGDQSTKIP------FARVN---HAK 127

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 736049347 171 AMIADNQaAIIGGRNIGDEYFGASSMLEFgdldVVVHGRVVNDISTEFDTFWN 223
Cdd:cd09107  128 YMVTDER-AYIGTSNWSGDYFYNTAGVSL----VINDPAIVQQLKDVFERDWN 175
PLDc_SMU_988_like_1 cd09154
Putative catalytic domain, repeat 1, of Streptococcus mutans uncharacterized protein SMU_988 ...
 74-223 4.43e-10

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


Pssm-ID: 197251 [Multi-domain]  Cd Length: 155  Bit Score: 58.31  E-value: 4.43e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347  74 LLAD--RADRSLDLQYYIWHDDLTGHALADAIIRAADRGVRVRVLLDDLGT----NADDRKLLEISshpHIEIRLFNPva 147
Cdd:cd09154   11 MLEDlkKAEKFIFMEYFIIEEGYMWDSILEILKEKAKEGVEVRIMYDDFGSittlPKDYPKELEKI---GIKCRVFNP-- 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 148 treFKKIgtvleFS-RVNRRMHNKAMIADNQAAIIGGRNIGDEYFGASSmlEFG---DLDVVVHGRVVNDISTEFDTFWN 223
Cdd:cd09154   86 ---FKPI-----LSlYMNNRDHRKITVIDGKVAFTGGINLADEYINKIE--RFGywkDTGIRLEGEAVWSLTVMFLEMWN 155
PLDc_vPLD3_4_5_like_1 cd09106
Putative catalytic domain, repeat 1, of vertebrate phospholipases, PLD3, PLD4 and PLD5, viral ...
 319-439 2.95e-09

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: 55.72  E-value: 2.95e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 319 EHELLIVSPY-------------LVPGAAMIERLRALTARGVRVTILTNS-----LASTDVAAVHAGYRRYRR----ELV 376
Cdd:cd09106   32 KKSIDIASFYwnlrgtdtnpdssAQEGEDIFNALLEAAKRGVKIRILQDKpskdkPDEDDLELAALGGAEVRSldftKLI 111

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 736049347 377 EAGVrlyerrpsgdksiskrliigssrasLHAKTYVFDRKSVFIGSMNLDPRSLRLNTEIGVY 439
Cdd:cd09106  112 GGGV-------------------------LHTKFWIVDGKHFYLGSANLDWRSLTQVKELGVY 149
PLDc_unchar1_1 cd09127
Putative catalytic domain, repeat 1, of uncharacterized phospholipase D-like proteins; ...
 334-451 7.57e-09

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: 54.19  E-value: 7.57e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 334 AMIERLRALTARGVRVTILTNSLASTDVAAVHAGYRRyrreLVEAGVRLyeRRPSGDksiskrliigSSRASLHAKTYVF 413
Cdd:cd09127   35 ALEKALAAAAKRGVRVRVLLEGGPVGGISRAEKLLDY----LNEAGVEV--RWTNGT----------ARYRYTHAKYIVV 98

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 736049347 414 DRKSVFIGSMNLDPRSLRLNTEIGVYCESPALAAQVAA 451
Cdd:cd09127   99 DDERALVLTENFKPSGFTGTRGFGVVTDDPAVVAEIAD 136
PLDc_unchar1_1 cd09127
Putative catalytic domain, repeat 1, of uncharacterized phospholipase D-like proteins; ...
 77-191 7.79e-09

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: 54.19  E-value: 7.79e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347  77 DRADRSLDLQYYiwhdDLTGHALADAIIRAADRGVRVRVLLDD--LGTNADDRKLLEISSHPHIEIRLFNPVATRefkki 154
Cdd:cd09127   18 ASAKRSILLKMY----EFTDPALEKALAAAAKRGVRVRVLLEGgpVGGISRAEKLLDYLNEAGVEVRWTNGTARY----- 88

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 736049347 155 gtvlefsrvnRRMHNKAMIADNQAAIIGGRNIGDEYF 191
Cdd:cd09127   89 ----------RYTHAKYIVVDDERALVLTENFKPSGF 115
PLDc_unchar3 cd09131
Putative catalytic domain of uncharacterized phospholipase D-like proteins; Putative catalytic ...
 98-185 1.20e-08

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: 53.88  E-value: 1.20e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347  98 ALADAIIRAADRGVRVRVLLDDlgTNADDrklleisshphiEIRLFNPVATREFKKIGTVLEFSRVNRRMHNKAMIADNQ 177
Cdd:cd09131   38 TLLEALIDAHKRGVDVKVVLED--SIDDD------------EVTEENDNTYRYLKDNGVEVRFDSPSVTTHTKLVVIDGR 103


                 ....*...
gi 736049347 178 AAIIGGRN 185
Cdd:cd09131  104 TVYVGSHN 111
PLDc_SF cd00138
Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D ...
 75-185 1.53e-08

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: 52.90  E-value: 1.53e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347  75 LADRADRSLDLQYYIWHDDLTGHaLADAIIRAADRGVRVRVLLDDLGTNA--DDRKLLEISSHPHIEIRLFNPVATRefk 152
Cdd:cd00138    6 LLKNAKESIFIATPNFSFNSADR-LLKALLAAAERGVDVRLIIDKPPNAAgsLSAALLEALLRAGVNVRSYVTPPHF--- 81

                         90       100       110
                 ....*....|....*....|....*....|...
gi 736049347 153 kigtvlefsrvNRRMHNKAMIADNQAAIIGGRN 185
Cdd:cd00138   82 -----------FERLHAKVVVIDGEVAYVGSAN 103
PLDc_Nuc_like cd09116
Catalytic domain of EDTA-resistant nuclease Nuc, vertebrate phospholipase D6, and similar ...
 67-185 1.82e-08

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: 53.07  E-value: 1.82e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347  67 DALDARVLLADRADRSLDLQYYIwhddLTGHALADAIIRAADRGVRVRVLLD-DLGTNADDRKLLEISSHPHIEIRlfnp 145
Cdd:cd09116    9 NLERLIVALIANAKSSIDVAMYA----LTDPEIAEALKRAAKRGVRVRIILDkDSLADNLSITLLALLSNLGIPVR---- 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 736049347 146 vaTREFKKIgtvlefsrvnrrMHNKAMIADNQAAIIGGRN 185
Cdd:cd09116   81 --TDSGSKL------------MHHKFIIIDGKIVITGSAN 106
PLDc_vPLD3_2 cd09147
Putative catalytic domain, repeat 2, of vertebrate phospholipase PLD3; Putative catalytic ...
 98-227 2.48e-08

Putative catalytic domain, repeat 2, of vertebrate phospholipase PLD3; Putative catalytic domain, repeat 2, of phospholipase D3 (PLD3, EC 3.1.4.4). The human protein is also known as Hu-K4 or HUK4 and it was identified as a human homolog of the vaccinia virus protein K4, which is encoded by the HindIII K4L gene. PLD3 is found in many human organs with highest expression levels found in the central nervous system. Due to the presence of two copies of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue), PLD3 has been assigned to the PLD superfamily although no catalytic activity has been detected experimentally. PLD3 is a membrane-bound protein that colocalizes with protein disulfide isomerase, an endoplasmic reticulum (ER) protein. Like other homologs of protein K4, PLD3 might alter the lipid content of associated membranes by selectively hydrolyzing phosphatidylcholine (PC) into the corresponding phosphatidic acid, which is thought to be involved in the regulation of lipid movement.


Pssm-ID: 197245  Cd Length: 186  Bit Score: 53.82  E-value: 2.48e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347  98 ALADAIIRAA-DRGVRVRVLLDDLGTNADDRK--------LLEISSHPHIEIRLFNPVATREFKKIgtvlEFSRVNrrmH 168
Cdd:cd09147   54 AIDDGLRRATyERGVKVRLLISCWGHSEPSMFaflrslaaLRDNTTHSDIQVKIFVVPADEAQKKI----PYARVN---H 126

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 736049347 169 NKAMIADnQAAIIGGRNIGDEYF--GASSMLEFGDLDVVVHGRVVNDISTEFDTFWNSPYA 227
Cdd:cd09147  127 NKYMVTD-RVAYIGTSNWSGDYFtnTAGSALVVNQTGRSASGTLQSQLQAVFERDWDSPYS 186
PLDc_unchar4 cd09132
Putative catalytic domain of uncharacterized phospholipase D-like proteins; Putative catalytic ...
 319-438 3.89e-08

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: 51.89  E-value: 3.89e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 319 EHELLIVSPYLVPGAAMIERLRALTARGVRVTILTNSLASTDVAAVHAGYRRYRRELveAGVRLYERrpSGDKSISKRli 398
Cdd:cd09132   12 ERSLLIVGYSAYKVSELLQALAAALERGVQVRVVVESSEKAGSVLSLDEDELMWPKL--AGATLYVW--PEKKRPGKR-- 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 736049347 399 igssrASLHAKTYVFDRKSVFIGSMNLDPRSLRLNTEIGV 438
Cdd:cd09132   86 -----ASLHAKVIVADRRRLLVTSANLTGAGMERNIEAGV 120
PRK13912 PRK13912
nuclease NucT; Provisional
 55-192 4.00e-08

nuclease NucT; Provisional


Pssm-ID: 184389 [Multi-domain]  Cd Length: 177  Bit Score: 53.24  E-value: 4.00e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347  55 GQDAFHLLS-DPVDALDARVLLADRADRSLDLQYYiwhdDLTGHALADAIIRAADRGVRVRVLLDDLGTNADDRKLLE-I 132
Cdd:PRK13912  20 AKSSLYFLPyEQKDALNKLVSLISNARSSIKIAIY----SFTHKDIAKALKSAAKRGVKISIIYDYESNHNNDQSTIGyL 95

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 133 SSHPHIEIRLFNPVATREFKKIGtvlefsrvnrRMHNKAMIADNQAAIIGGRNIGDEYFG 192
Cdd:PRK13912  96 DKYPNIKVCLLKGLKAKNGKYYG----------IMHQKVAIIDDKIVVLGSANWSKNAFE 145
PLDc_Nuc cd09170
Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar ...
 77-182 1.76e-07

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: 50.21  E-value: 1.76e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347  77 DRADRSLDLQYYiwhdDLTGHALADAIIRAADRGVRVRVLLDDLGTNADDRKLLEISSHpHIEIRLFNPVATrefkkigt 156
Cdd:cd09170   21 DSARRSIDVAAY----SFTSPPIARALIAAKKRGVDVRVVLDKSQAGGKYSALNYLANA-GIPVRIDDNYAI-------- 87

                         90       100
                 ....*....|....*....|....*.
gi 736049347 157 vlefsrvnrrMHNKAMIADNQAAIIG 182
Cdd:cd09170   88 ----------MHNKVMVIDGKTVITG 103
PHA03003 PHA03003
palmytilated EEV membrane glycoprotein; Provisional
 69-230 3.47e-07

palmytilated EEV membrane glycoprotein; Provisional


Pssm-ID: 177506 [Multi-domain]  Cd Length: 369  Bit Score: 52.36  E-value: 3.47e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347  69 LDARVLLA--DRADRSLDLQYY-----IWHDDLTGH--ALADAIIRAA-DRGVRVRVLL-----DDLGTNADDRKLLEIS 133
Cdd:PHA03003 216 LDADVVLHkiKSAKKSIDLELLslvpvIREDDKTTYwpDIYNALIRAAiNRGVKVRLLVgswkkNDVYSMASVKSLQALC 295

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 134 SHPHIEIRLFnpvatrefkkigtvlefsrvnrRMHN--KAMIADNQAAIIGGRNIGDEYFGASSMLEFGdldvVVHGRVV 211
Cdd:PHA03003 296 VGNDLSVKVF----------------------RIPNntKLLIVDDEFAHITSANFDGTHYLHHAFVSFN----TIDKELV 349

                        170
                 ....*....|....*....
gi 736049347 212 NDISTEFDTFWNSPYAYSV 230
Cdd:PHA03003 350 KELSAIFERDWTSSYSKPL 368
PLDc_unchar6 cd09176
Putative catalytic domain of uncharacterized hypothetical proteins with one or two copies of ...
 310-439 7.24e-07

Putative catalytic domain of uncharacterized hypothetical proteins with one or two copies of the HKD motif; Putative catalytic domain of uncharacterized hypothetical proteins with similarity to phospholipase D (PLD, EC 3.1.4.4). 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 one or two copies of the HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the PLD superfamily.


Pssm-ID: 197273 [Multi-domain]  Cd Length: 114  Bit Score: 48.11  E-value: 7.24e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 310 QLRALALRPEHELLIVSPYLvpgaAMIERLRALTAR-GVRVTILTnSLASTDVAAVHAGYRryrrelveaGVRLYERRPS 388
Cdd:cd09176    2 GLGGLIREAAKRLLVISPFI----DLGNALKELAEAlPAKIRVLI-SRSEELAALGASDLE---------GFDLLLALDD 67

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 736049347 389 GDKSISKRliigssrasLHAKTYVFDRKS---VFIGSMNL-DPRSLRLNTEIGVY 439
Cdd:cd09176   68 AEILVLRG---------LHAKLYIAETGDgthVIIGSANAtEAAAAGNNVEFGVL 113
PLDc_vPLD4_2 cd09148
Putative catalytic domain, repeat 2, of vertebrate phospholipase PLD4; Putative catalytic ...
 99-227 1.44e-06

Putative catalytic domain, repeat 2, of vertebrate phospholipase PLD4; Putative catalytic domain, repeat 2, of vertebrate phospholipases D4 (PLD4, EC 3.1.4.4), homologs of the vaccinia virus protein K4 which is encoded by the HindIII K4L gene. Due to the presence of two copies of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue), PLD4 has been assigned to PLD superfamily although no catalytic activity has been detected to date. Unlike PLD1 and PLD2, PLD4 does not contain Phox (PX) and Pleckstrin homology (PH) domains but has a putative transmembrane domain. Like other vertebrate homologs of protein K4, PLD4 might be associated with Golgi membranes and alter their lipid content by selectively hydrolyze phosphatidylcholine (PC) into corresponding phosphatidic acid, which is thought to be involved in the regulation of lipid movement.


Pssm-ID: 197246  Cd Length: 187  Bit Score: 48.69  E-value: 1.44e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347  99 LADAIIRAA-DRGVRVRVLLDdLGTNADD------RKLLEISSHPH---IEIRLF-NPVATRefkkigTVLEFSRVNrrm 167
Cdd:cd09148   55 LDNALRAAAfDRRVLIRLLIS-CGRHSDPdmfpflRSLNALSNPPLsisVHVKLFiVPVGNQ------TNIPYSRVN--- 124

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 736049347 168 HNKAMIADnQAAIIGGRNIGDEYFGASSMLEFGDLDVVVHGR----VVNDISTEFDTFWNSPYA 227
Cdd:cd09148  125 HNKFMVTD-KAAYIGTSNWSEDYFLNTAGVGLVILQSPGANEemlpVQEQLRSLFERDWSSPYA 187
PLDc_EcCLS_like_1 cd09152
Catalytic domain, repeat 1, of Escherichia coli cardiolipin synthase and similar proteins; ...
 332-431 1.93e-06

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: 47.97  E-value: 1.93e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 332 GAAMIERLRALTARGVRVTILTNSLASTDVaavhaGYRRYRRELVEAGVRLYERRPSGdksiskRLIIGSSRASL--HAK 409
Cdd:cd09152   41 GDRVAEALERAAKRGVTCRLLLDAVGSRAF-----FRSSLWKRLREAGVEVVEALPLR------LFRRRLARFDLrnHRK 109

                         90       100
                 ....*....|....*....|...
gi 736049347 410 TYVFDRKSVFIGSMNL-DPRSLR 431
Cdd:cd09152  110 IAVIDGRIAYTGSQNIiDPEFFK 132
PLDc_N_DEXD_b1 cd09203
N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family ...
 336-425 8.27e-06

N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain; N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain. All members of this subfamily are uncharacterized. Other characterized members of the superfamily that have a related domain architecture ( containing a DEAD/DEAH box helicase domain), include the DNA/RNA helicase superfamily II (SF2) and Res-subunit of type III restriction endonucleases. In addition to the helicase-like region, members of this subfamily also contain one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) in the N-terminal putative catalytic domain. The HKD motif characterizes the phospholipase D (PLD, EC 3.1.4.4) superfamily.


Pssm-ID: 197297 [Multi-domain]  Cd Length: 143  Bit Score: 45.69  E-value: 8.27e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 336 IERLRALTARGVRVTILTNS-LASTDVAAVHAgyrryRRELVEAGVRL-YERRpsgdksiskrliigssRASLHAKTYVF 413
Cdd:cd09203   33 LDALKEFTDRGIPLRVITTTyMGATDAKALEA-----LAELPGTEVKVsYDTR----------------RTRLHAKAYLF 91

                         90
                 ....*....|....*.
gi 736049347 414 DRKS----VFIGSMNL 425
Cdd:cd09203   92 HRNTgfstAYIGSSNL 107
PLDc_Bfil_DEXD_like cd09117
Catalytic domain of type II restriction endonucleases BfiI and NgoFVII, and uncharacterized ...
 321-440 1.14e-05

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: 44.69  E-value: 1.14e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 321 ELLIVSPYLVPGAAmIERLRALTARGvRVTILTNSLASTDVAAVHAGYRRYRRELVEagVRLYERRPSgdksiskrliig 400
Cdd:cd09117   16 TIRIAVAFASAGGA-IKLLDKFREGK-KIRLIVGLDFGGTSPADFALKLLLALGNLN--VRIFDAGPL------------ 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 736049347 401 ssrasLHAKTYVF---DRKSVFIGSMNLDPRSLRLNTEIGVYC 440
Cdd:cd09117   80 -----LHAKLYLFendDPTRAIVGSANLTQGGLSGNIEAAVVI 117
PLDc_unchar3 cd09131
Putative catalytic domain of uncharacterized phospholipase D-like proteins; Putative catalytic ...
 339-451 1.47e-05

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


Pssm-ID: 197229 [Multi-domain]  Cd Length: 143  Bit Score: 45.02  E-value: 1.47e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 339 LRALTA---RGVRVT-ILTNSLASTDVAAVH-AGYRRYRRELVEagVRLyerrpsgdksiskrliiGSSRASLHAKTYVF 413
Cdd:cd09131   40 LEALIDahkRGVDVKvVLEDSIDDDEVTEENdNTYRYLKDNGVE--VRF-----------------DSPSVTTHTKLVVI 100

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 736049347 414 DRKSVFIGSMNLDPRSLRLNTEIGVYCESPALAAQVAA 451
Cdd:cd09131  101 DGRTVYVGSHNWTYSALDYNHEASVLIESPEVADFAIN 138
PLDc_vPLD6_like cd09171
Catalytic domain of vertebrate phospholipase D6 and similar proteins; Catalytic domain of ...
 53-185 1.78e-05

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: 44.52  E-value: 1.78e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347  53 HPGQDAFHLLsdpvdaldARVLLAdrADRSLDL-QYYIWHDDLtghalADAIIRAADRGVRVRVLLDDlgTNADDRKlle 131
Cdd:cd09171    4 FPGETSLSKL--------LRYLLS--ARKSLDVcVFTITCDDL-----ADAILDLHRRGVRVRIITDD--DQMEDKG--- 63

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 736049347 132 isshphIEIRLfnpvatreFKKIGTVLEFSRVNRRMHNKAMIADNQAAIIGGRN 185
Cdd:cd09171   64 ------SDIGK--------LRKAGIPVRTDLSSGHMHHKFAVIDGKILITGSFN 103
PLDc_vPLD3_4_5_like_1 cd09106
Putative catalytic domain, repeat 1, of vertebrate phospholipases, PLD3, PLD4 and PLD5, viral ...
 59-185 1.86e-05

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: 44.93  E-value: 1.86e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347  59 FHLLSDPVDALDARVLLADRADRSLDLQYYIW---HDDLT-------GHALADAIIRAADRGVRVRVLLDDLGTNADDRK 128
Cdd:cd09106   11 FLSSSSHLSTFEAWMELISSAKKSIDIASFYWnlrGTDTNpdssaqeGEDIFNALLEAAKRGVKIRILQDKPSKDKPDED 90

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 736049347 129 LLEISSHPHIEIRlfnpvatrefkkigtVLEFSRVNR--RMHNKAMIADNQAAIIGGRN 185
Cdd:cd09106   91 DLELAALGGAEVR---------------SLDFTKLIGggVLHTKFWIVDGKHFYLGSAN 134
PLDc_Nuc_like_unchar2 cd09174
Putative catalytic domain of uncharacterized hypothetical proteins closely related to Nuc, , ...
 94-186 2.00e-05

Putative catalytic domain of uncharacterized hypothetical proteins closely related to Nuc, , an endonuclease from Salmonella typhimurium; Putative catalytic domain 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: 197271 [Multi-domain]  Cd Length: 136  Bit Score: 44.23  E-value: 2.00e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347  94 LTGHALADAIIRAADRGVRVRVLLDDLGTNADDRKLLEISSHPHIEIRLFNpvatrefkkigtvlefSRVNRRMHNKAMI 173
Cdd:cd09174   30 FTNKDIFNALKNKKKEGVNIQIIINDDDINKKDVLILDEDSFEIYKLPGNG----------------SRYGNLMHNKFCV 93

                         90
                 ....*....|...
gi 736049347 174 ADNQAAIIGGRNI 186
Cdd:cd09174   94 IDFKTVITGSYNW 106
PLDc_Nuc_like cd09116
Catalytic domain of EDTA-resistant nuclease Nuc, vertebrate phospholipase D6, and similar ...
 336-448 2.01e-05

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: 44.21  E-value: 2.01e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 336 IERLRALTARGVRVTILTNSlastdvaavhaGYRRYRRELVEAGVrlyerrpsgDKSISKRLIIGSSRASLHAKTYVFDR 415
Cdd:cd09116   38 AEALKRAAKRGVRVRIILDK-----------DSLADNLSITLLAL---------LSNLGIPVRTDSGSKLMHHKFIIIDG 97

                         90       100       110
                 ....*....|....*....|....*....|...
gi 736049347 416 KSVFIGSMNLDPRSLRLNTEIGVYCESPALAAQ 448
Cdd:cd09116   98 KIVITGSANWTKSGFHRNDENLLIIDDPKLAAS 130
PLDc smart00155
Phospholipase D. Active site motifs; Phosphatidylcholine-hydrolyzing phospholipase D (PLD) ...
 406-429 2.28e-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: 41.22  E-value: 2.28e-05
                           10        20
                   ....*....|....*....|....
gi 736049347   406 LHAKTYVFDRKSVFIGSMNLDPRS 429
Cdd:smart00155   5 LHTKLMIVDDEIAYIGSANLDGRS 28
PLDc_Nuc_like_unchar1_1 cd09172
Putative catalytic domain, repeat 1, of uncharacterized hypothetical proteins similar to Nuc, ...
 305-447 2.32e-05

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: 44.27  E-value: 2.32e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 305 GHLLPQLRALALRPEHELLIVSpYLVPGAAMIERLRALTARGVRVTILtnslasTDVAAVHAGYRRYRRELveagvrlye 384
Cdd:cd09172    8 REALLAFLDEARSAGSSIRLAI-YELDDPEIIDALKAAKDRGVRVRII------LDDSSVTGDPTEESAAA--------- 71

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 736049347 385 RRPSGDKSISKRliiGSSRASLHAKTYVFDRK----SVFIGSMNLDPRSLRLNTEIGVYCESPALAA 447
Cdd:cd09172   72 TLSKGPGALVKR---RHSSGLMHNKFLVVDRKdgpnRVLTGSTNFTTSGLYGQSNNVLIFRNPAFAA 135
PLDc_C_DEXD_like cd09126
C-terminal putative phospholipase D-like domain of uncharacterized prokaryotic HKD family ...
 320-425 4.83e-05

C-terminal putative phospholipase D-like domain of uncharacterized prokaryotic HKD family nucleases fused to DEAD/DEAH box helicases; C-terminal putative phospholipase D (PLD)-like domain of uncharacterized prokaryotic HKD family nucleases fused to a DEAD/DEAH box helicase domain. All members of this subfamily are uncharacterized. In addition to the helicase-like region, members of this family also contain a PLD-like domain in the C-terminal region, which is characterized by a variant HKD (H-x-K-x(4)-D motif, where x represents any amino acid residue) motif. Due to the lack of key residues related to PLD activity in the variant HKD motif, members of this subfamily are most unlikely to carry PLD activity.


Pssm-ID: 197224 [Multi-domain]  Cd Length: 126  Bit Score: 43.01  E-value: 4.83e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 320 HELLIVSPYLVPG--AAMIERLRALTARGVRVTILTNSlastdvaavHAGYRRYRRELVEAGVRLyerrpsgdksiskrl 397
Cdd:cd09126   22 KSIIISSPYVSQKriTKLINLLKEAQERGVEVTVVTRE---------PKEYKELIEELRSAGVKV--------------- 77

                         90       100
                 ....*....|....*....|....*...
gi 736049347 398 iigSSRASLHAKTYVFDRKSVFIGSMNL 425
Cdd:cd09126   78 ---KLKEEIHEKFAIIDKKIVWYGSINL 102
YrhO COG1378
Sugar-specific transcriptional regulator TrmB [Transcription];
47-192 5.68e-05

Sugar-specific transcriptional regulator TrmB [Transcription];


Pssm-ID: 440988 [Multi-domain]  Cd Length: 238  Bit Score: 44.63  E-value: 5.68e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347  47 RAQAAAHPGQDAFHLLSDPvDALDARVL-LADRADRSLDLqyYIWHDDLTGHALADAIIRAADRGVRVRVLLDDlgtnaD 125
Cdd:COG1378   97 LYEELREPEEELVWVVKGR-EAILERLReLIASAEEEILI--VLSPPELLLEELEEALEEALERGVKVRVLVSP-----E 168

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 736049347 126 DRKLLEISSHPHIEIrlfnpvatrefkkigtvlefsRVNRRMHNKAMIADNQAAIIGGRNIGDEYFG 192
Cdd:COG1378  169 VLEVPERLEEEGEEV---------------------RVLPGLPGRLLIVDDKEALISVSEPDGEETA 214
PLDc_vPLD1_2_like_2 cd09105
Catalytic domain, repeat 2, of vertebrate phospholipases, PLD1 and PLD2, and similar proteins; ...
 334-438 6.23e-05

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: 43.06  E-value: 6.23e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 334 AMIERLRAltARGVRVTILTNSLASTDVAAVHAGYRRYRRELVEAgvrlyERRPSGDKSIS---KRLIIGSSRASL---H 407
Cdd:cd09105   39 ALAEALKA--NPGLRVVLVLPALPDAVAFGADDGLDALALLALLL-----LADAAPDRVAVfslATHRRGLLGGPPiyvH 111

                         90       100       110
                 ....*....|....*....|....*....|.
gi 736049347 408 AKTYVFDRKSVFIGSMNLDPRSLRLNTEIGV 438
Cdd:cd09105  112 SKVVIVDDEWATVGSANLNRRSMTWDTELNL 142
PLDc_vPLD4_1 cd09145
Putative catalytic domain, repeat 1, of vertebrate phospholipase PLD4; Putative catalytic ...
 331-438 1.45e-04

Putative catalytic domain, repeat 1, of vertebrate phospholipase PLD4; Putative catalytic domain, repeat 1, of vertebrate phospholipases D4 (PLD4, EC 3.1.4.4), homologs of the vaccinia virus protein K4 which is encoded by the HindIII K4L gene. Due to the presence of two copies of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue), PLD4 has been assigned to PLD superfamily although no catalytic activity has been detected to date. Unlike PLD1 and PLD2, PLD4 does not contain Phox (PX) and Pleckstrin homology (PH) domains but has a putative transmembrane domain. Like other vertebrate homologs of protein K4, PLD4 might be associated with Golgi membranes and alter their lipid content by selectively hydrolyze phosphatidylcholine (PC) into corresponding phosphatidic acid, which is thought to be involved in the regulation of lipid movement.


Pssm-ID: 197243 [Multi-domain]  Cd Length: 170  Bit Score: 42.59  E-value: 1.45e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 331 PGAAMIERLRALTARGVRVTILTNS----LASTDVaavhagyrryrrelveagvRLYERRPSGDKSIS-KRLiigsSRAS 405
Cdd:cd09145   59 PGEDILKELAELLSRNVSVRAAASIptlaANSTDL-------------------KILRQKGAHVRKVNfGRL----TGGV 115

                         90       100       110
                 ....*....|....*....|....*....|...
gi 736049347 406 LHAKTYVFDRKSVFIGSMNLDPRSLRLNTEIGV 438
Cdd:cd09145  116 LHSKFWIIDKKHIYVGSANMDWRSLTQVKELGA 148
PLDc_Nuc_like_unchar1_1 cd09172
Putative catalytic domain, repeat 1, of uncharacterized hypothetical proteins similar to Nuc, ...
 68-223 2.53e-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: 2.53e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347  68 ALDARVLLADRADRSlDLQYYIWHDDLTGHALADAIIRAADRGVRVRVLLDDLGTNADDRKLLEISSHPHIEIRLfnpVA 147
Cdd:cd09172    7 LREALLAFLDEARSA-GSSIRLAIYELDDPEIIDALKAAKDRGVRVRIILDDSSVTGDPTEESAAATLSKGPGAL---VK 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 148 TREFKKIgtvlefsrvnrrMHNKAMIADN----QAAIIGGRNigdeyFGASSMleFGDLDvVVHGRVVNDISTEFDTFWN 223
Cdd:cd09172   83 RRHSSGL------------MHNKFLVVDRkdgpNRVLTGSTN-----FTTSGL--YGQSN-NVLIFRNPAFAAAYLAYWN 142
COG3886 COG3886
HKD family nuclease [Replication, recombination and repair];
336-425 2.64e-04

HKD family nuclease [Replication, recombination and repair];


Pssm-ID: 443094 [Multi-domain]  Cd Length: 941  Bit Score: 43.82  E-value: 2.64e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 336 IERLRALTARGVRVTILTNS-LASTDVAAVhagyrRYRRELVEAGVRLYERRpsgdksiskrliigssRASLHAKTYVFD 414
Cdd:COG3886   61 LDALKELLERGVKGRILTSTyLGFTEPKAL-----RELLDLPNIEVRVSYDR----------------KTRFHAKAYIFE 119

                         90
                 ....*....|....
gi 736049347 415 RK---SVFIGSMNL 425
Cdd:COG3886  120 RTgygTAIIGSSNL 133
PLDc smart00155
Phospholipase D. Active site motifs; Phosphatidylcholine-hydrolyzing phospholipase D (PLD) ...
 163-190 3.91e-04

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


Pssm-ID: 197546 [Multi-domain]  Cd Length: 28  Bit Score: 37.75  E-value: 3.91e-04
                           10        20
                   ....*....|....*....|....*...
gi 736049347   163 VNRRMHNKAMIADNQAAIIGGRNIGDEY 190
Cdd:smart00155   1 YDGVLHTKLMIVDDEIAYIGSANLDGRS 28
PLDc_CLS_unchar1_1 cd09156
Putative catalytic domain, repeat 1, of uncharacterized proteins similar to bacterial ...
 332-426 5.22e-04

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: 40.71  E-value: 5.22e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 332 GAAMIERLRALTARGVRVTILTNSLAStdvaavHAGYRRYRRELVEAGVRLYERRPSGDKSiskrliiGSSRASL--HAK 409
Cdd:cd09156   34 GRRVIDALARKAREGVEVRLLLDALGS------FFLSRRALKKLRAAGGKVAFFMPVFRLP-------FRGRTNLrnHRK 100

                         90
                 ....*....|....*..
gi 736049347 410 TYVFDRKSVFIGSMNLD 426
Cdd:cd09156  101 IAIADGSTAISGGMNLA 117
PHA03003 PHA03003
palmytilated EEV membrane glycoprotein; Provisional
 332-458 5.43e-04

palmytilated EEV membrane glycoprotein; Provisional


Pssm-ID: 177506 [Multi-domain]  Cd Length: 369  Bit Score: 42.34  E-value: 5.43e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 332 GAAMIERLRALTARGVRVTILtnslasTDVAAVHAGYrryrRELVEAGVRLYERRpsgdksISKRLIIGSSRASLhaktY 411
Cdd:PHA03003  62 GRLILDKLKEAAESGVKVTIL------VDEQSGDKDE----EELQSSNINYIKVD------IGKLNNVGVLLGSF----W 121

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 736049347 412 VFDRKSVFIGSMNLDPRSLRLNTEIGVYCESPALaaqvAADLEPRLD 458
Cdd:PHA03003 122 VSDDRRCYIGNASLTGGSISTIKTLGVYSTYPPL----ATDLRRRFD 164
PLDc_N_DEXD_b cd09180
N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family ...
 306-439 9.52e-04

N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain; N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain. All members of this subfamily are uncharacterized. Other characterized members of the superfamily that have a related domain architecture ( containing a DEAD/DEAH box helicase domain), include the DNA/RNA helicase superfamily II (SF2) and Res-subunit of type III restriction endonucleases. In addition to the helicase-like region, members of this subfamily also contain one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) in the N-terminal putative catalytic domain. The HKD motif characterizes the phospholipase D (PLD, EC 3.1.4.4) superfamily. A few family members contain additional domains, like a C-terminal peptidase S24-like domain.


Pssm-ID: 197277 [Multi-domain]  Cd Length: 142  Bit Score: 39.63  E-value: 9.52e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 306 HLLPQLRALALRPEHELLIVSPYLVPGAAMIER-LRALTARGVRVTILTnslaSTDVAAVHAGYRRYRRELVEAGVRLYE 384
Cdd:cd09180    2 KLLSELKNEMETADSVDFIVSFISESGIQLLIPeLEELINKGVPIRIIT----STYLGITEPKALRELADYDNVEVKIYN 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 736049347 385 RRPsgdksiskrliigssRASLHAKTYVFDRK----SVFIGSMNLDPRSLRLNTEIGVY 439
Cdd:cd09180   78 NIK---------------SESFHAKAYLFEREtgysSAIIGSSNLSQSALTTGIEWNVR 121
PLDc_unchar2_2 cd09130
Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins; ...
 101-223 1.52e-03

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


Pssm-ID: 197228 [Multi-domain]  Cd Length: 157  Bit Score: 39.15  E-value: 1.52e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 101 DAIIRAADRGVRVRVLLdDLGTNADDRK---------LLEI--SSHPHIEIRLFNpvatrefkkigTVLEfsrvnrRMHN 169
Cdd:cd09130   37 KALIDAANRGVDVRLIL-DPNKDAFGREkngipnrpvAAELmkKTKGKIQIRWYN-----------TGGE------QFHT 98

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 736049347 170 KAMIADN--QAAIIGG------RNIGDeYFGASSMLEFGDLDvvvhGRVVNDISTEFDTFWN 223
Cdd:cd09130   99 KLLLIKKkgQAIIIGGsanftrRNLRD-YNLETDLKILAPND----SPVSKDVDAYFDRLWN 155
PLDc pfam00614
Phospholipase D Active site motif; Phosphatidylcholine-hydrolysing phospholipase D (PLD) ...
 405-429 1.76e-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: 35.86  E-value: 1.76e-03
                          10        20
                  ....*....|....*....|....*
gi 736049347  405 SLHAKTYVFDRKSVFIGSMNLDPRS 429
Cdd:pfam00614   4 RLHRKIVVVDDELAYIGGANLDGRS 28
PLDc_yjhR_C_like cd09118
C-terminal domain of Escherichia coli uncharacterized protein yjhR and similar proteins; ...
 310-424 1.77e-03

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


Pssm-ID: 197217 [Multi-domain]  Cd Length: 144  Bit Score: 38.83  E-value: 1.77e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 310 QLRALALRPEHELLIVSPYL----VPGAAMIERLRALTARGVRVTILTNS-LASTDVAAVHAGYRRYRRELVEAGVRLYE 384
Cdd:cd09118    5 FLLKALATVRERIVIVSPWIsldaLEADGLLEAIREAVSRGVDVTIYTDPhLNTGDANDTKANLEDAAEALAEAGIRIHE 84

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 736049347 385 RRpsgdksiskrliigssraSLHAKTYVFDRKSVFIGSMN 424
Cdd:cd09118   85 VN------------------GVHSKIVIVDNHLLAVGSFN 106
COG3218 COG3218
ABC-type uncharacterized transport system, auxiliary component [General function prediction ...
 1-151 2.39e-03

ABC-type uncharacterized transport system, auxiliary component [General function prediction only];


Pssm-ID: 442451  Cd Length: 202  Bit Score: 39.21  E-value: 2.39e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347   1 MTMLRSWGAILSLLMLAACASLPPqvdRTPTHAYtdtgntRLGVAFRAQAAAHPGQDAfhLLSDPVDALDA----RVLLA 76
Cdd:COG3218    4 RRLLRLLLLLLLALLLAGCSSLPA---PPPPTLY------DLTPPLPAAAAAGPLPAQ--LLVAEPTAPGAldsdRIVVR 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347  77 DRADRSLDLQYYIWHDDLTgHALADAIIRA-ADRGVRVRVLLDDLGTNADDRKLLEI--------SSHPHIEIRLF---- 143
Cdd:COG3218   73 PDPGQLQYYAGARWADPPP-RLLQDLLVEAlEASGRFRAVGRPGSGLAADYRLEGELrdfeqdfdGGAPRAVVELRarlv 151

                        170
                 ....*....|...
gi 736049347 144 -----NPVATREF 151
Cdd:COG3218  152 ddrdgRVVASRRF 164
PLDc_CLS_1 cd09110
Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Catalytic ...
 333-425 2.55e-03

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: 38.61  E-value: 2.55e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 333 AAMIERLRaltaRGVRVTILTNSLAStdvaavHAGYRRYRRELVEAGVRLYERRPsgdksISKRLIIGSSRASLHAKTYV 412
Cdd:cd09110   39 DALIEKAR----RGVEVRLLYDGFGS------LGLSRRFLRELREAGVEVRAFNP-----LSFPLFLLRLNYRNHRKILV 103

                         90
                 ....*....|...
gi 736049347 413 FDRKSVFIGSMNL 425
Cdd:cd09110  104 IDGKIAFVGGFNI 116
PLDc_unchar5 cd09133
Putative catalytic domain of uncharacterized hypothetical proteins with one or two copies of ...
 321-424 6.09e-03

Putative catalytic domain of uncharacterized hypothetical proteins with one or two copies of the HKD motif; Putative catalytic domain of uncharacterized hypothetical proteins with similarity to phospholipase D (PLD, EC 3.1.4.4). 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 one or two copies of the HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the PLD superfamily.


Pssm-ID: 197231 [Multi-domain]  Cd Length: 127  Bit Score: 36.92  E-value: 6.09e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347 321 ELLIVSPYLVP--GAAMIERLRALTARGVRVTIL--TNSLASTDVAAVHAGYRRYRRELVEAGVRLYERRPSGdksiskr 396
Cdd:cd09133   16 RVIIHSPWLGNavFENLLEALEKAAERGVKIDILwgISSDEEKEKKALSEIAEKLLADRGLRGGVNVHLRTTG------- 88

                         90       100
                 ....*....|....*....|....*...
gi 736049347 397 liigssrasLHAKTYVFDRKSVFIGSMN 424
Cdd:cd09133   89 ---------SHAKFLVCDDWFALVGSCN 107
PLDc_Nuc_like_unchar1_2 cd09173
Putative catalytic domain, repeat 2, of uncharacterized hypothetical proteins similar to Nuc, ...
 93-176 7.57e-03

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: 37.33  E-value: 7.57e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347  93 DLTGHALADAIIRAADRGVRVRVLLDDLGT---NADDRKLLEISSHPHIEIRLFNPVATREfkkigtvLEFSRVNRRMHN 169
Cdd:cd09173   31 DFSDGALLDALLAAADAGLFVRGLVDKRFGgryYSAAADMGGIDPVYPAALAPDEPEKFVG-------EPLLGVGDKLHH 103


                 ....*..
gi 736049347 170 KAMIADN 176
Cdd:cd09173  104 KFMVIDP 110
PLDc_PGS1_euk_1 cd09135
Catalytic domain, repeat 1, of eukaryotic PhosphatidylGlycerophosphate Synthases; Catalytic ...
 97-191 9.82e-03

Catalytic domain, repeat 1, of eukaryotic PhosphatidylGlycerophosphate Synthases; Catalytic domain, repeat 1, of eukaryotic phosphatidylglycerophosphate (PGP) synthases, also called CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase (EC 2.7.8.5). Eukaryotic PGP synthases are different and unrelated to prokaryotic PGP synthases and yeast phosphatidylserine synthase. They catalyze the synthesis of PGP from CDP-diacylglycerol and sn-glycerol 3-phosphate, the committed and rate-limiting step in the biosynthesis of cardiolipin (CL), which is an essential component of many mitochondrial functions in eukaryotes. Members in this subfamily all have two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. They may utilize a common two-step ping-pong catalytic mechanism involving a substrate-enzyme intermediate to cleave phosphodiester bonds. The two motifs are suggested to constitute the active site involved in the phosphatidyl group transfer.


Pssm-ID: 197233 [Multi-domain]  Cd Length: 170  Bit Score: 37.14  E-value: 9.82e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736049347  97 HALADAIIRAADR--GVRVRVLLDDL-GT--NADDRKLLEISSHPH-----IEIRLFNPVATREFKKigtVLEFSRVNRR 166
Cdd:cd09135   40 QELVDALQEALERnpNLKVSILLDYLrGTrgEPNSRTASLLLPLLKlfpdrVRVSLYHTPNLRGLLK---KLLPERFNEI 116

                         90       100
                 ....*....|....*....|....*...
gi 736049347 167 ---MHNKAMIADNqAAIIGGRNIGDEYF 191
Cdd:cd09135  117 iglQHMKLYIFDD-DVILSGANLSDDYF 143
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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