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Conserved domains on  [gi|446001333|ref|WP_000079188|]
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MULTISPECIES: phospholipase D family protein [Acinetobacter]

Protein Classification

phospholipase D family protein( domain architecture ID 10173503)

phospholipase D (PLD) family protein similar to Escherichia coli cardiolipin synthase C that catalyzes the synthesis of cardiolipin from phosphatidylglycerol and phosphatidylethanolamine

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 ...
 310-537 3.56e-90

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: 275.64  E-value: 3.56e-90
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 310 VKDSPDKIRSKAKKEEHLNFQLINHLEKPESNVDLISAYFIPEKQGAKILSTLAKEGVEVRVLTNSFKANDVAVVHAFYG 389
Cdd:cd09113    1 LSDPPEKALKEAGPEPVLAYQLAELLKNAKREVLIVSPYFVPGDEGVALLAELARRGVRVRILTNSLAATDVPAVHSGYA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 390 KYRKELLKNGVQLYEFLPTPDKRDLnkntdelatkaKVNMKGLSRSSLHTKLMALD-EQVFIGSFNFDPRSAYLNTEIGV 468
Cdd:cd09113   81 RYRKRLLKAGVELYELKPDAAKRKR-----------LRGLFGSSRASLHAKSFVIDdRLVFVGSFNLDPRSAYLNTEMGL 149

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446001333 469 ILDSPSLAKTIHHTMDENLNKYAYKLKLDPNNHIYWQQETPKGPVIYKKEPEMKWWQKAGMKLLSWLPL 537
Cdd:cd09113  150 VIDSPELAAQLRAAMEEDLAPSAYWVLLLDDGGLVWETEEDGKEKEYDSEPETSFWRRLGAWLLSLLPI 218
PLDc_ymdC_like_1 cd09111
Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and ...
 82-243 8.53e-89

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: 270.17  E-value: 8.53e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333  82 LNDPLEALAARLRLIDKAEKTLDLQYYIWDNDKVGALALHAIIRAADRGVKVRLLIDDNNAKKMEGVLLALSQHKNIEVK 161
Cdd:cd09111    1 LEDGLDALAARLALIRSAERSIDLQYYIWHDDESGRLLLGELLEAADRGVRVRLLLDDLGTSGRDRLLAALDAHPNIEVR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 162 LFNPYRFRKYRAMDMILDLKRINRRMHNKSFIADNQVALIGGRNMTNQYYNVSDSYQFSDVDVMLVGAAVDDIVNSFDDY 241
Cdd:cd09111   81 LFNPFRNRGGRLLEFLTDFSRLNRRMHNKLFIVDGAVAIVGGRNIGDEYFGASPEVNFRDLDVLAVGPVVRQLSESFDTY 160


                 ..
gi 446001333 242 WN 243
Cdd:cd09111  161 WN 162
 
Name Accession Description Interval E-value
PLDc_ymdC_like_2 cd09113
Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and ...
 310-537 3.56e-90

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: 275.64  E-value: 3.56e-90
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 310 VKDSPDKIRSKAKKEEHLNFQLINHLEKPESNVDLISAYFIPEKQGAKILSTLAKEGVEVRVLTNSFKANDVAVVHAFYG 389
Cdd:cd09113    1 LSDPPEKALKEAGPEPVLAYQLAELLKNAKREVLIVSPYFVPGDEGVALLAELARRGVRVRILTNSLAATDVPAVHSGYA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 390 KYRKELLKNGVQLYEFLPTPDKRDLnkntdelatkaKVNMKGLSRSSLHTKLMALD-EQVFIGSFNFDPRSAYLNTEIGV 468
Cdd:cd09113   81 RYRKRLLKAGVELYELKPDAAKRKR-----------LRGLFGSSRASLHAKSFVIDdRLVFVGSFNLDPRSAYLNTEMGL 149

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446001333 469 ILDSPSLAKTIHHTMDENLNKYAYKLKLDPNNHIYWQQETPKGPVIYKKEPEMKWWQKAGMKLLSWLPL 537
Cdd:cd09113  150 VIDSPELAAQLRAAMEEDLAPSAYWVLLLDDGGLVWETEEDGKEKEYDSEPETSFWRRLGAWLLSLLPI 218
PLDc_ymdC_like_1 cd09111
Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and ...
 82-243 8.53e-89

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: 270.17  E-value: 8.53e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333  82 LNDPLEALAARLRLIDKAEKTLDLQYYIWDNDKVGALALHAIIRAADRGVKVRLLIDDNNAKKMEGVLLALSQHKNIEVK 161
Cdd:cd09111    1 LEDGLDALAARLALIRSAERSIDLQYYIWHDDESGRLLLGELLEAADRGVRVRLLLDDLGTSGRDRLLAALDAHPNIEVR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 162 LFNPYRFRKYRAMDMILDLKRINRRMHNKSFIADNQVALIGGRNMTNQYYNVSDSYQFSDVDVMLVGAAVDDIVNSFDDY 241
Cdd:cd09111   81 LFNPFRNRGGRLLEFLTDFSRLNRRMHNKLFIVDGAVAIVGGRNIGDEYFGASPEVNFRDLDVLAVGPVVRQLSESFDTY 160


                 ..
gi 446001333 242 WN 243
Cdd:cd09111  161 WN 162
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 67-505 2.08e-86

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: 271.43  E-value: 2.08e-86
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333  67 TPLREKNPNLTG--YHLLNDPLEALAARLRLIDKAEKTLDLQYYIWDNDKVGALALHAIIRAADRGVKVRLLIDDNNAKK 144
Cdd:COG1502    3 APLAAGLPLVGGnrVTLLVDGDEAFAALLEAIEAARRSIDLEYYIFDDDEVGRRLADALIAAARRGVKVRVLLDGIGSRA 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 145 MEGVLLALSQHKNIEVKLFNPYRFRkyramdmildLKRINRRMHNKSFIADNQVALIGGRNMTNQYYNVSDSY-QFSDVD 223
Cdd:COG1502   83 LNRDFLRRLRAAGVEVRLFNPVRLL----------FRRLNGRNHRKIVVIDGRVAFVGGANITDEYLGRDPGFgPWRDTH 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 224 VMLVGAAVDDIVNSFDDYWNHEyaysvqsivsaqqhrlryeslKQQLDAHYQQAtvqnfldltsrshafdkwldrnikfD 303
Cdd:COG1502  153 VRIEGPAVADLQAVFAEDWNFA---------------------TGEALPFPEPA-------------------------G 186

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 304 WVKAEVVKDSPDkirskaKKEEHLNFQLINHLEKPESNVDLISAYFIPEKQGAKILSTLAKEGVEVRVLTNSfkANDVAV 383
Cdd:COG1502  187 DVRVQVVPSGPD------SPRETIERALLAAIASARRRIYIETPYFVPDRSLLRALIAAARRGVDVRILLPA--KSDHPL 258

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 384 VHAFYGKYRKELLKNGVQLYEFLPtpdkrdlnkntdelatkakvnmkglsrSSLHTKLMALDEQ-VFIGSFNFDPRSAYL 462
Cdd:COG1502  259 VHWASRSYYEELLEAGVRIYEYEP---------------------------GFLHAKVMVVDDEwALVGSANLDPRSLRL 311

                        410       420       430       440
                 ....*....|....*....|....*....|....*....|...
gi 446001333 463 NTEIGVILDSPSLAKTIHHTMDENLNKyAYKLKLDPNNHIYWQ 505
Cdd:COG1502  312 NFEVNLVIYDPEFAAQLRARFEEDLAH-SREVTLEEWRKRPLR 353
cls PRK01642
cardiolipin synthetase; Reviewed
 80-477 4.62e-24

cardiolipin synthetase; Reviewed


Pssm-ID: 234967 [Multi-domain]  Cd Length: 483  Bit Score: 105.25  E-value: 4.62e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333  80 HLLNDPLEALAARLRLIDKAEKTLDLQYYIWDNDKVGALALHAIIRAADRGVKVRLLIDD---------NNAKKME--GV 148
Cdd:PRK01642 119 RLLTNGDETFQAIIRDIELARHYILMEFYIWRPDGLGDQVAEALIAAAKRGVRVRLLYDSigsfaffrsPYPEELRnaGV 198

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 149 LLALSQHKNievklfnpyRFRKYRamdmildlKRINRRMHNKSFIADNQVALIGGRNMTNQYYNVSDSY--QFSDVDVML 226
Cdd:PRK01642 199 EVVEFLKVN---------LGRVFR--------RRLDLRNHRKIVVIDGYIAYTGSMNVVDPEYFKQDPGvgQWRDTHVRI 261

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 227 VGAAVDD--IVNSFDDYWnheyaysvqsivsAQQHRLRYES--LKQQLDAHYQQATVQnfldltsrshafdkwldrnikf 302
Cdd:PRK01642 262 EGPVVTAlqLIFAEDWEW-------------ETGERILPPPpdVLIMPFEEASGHTVQ---------------------- 306

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 303 dwvkaeVVKDSPdkirskAKKEE---HLNFQLINHLEKpesNVDLISAYFIPEKQgakILSTL---AKEGVEVRVLTNSF 376
Cdd:PRK01642 307 ------VIASGP------GDPEEtihQFLLTAIYSARE---RLWITTPYFVPDED---LLAALktaALRGVDVRIIIPSK 368

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 377 kaNDVAVV----HAFYGkyrkELLKNGVQLYEFLPtpdkrdlnkntdelatkakvnmkGLsrssLHTKLMALDEQV-FIG 451
Cdd:PRK01642 369 --NDSLLVfwasRAFFT----ELLEAGVKIYRYEG-----------------------GL----LHTKSVLVDDELaLVG 415

                        410       420
                 ....*....|....*....|....*.
gi 446001333 452 SFNFDPRSAYLNTEIGVILDSPSLAK 477
Cdd:PRK01642 416 TVNLDMRSFWLNFEITLVIDDTGFAA 441
PLDc_2 pfam13091
PLD-like domain;
331-477 3.17e-21

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 89.66  E-value: 3.17e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333  331 LINHLEKPESNVDLISAYFIPEKQGAKILSTLAKEGVEVRVLTNSFKANDVAVVHAFYGKYRkELLKNGVQLYEFLPTPd 410
Cdd:pfam13091   1 LIDLINSAKKSIDIATYYFVPDREIIDALIAAAKRGVDVRIILDSNKDDAGGPKKASLKELR-SLLRAGVEIREYQSFL- 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446001333  411 krdlnkntdelatkakvnmkglsrSSLHTKLMALDEQ-VFIGSFNFDPRSAYLNTEIGVILDSPSLAK 477
Cdd:pfam13091  79 ------------------------RSMHAKFYIIDGKtVIVGSANLTRRALRLNLENNVVIKDPELAQ 122
PLDc_2 pfam13091
PLD-like domain;
93-209 4.35e-12

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 63.46  E-value: 4.35e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333   93 LRLIDKAEKTLDLQ-YYIWDNDKVgalaLHAIIRAADRGVKVRLLIDDNNA------KKMEGVLLALSQHKnIEVKLFNP 165
Cdd:pfam13091   2 IDLINSAKKSIDIAtYYFVPDREI----IDALIAAAKRGVDVRIILDSNKDdaggpkKASLKELRSLLRAG-VEIREYQS 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 446001333  166 YrfrkyramdmildlkriNRRMHNKSFIADNQVALIGGRNMTNQ 209
Cdd:pfam13091  77 F-----------------LRSMHAKFYIIDGKTVIVGSANLTRR 103
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 93-262 2.37e-09

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: 59.19  E-value: 2.37e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333  93 LRLIDKAEKTLDLQ--YYIWDNDkvgalALHAIIRAADRGVKVRLLIDDNNAKKMegVLLALSQH------KNIEVKLFN 164
Cdd:COG1502  209 LAAIASARRRIYIEtpYFVPDRS-----LLRALIAAARRGVDVRILLPAKSDHPL--VHWASRSYyeelleAGVRIYEYE 281

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 165 PyrfrkyramdmildlkrinRRMHNKSFIADNQVALIGGRNMTNQ--YYNvsdsyqfSDVDVMLVGAAV-DDIVNSFDDY 241
Cdd:COG1502  282 P-------------------GFLHAKVMVVDDEWALVGSANLDPRslRLN-------FEVNLVIYDPEFaAQLRARFEED 335

                        170       180
                 ....*....|....*....|.
gi 446001333 242 WNHEYAYSVQSIVSAQQHRLR 262
Cdd:COG1502  336 LAHSREVTLEEWRKRPLRRLR 356
PRK13912 PRK13912
nuclease NucT; Provisional
 79-207 2.31e-06

nuclease NucT; Provisional


Pssm-ID: 184389 [Multi-domain]  Cd Length: 177  Bit Score: 47.85  E-value: 2.31e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333  79 YHLLNDPLEALAARLRLIDKAEKTLDLQYYIWDNDKVGalalHAIIRAADRGVKVRLLID-DNNAKKMEGVLLALSQHKN 157
Cdd:PRK13912  25 YFLPYEQKDALNKLVSLISNARSSIKIAIYSFTHKDIA----KALKSAAKRGVKISIIYDyESNHNNDQSTIGYLDKYPN 100

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 446001333 158 IEVKLFNPYRFRKyramdmildlKRINRRMHNKSFIADNQVALIGGRNMT 207
Cdd:PRK13912 101 IKVCLLKGLKAKN----------GKYYGIMHQKVAIIDDKIVVLGSANWS 140
PLDc smart00155
Phospholipase D. Active site motifs; Phosphatidylcholine-hydrolyzing phospholipase D (PLD) ...
 437-459 2.07e-03

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: 35.83  E-value: 2.07e-03
                           10        20
                   ....*....|....*....|....
gi 446001333   437 LHTKLMALD-EQVFIGSFNFDPRS 459
Cdd:smart00155   5 LHTKLMIVDdEIAYIGSANLDGRS 28
 
Name Accession Description Interval E-value
PLDc_ymdC_like_2 cd09113
Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and ...
 310-537 3.56e-90

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: 275.64  E-value: 3.56e-90
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 310 VKDSPDKIRSKAKKEEHLNFQLINHLEKPESNVDLISAYFIPEKQGAKILSTLAKEGVEVRVLTNSFKANDVAVVHAFYG 389
Cdd:cd09113    1 LSDPPEKALKEAGPEPVLAYQLAELLKNAKREVLIVSPYFVPGDEGVALLAELARRGVRVRILTNSLAATDVPAVHSGYA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 390 KYRKELLKNGVQLYEFLPTPDKRDLnkntdelatkaKVNMKGLSRSSLHTKLMALD-EQVFIGSFNFDPRSAYLNTEIGV 468
Cdd:cd09113   81 RYRKRLLKAGVELYELKPDAAKRKR-----------LRGLFGSSRASLHAKSFVIDdRLVFVGSFNLDPRSAYLNTEMGL 149

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446001333 469 ILDSPSLAKTIHHTMDENLNKYAYKLKLDPNNHIYWQQETPKGPVIYKKEPEMKWWQKAGMKLLSWLPL 537
Cdd:cd09113  150 VIDSPELAAQLRAAMEEDLAPSAYWVLLLDDGGLVWETEEDGKEKEYDSEPETSFWRRLGAWLLSLLPI 218
PLDc_ymdC_like_1 cd09111
Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and ...
 82-243 8.53e-89

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: 270.17  E-value: 8.53e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333  82 LNDPLEALAARLRLIDKAEKTLDLQYYIWDNDKVGALALHAIIRAADRGVKVRLLIDDNNAKKMEGVLLALSQHKNIEVK 161
Cdd:cd09111    1 LEDGLDALAARLALIRSAERSIDLQYYIWHDDESGRLLLGELLEAADRGVRVRLLLDDLGTSGRDRLLAALDAHPNIEVR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 162 LFNPYRFRKYRAMDMILDLKRINRRMHNKSFIADNQVALIGGRNMTNQYYNVSDSYQFSDVDVMLVGAAVDDIVNSFDDY 241
Cdd:cd09111   81 LFNPFRNRGGRLLEFLTDFSRLNRRMHNKLFIVDGAVAIVGGRNIGDEYFGASPEVNFRDLDVLAVGPVVRQLSESFDTY 160


                 ..
gi 446001333 242 WN 243
Cdd:cd09111  161 WN 162
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 67-505 2.08e-86

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: 271.43  E-value: 2.08e-86
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333  67 TPLREKNPNLTG--YHLLNDPLEALAARLRLIDKAEKTLDLQYYIWDNDKVGALALHAIIRAADRGVKVRLLIDDNNAKK 144
Cdd:COG1502    3 APLAAGLPLVGGnrVTLLVDGDEAFAALLEAIEAARRSIDLEYYIFDDDEVGRRLADALIAAARRGVKVRVLLDGIGSRA 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 145 MEGVLLALSQHKNIEVKLFNPYRFRkyramdmildLKRINRRMHNKSFIADNQVALIGGRNMTNQYYNVSDSY-QFSDVD 223
Cdd:COG1502   83 LNRDFLRRLRAAGVEVRLFNPVRLL----------FRRLNGRNHRKIVVIDGRVAFVGGANITDEYLGRDPGFgPWRDTH 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 224 VMLVGAAVDDIVNSFDDYWNHEyaysvqsivsaqqhrlryeslKQQLDAHYQQAtvqnfldltsrshafdkwldrnikfD 303
Cdd:COG1502  153 VRIEGPAVADLQAVFAEDWNFA---------------------TGEALPFPEPA-------------------------G 186

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 304 WVKAEVVKDSPDkirskaKKEEHLNFQLINHLEKPESNVDLISAYFIPEKQGAKILSTLAKEGVEVRVLTNSfkANDVAV 383
Cdd:COG1502  187 DVRVQVVPSGPD------SPRETIERALLAAIASARRRIYIETPYFVPDRSLLRALIAAARRGVDVRILLPA--KSDHPL 258

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 384 VHAFYGKYRKELLKNGVQLYEFLPtpdkrdlnkntdelatkakvnmkglsrSSLHTKLMALDEQ-VFIGSFNFDPRSAYL 462
Cdd:COG1502  259 VHWASRSYYEELLEAGVRIYEYEP---------------------------GFLHAKVMVVDDEwALVGSANLDPRSLRL 311

                        410       420       430       440
                 ....*....|....*....|....*....|....*....|...
gi 446001333 463 NTEIGVILDSPSLAKTIHHTMDENLNKyAYKLKLDPNNHIYWQ 505
Cdd:COG1502  312 NFEVNLVIYDPEFAAQLRARFEEDLAH-SREVTLEEWRKRPLR 353
PLDc_CLS_1 cd09110
Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Catalytic ...
 87-243 4.30e-35

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: 128.75  E-value: 4.30e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333  87 EALAARLRLIDKAEKTLDLQYYIWDNDKVGALALHAIIRAADRGVKVRLLIDDNNAKKM-EGVLLALSQHkNIEVKLFNP 165
Cdd:cd09110    5 EFFPALLEAIRAARHSIHLEYYIFRDDEIGRRFRDALIEKARRGVEVRLLYDGFGSLGLsRRFLRELREA-GVEVRAFNP 83

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446001333 166 YRFRkyramdmiLDLKRINRRMHNKSFIADNQVALIGGRNMTNQYYNVSDSYQ-FSDVDVMLVGAAVDDIVNSFDDYWN 243
Cdd:cd09110   84 LSFP--------LFLLRLNYRNHRKILVIDGKIAFVGGFNIGDEYLGKDPGFGpWRDTHVRIEGPAVADLQAAFLEDWY 154
cls PRK01642
cardiolipin synthetase; Reviewed
 80-477 4.62e-24

cardiolipin synthetase; Reviewed


Pssm-ID: 234967 [Multi-domain]  Cd Length: 483  Bit Score: 105.25  E-value: 4.62e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333  80 HLLNDPLEALAARLRLIDKAEKTLDLQYYIWDNDKVGALALHAIIRAADRGVKVRLLIDD---------NNAKKME--GV 148
Cdd:PRK01642 119 RLLTNGDETFQAIIRDIELARHYILMEFYIWRPDGLGDQVAEALIAAAKRGVRVRLLYDSigsfaffrsPYPEELRnaGV 198

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 149 LLALSQHKNievklfnpyRFRKYRamdmildlKRINRRMHNKSFIADNQVALIGGRNMTNQYYNVSDSY--QFSDVDVML 226
Cdd:PRK01642 199 EVVEFLKVN---------LGRVFR--------RRLDLRNHRKIVVIDGYIAYTGSMNVVDPEYFKQDPGvgQWRDTHVRI 261

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 227 VGAAVDD--IVNSFDDYWnheyaysvqsivsAQQHRLRYES--LKQQLDAHYQQATVQnfldltsrshafdkwldrnikf 302
Cdd:PRK01642 262 EGPVVTAlqLIFAEDWEW-------------ETGERILPPPpdVLIMPFEEASGHTVQ---------------------- 306

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 303 dwvkaeVVKDSPdkirskAKKEE---HLNFQLINHLEKpesNVDLISAYFIPEKQgakILSTL---AKEGVEVRVLTNSF 376
Cdd:PRK01642 307 ------VIASGP------GDPEEtihQFLLTAIYSARE---RLWITTPYFVPDED---LLAALktaALRGVDVRIIIPSK 368

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 377 kaNDVAVV----HAFYGkyrkELLKNGVQLYEFLPtpdkrdlnkntdelatkakvnmkGLsrssLHTKLMALDEQV-FIG 451
Cdd:PRK01642 369 --NDSLLVfwasRAFFT----ELLEAGVKIYRYEG-----------------------GL----LHTKSVLVDDELaLVG 415

                        410       420
                 ....*....|....*....|....*.
gi 446001333 452 SFNFDPRSAYLNTEIGVILDSPSLAK 477
Cdd:PRK01642 416 TVNLDMRSFWLNFEITLVIDDTGFAA 441
PLDc_2 pfam13091
PLD-like domain;
331-477 3.17e-21

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 89.66  E-value: 3.17e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333  331 LINHLEKPESNVDLISAYFIPEKQGAKILSTLAKEGVEVRVLTNSFKANDVAVVHAFYGKYRkELLKNGVQLYEFLPTPd 410
Cdd:pfam13091   1 LIDLINSAKKSIDIATYYFVPDREIIDALIAAAKRGVDVRIILDSNKDDAGGPKKASLKELR-SLLRAGVEIREYQSFL- 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446001333  411 krdlnkntdelatkakvnmkglsrSSLHTKLMALDEQ-VFIGSFNFDPRSAYLNTEIGVILDSPSLAK 477
Cdd:pfam13091  79 ------------------------RSMHAKFYIIDGKtVIVGSANLTRRALRLNLENNVVIKDPELAQ 122
PLDc_ybhO_like_2 cd09159
Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; ...
 342-487 1.04e-20

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


Pssm-ID: 197256 [Multi-domain]  Cd Length: 170  Bit Score: 89.13  E-value: 1.04e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 342 VDLISAYFIPekqGAKILSTL---AKEGVEVRVLTNSfKANDVAVVHAFYGKYRKeLLKNGVQLYEFLPTPdkrdlnknt 418
Cdd:cd09159   27 IWIANAYFVP---DRRLRRALieaARRGVDVRLLLPG-KSDDPLTVAASRALYGK-LLRAGVRIFEYQPSM--------- 92

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 419 delatkakvnmkglsrssLHTKLMALDEQ-VFIGSFNFDPRSAYLNTEIGVILDSPSLAKTIHHTMDENL 487
Cdd:cd09159   93 ------------------LHAKTAVIDGDwATVGSSNLDPRSLRLNLEANLVVEDPAFAAQLEELFEEDL 144
PLDc_EcCLS_like_1 cd09152
Catalytic domain, repeat 1, of Escherichia coli cardiolipin synthase and similar proteins; ...
 80-226 4.99e-19

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: 84.18  E-value: 4.99e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333  80 HLLNDPLEALAARLRLIDKAEKTLDLQYYIWDNDKVGALALHAIIRAADRGVKVRLLIDDNNAKKM-EGVLLALSQHKNI 158
Cdd:cd09152    5 ELLTDYDAVIDRLIADIDAAKHHVHLLFYIWADDGTGDRVAEALERAAKRGVTCRLLLDAVGSRAFfRSSLWKRLREAGV 84

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 159 EVKLFNPYRF--RKYRAMDMildlkrinrRMHNKSFIADNQVALIGGRNMTNQYYNVSDSYQFSdVDVML 226
Cdd:cd09152   85 EVVEALPLRLfrRRLARFDL---------RNHRKIAVIDGRIAYTGSQNIIDPEFFKKAGGGPW-VDLMV 144
PLDc_CLS_unchar2_1 cd09157
Putative catalytic domain, repeat 1, of uncharacterized proteins similar to bacterial ...
 87-243 1.64e-18

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: 82.61  E-value: 1.64e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333  87 EALAARLRLIDKAEKTLDLQYYIWDNDKVGALALHAIIRAADRGVKVRLLIDDNNAKKMEGVLLALSQHKNIEVKLFNPY 166
Cdd:cd09157    5 EAYPAMLEAIDAARHSIALSSYIFDNDGVGREFVDALAEAVARGVDVRVLIDGVGARYSRPSIRRRLRRAGVPVARFLPP 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 167 RfrkyramdMILDLKRINRRMHNKSFIADNQVALIGGrnMtnqyyNVSDSYQ--------FSDVDVMLVGAAVDDIVNSF 238
Cdd:cd09157   85 R--------LPPRLPFINLRNHRKILVVDGRTGFTGG--M-----NIRDGHLvaddpknpVQDLHFRVEGPVVAQLQEVF 149


                 ....*
gi 446001333 239 DDYWN 243
Cdd:cd09157  150 AEDWY 154
PLDc_CLS_unchar1_1 cd09156
Putative catalytic domain, repeat 1, of uncharacterized proteins similar to bacterial ...
 84-243 1.92e-18

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: 82.31  E-value: 1.92e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333  84 DPLEALAARLRLIDKAEKTLDLQYYIWDNDKVGALALHAIIRAADRGVKVRLLIDDNNAKKM-EGVLLALSqHKNIEVKL 162
Cdd:cd09156    2 DGVEAYQALIQLIESAKHSIDVCTFILGDDATGRRVIDALARKAREGVEVRLLLDALGSFFLsRRALKKLR-AAGGKVAF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 163 FNPYRFRKYRAmdmildlkRINRRMHNKSFIADNQVALIGGRNMTNQYYN-VSDSYQFSDVDVMLVGAAVDDIVNSFDDY 241
Cdd:cd09156   81 FMPVFRLPFRG--------RTNLRNHRKIAIADGSTAISGGMNLANEYMGpEPDDGRWVDLSFLIEGPAVAQYQEVFRSD 152


                 ..
gi 446001333 242 WN 243
Cdd:cd09156  153 WA 154
PLDc_CLS_2 cd09112
catalytic domain repeat 2 of bacterial cardiolipin synthase and similar proteins; This CD ...
 310-489 4.18e-16

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


Pssm-ID: 197211 [Multi-domain]  Cd Length: 174  Bit Score: 76.36  E-value: 4.18e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 310 VKDSPDKIRSKAKkeeHLNFQLINHLEKpesNVDLISAYFIPEKQGAKILSTLAKEGVEVRVLTnSFKANDVAVVHAFYg 389
Cdd:cd09112    1 VSSGPDSDWSSIE---QAYLKAINSAKK---SIYIQTPYFIPDESLLEALKTAALSGVDVRIMI-PGKPDHKLVYWASR- 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 390 KYRKELLKNGVQLYEFlptpdkrdlnkntdelatkakvnmkglSRSSLHTKLMALD-EQVFIGSFNFDPRSAYLNTEIGV 468
Cdd:cd09112   73 SYFEELLKAGVKIYEY---------------------------NKGFLHSKTLIVDdEIASVGTANLDIRSFELNFEVNA 125

                        170       180
                 ....*....|....*....|.
gi 446001333 469 ILDSPSLAKTIHHTMDENLNK 489
Cdd:cd09112  126 VIYDKEVAKKLEEIFEEDLKD 146
PRK12452 PRK12452
cardiolipin synthase;
77-477 4.72e-15

cardiolipin synthase;


Pssm-ID: 171510 [Multi-domain]  Cd Length: 509  Bit Score: 77.65  E-value: 4.72e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333  77 TGYHLLNDPLEALAARLRLIDKAEKTLDLQYYIWDNDKVGALALHAIIRAADRGVKVRLLIDDNNAKKMEGVLLALSQHK 156
Cdd:PRK12452 140 TTTKLLTNGDQTFSEILQAIEQAKHHIHIQYYIYKSDEIGTKVRDALIKKAKDGVIVRFLYDGLGSNTLRRRFLQPMKEA 219

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 157 NIEVKLFNPyrfrkyraMDMILDLKRINRRMHNKSFIADNQVALIGGRNMTNQYYNVSDSYQF-SDVDVMLVGAAVDDIV 235
Cdd:PRK12452 220 GIEIVEFDP--------IFSAWLLETVNYRNHRKIVIVDGEIGFTGGLNVGDEYLGRSKKFPVwRDSHLKVEGKALYKLQ 291

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 236 NSFDDYWnheyaysvqsivsaqqhrlRYESLKQQLDAHYQQATVQNF--LDLTSRSHAfdkwldrnikfdwvkAEVVKDS 313
Cdd:PRK12452 292 AIFLEDW-------------------LYASSGLNTYSWDPFMNRQYFpgKEISNAEGA---------------VQIVASG 337

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 314 PdkirskAKKEEHLNFQLINHLEKPESNVDLISAYFIPEKQGAKILSTLAKEGVEVRVLTNSfKANDVAvvhAFYG--KY 391
Cdd:PRK12452 338 P------SSDDKSIRNTLLAVMGSAKKSIWIATPYFIPDQETLTLLRLSAISGIDVRILYPG-KSDSII---SDQAsqSY 407

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 392 RKELLKNGVQLYEFlptpdkrdlnkntdelatkakvnmkglSRSSLHTKLMALDEQV-FIGSFNFDPRSAYLNTEI-GVI 469
Cdd:PRK12452 408 FTPLLKAGASIYSY---------------------------KDGFMHAKIVLVDDKIaTIGTANMDVRSFELNYEIiSVL 460


                 ....*...
gi 446001333 470 LDSPSLAK 477
Cdd:PRK12452 461 YESETVHD 468
PLDc_PaCLS_like_1 cd09155
Putative catalytic domain, repeat 1, of Pseudomonas aeruginosa cardiolipin synthase and ...
 90-242 2.82e-14

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: 70.35  E-value: 2.82e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333  90 AARLRLIDKAEKTLDLQYYIWDNDKVGALALHAIIRAADRGVKVRLLIDDNNAKKMEGVLLALSQHKNIEVKLFNPYRFR 169
Cdd:cd09155    8 AAIFEAIASAEEYILVQFYIIRDDDLGRELKDALIARAQAGVRVYLLYDEIGSHSLSRSYIERLRKAGVEVSAFNTTRGW 87

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446001333 170 KYRAmdmildlkRINRRMHNKSFIADNQVALIGGRNMTNQYYNVSDSY-QFSDVDVMLVGAAVDDIVNSF--DDYW 242
Cdd:cd09155   88 GNRF--------QLNFRNHRKIVVVDGQTAFVGGHNVGDEYLGRDPRLgPWRDTHVKLEGPAVQQLQLSFaeDWYW 155
PRK11263 PRK11263
cardiolipin synthase ClsB;
96-485 9.10e-14

cardiolipin synthase ClsB;


Pssm-ID: 236888 [Multi-domain]  Cd Length: 411  Bit Score: 73.06  E-value: 9.10e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333  96 IDKAEKTLDLQYYIWDNDKVGaLALH-AIIRAADRGVKVRLLIDDNNAKKMEGVLLALSQHKNIEVKLFNPYRfrkyRAM 174
Cdd:PRK11263  27 IAAAQEEILLETFILFEDKVG-KQLHaALLAAAQRGVKVEVLVDGYGSPDLSDEFVNELTAAGVRFRYFDPRP----RLL 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 175 DMildlkRIN--RRMHNKSFIADNQVALIGGRNmtnqyYNVSDSYQFS-----DVDVMLVGAAVDDIvnsfddywnheYA 247
Cdd:PRK11263 102 GM-----RTNlfRRMHRKIVVIDGRIAFVGGIN-----YSADHLSDYGpeakqDYAVEVEGPVVADI-----------HQ 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 248 YSVQSIVSAQQHRLRYESLKQQLDAHYQQATVQNFLDLTSRSHAFDkwldrnIKFDWVKAevvkdspdkIRSkAKKEehl 327
Cdd:PRK11263 161 FELEALPGQSAARRWWRRHHRAEENRQPGEAQALLVWRDNEEHRDD------IERHYLKA---------LRQ-ARRE--- 221

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 328 nfqlinhlekpesnVDLISAYFIPekqGAKILSTL---AKEGVEVRVLTNSfkANDVAVVHAFYGKYRKELLKNGVQLYE 404
Cdd:PRK11263 222 --------------VIIANAYFFP---GYRLLRALrnaARRGVRVRLILQG--EPDMPIVRVGARLLYNYLLKGGVQIYE 282

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 405 FLPTPdkrdlnkntdelatkakvnmkglsrssLHTKLmAL--DEQVFIGSFNFDPRSAYLNTEIGVILDSPSLAKTIHHT 482
Cdd:PRK11263 283 YCRRP---------------------------LHGKV-ALmdDHWATVGSSNLDPLSLSLNLEANLIIRDRAFNQTLRDN 334


                 ...
gi 446001333 483 MDE 485
Cdd:PRK11263 335 LNG 337
PLDc_unchar1_1 cd09127
Putative catalytic domain, repeat 1, of uncharacterized phospholipase D-like proteins; ...
 93-211 2.10e-13

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: 67.29  E-value: 2.10e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333  93 LRLIDKAEKTLDLQYYIWDNDKVgalaLHAIIRAADRGVKVRLLIDDNNAKKM---EGVLLALSQHkNIEVKLFNP-YRF 168
Cdd:cd09127   14 VDAIASAKRSILLKMYEFTDPAL----EKALAAAAKRGVRVRVLLEGGPVGGIsraEKLLDYLNEA-GVEVRWTNGtARY 88

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 446001333 169 RKYramdmildlkrinrrmHNKSFIADNQVALIGGRNMTNQYY 211
Cdd:cd09127   89 RYT----------------HAKYIVVDDERALVLTENFKPSGF 115
PLDc_SF cd00138
Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D ...
 93-209 1.35e-12

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: 64.46  E-value: 1.35e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333  93 LRLIDKAEKTLDLQYYIWDNDKVGALaLHAIIRAADRGVKVRLLIDDNNAKK--MEGVLLALSQHKNIEVKLFNpyrfrk 170
Cdd:cd00138    4 LELLKNAKESIFIATPNFSFNSADRL-LKALLAAAERGVDVRLIIDKPPNAAgsLSAALLEALLRAGVNVRSYV------ 76

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 446001333 171 yramdmilDLKRINRRMHNKSFIADNQVALIGGRNMTNQ 209
Cdd:cd00138   77 --------TPPHFFERLHAKVVVIDGEVAYVGSANLSTA 107
PLDc_EcCLS_like_2 cd09158
Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase and similar proteins; ...
 348-489 4.00e-12

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: 64.52  E-value: 4.00e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 348 YFIPEKQGAKILSTLAKEGVEVRVLTnSFKaNDVAVVHAFYGKYRKELLKNGVQLYEFLPtpdkrdlnkntdelatkakv 427
Cdd:cd09158   33 YFVPDESLLQALCTAALRGVEVTLIL-PAK-NDSFLVGAASRSYYEELLEAGVKIYLYRG-------------------- 90

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446001333 428 nmkGLsrssLHTKLMALDEQV-FIGSFNFDPRSAYLNTEIGVILDSPSLAKTIHHTMDENLNK 489
Cdd:cd09158   91 ---GL----LHAKTVTVDDEVaLVGSSNFDIRSFALNFEISLILYDKEFTAQLRAIQERYLAR 146
PLDc_2 pfam13091
PLD-like domain;
93-209 4.35e-12

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 63.46  E-value: 4.35e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333   93 LRLIDKAEKTLDLQ-YYIWDNDKVgalaLHAIIRAADRGVKVRLLIDDNNA------KKMEGVLLALSQHKnIEVKLFNP 165
Cdd:pfam13091   2 IDLINSAKKSIDIAtYYFVPDREI----IDALIAAAKRGVDVRIILDSNKDdaggpkKASLKELRSLLRAG-VEIREYQS 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 446001333  166 YrfrkyramdmildlkriNRRMHNKSFIADNQVALIGGRNMTNQ 209
Cdd:pfam13091  77 F-----------------LRSMHAKFYIIDGKTVIVGSANLTRR 103
PLDc_Nuc_like cd09116
Catalytic domain of EDTA-resistant nuclease Nuc, vertebrate phospholipase D6, and similar ...
 93-244 1.64e-11

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


Pssm-ID: 197215 [Multi-domain]  Cd Length: 138  Bit Score: 61.93  E-value: 1.64e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333  93 LRLIDKAEKTLDLQYYIWDNDKVGAlalhAIIRAADRGVKVRLLID-DNNAKKMEGVLLALSQHKNIEVKlfnpyrfrky 171
Cdd:cd09116   15 VALIANAKSSIDVAMYALTDPEIAE----ALKRAAKRGVRVRIILDkDSLADNLSITLLALLSNLGIPVR---------- 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446001333 172 ramdmildLKRINRRMHNKSFIADNQVALIGGRNMTNQ--YYNVSDSYQFSDvdvmlvgaavDDIVNSFDDYWNH 244
Cdd:cd09116   81 --------TDSGSKLMHHKFIIIDGKIVITGSANWTKSgfHRNDENLLIIDD----------PKLAASFEEEFNR 137
PLDc_SMU_988_like_1 cd09154
Putative catalytic domain, repeat 1, of Streptococcus mutans uncharacterized protein SMU_988 ...
 87-243 9.79e-11

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: 60.24  E-value: 9.79e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333  87 EALAARLRLIDKAEKTLDLQYYI------WDNdkvgalALHAIIRAADRGVKVRLLIDD---------NNAKKMEgvlla 151
Cdd:cd09154    6 DMFEDMLEDLKKAEKFIFMEYFIieegymWDS------ILEILKEKAKEGVEVRIMYDDfgsittlpkDYPKELE----- 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 152 lsqHKNIEVKLFNPYRfrkyramdMILDLkRINRRMHNKSFIADNQVALIGGRNMTNQYYNVSDSY-QFSDVDVMLVGAA 230
Cdd:cd09154   75 ---KIGIKCRVFNPFK--------PILSL-YMNNRDHRKITVIDGKVAFTGGINLADEYINKIERFgYWKDTGIRLEGEA 142

                        170
                 ....*....|...
gi 446001333 231 VDDIVNSFDDYWN 243
Cdd:cd09154  143 VWSLTVMFLEMWN 155
PLDc_CLS_unchar2_2 cd09163
Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial ...
 310-479 1.83e-10

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: 59.88  E-value: 1.83e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 310 VKDSPDKirskakKEEHLNFQLINHLEKPESNVDLISAYFIPEKQGAKILSTLAKEGVEVRVLTNsfKANDVAVVH-AFY 388
Cdd:cd09163    1 IPDGPDE------DLDKLRWTLLGAISAARHSIRIMTPYFLPDRTLITALQAAALRGVEVDIVLP--ERNNLPLVDwAMR 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 389 GKYRkELLKNGVQLYEflpTPDKRDlnkntdelatkakvnmkglsrsslHTKLMALDEQ-VFIGSFNFDPRSAYLNTEIG 467
Cdd:cd09163   73 ANLW-ELLEHGVRIYL---QPPPFD------------------------HSKLMVVDGAwALIGSANWDPRSLRLNFELN 124

                        170
                 ....*....|..
gi 446001333 468 VILDSPSLAKTI 479
Cdd:cd09163  125 LEVYDTALAGQL 136
PLDc_vPLD3_4_5_like_1 cd09106
Putative catalytic domain, repeat 1, of vertebrate phospholipases, PLD3, PLD4 and PLD5, viral ...
 93-207 4.98e-10

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: 58.03  E-value: 4.98e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333  93 LRLIDKAEKTLDLQYYIWDND----------KVGALALHAIIRAADRGVKVRLLIDDNNAKKMEGVLLALSQHKNIEVkl 162
Cdd:cd09106   25 MELISSAKKSIDIASFYWNLRgtdtnpdssaQEGEDIFNALLEAAKRGVKIRILQDKPSKDKPDEDDLELAALGGAEV-- 102

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 446001333 163 fnpyrfrkyRAMDMilDLKRINRRMHNKSFIADNQVALIGGRNMT 207
Cdd:cd09106  103 ---------RSLDF--TKLIGGGVLHTKFWIVDGKHFYLGSANLD 136
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 93-262 2.37e-09

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: 59.19  E-value: 2.37e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333  93 LRLIDKAEKTLDLQ--YYIWDNDkvgalALHAIIRAADRGVKVRLLIDDNNAKKMegVLLALSQH------KNIEVKLFN 164
Cdd:COG1502  209 LAAIASARRRIYIEtpYFVPDRS-----LLRALIAAARRGVDVRILLPAKSDHPL--VHWASRSYyeelleAGVRIYEYE 281

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 165 PyrfrkyramdmildlkrinRRMHNKSFIADNQVALIGGRNMTNQ--YYNvsdsyqfSDVDVMLVGAAV-DDIVNSFDDY 241
Cdd:COG1502  282 P-------------------GFLHAKVMVVDDEWALVGSANLDPRslRLN-------FEVNLVIYDPEFaAQLRARFEED 335

                        170       180
                 ....*....|....*....|.
gi 446001333 242 WNHEYAYSVQSIVSAQQHRLR 262
Cdd:COG1502  336 LAHSREVTLEEWRKRPLRRLR 356
PLDc_SF cd00138
Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D ...
 330-470 1.63e-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: 1.63e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 330 QLINHLEKPESNVDLISAYFIPEKQG--AKILSTLAKEGVEVRVLTNsfKANDVAVVHAfyGKYRKELLKNGVQLYEFLP 407
Cdd:cd00138    2 ALLELLKNAKESIFIATPNFSFNSADrlLKALLAAAERGVDVRLIID--KPPNAAGSLS--AALLEALLRAGVNVRSYVT 77

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446001333 408 TPDKRdlnkntdelatkakvnmkglsrSSLHTKLMALDEQVF-IGSFNFDPRSAYLNTEIGVIL 470
Cdd:cd00138   78 PPHFF----------------------ERLHAKVVVIDGEVAyVGSANLSTASAAQNREAGVLV 119
PLDc_vPLD3_4_5_like_2 cd09107
Putative catalytic domain, repeat 2, of vertebrate phospholipases, PLD3, PLD4 and PLD5, viral ...
 89-211 2.25e-08

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


Pssm-ID: 197206 [Multi-domain]  Cd Length: 175  Bit Score: 53.80  E-value: 2.25e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333  89 LAARLRLIDKAEKTLDLQ--------------YYIWDNDKvgalalhAIIRAA-DRGVKVRLLI--DDNNAKKMEGVLLA 151
Cdd:cd09107   18 LDALLSTIDSAKKFIDISvmdyvplsryadprKYWPVIDN-------ALRRAAvDRGVKVRLLVsnWKHTDPSMDAFLKS 90

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 152 LSQHK------NIEVKLF----NPYRFRKYRamdmildlkrinRRMHNKSFIADNQvALIGGRNMTNQYY 211
Cdd:cd09107   91 LQLLKsgvgngDIEVKIFtvpgDQSTKIPFA------------RVNHAKYMVTDER-AYIGTSNWSGDYF 147
PLDc_SMU_988_like_2 cd09160
Putative catalytic domain, repeat 2, of Streptococcus mutans uncharacterized protein SMU_988 ...
 325-476 4.82e-08

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: 52.88  E-value: 4.82e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 325 EHLNFQLINHLEKpesNVDLISAYFIPEKQGAKILSTLAKEGVEVRVLTNSFKanDVAVVHAFYGKYRKELLKNGVQLYE 404
Cdd:cd09160   13 ENVYLDLINQAKD---YVYITTPYLILDDEMLDALCLAAKRGVDVRIITPHIP--DKKYVFLVTRSNYPELLEAGVKIYE 87

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446001333 405 FLPtpdkrdlnkntdelatkakvnmkGLsrssLHTKLMALDEQV-FIGSFNFDPRSAYLNTEIGV-ILDSPSLA 476
Cdd:cd09160   88 YTP-----------------------GF----IHAKTFVSDDKAaVVGTINLDYRSLYLHFECGVyMYDTPVIS 134
PLDc_unchar1_2 cd09128
Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins; ...
 78-207 8.91e-08

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: 51.51  E-value: 8.91e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333  78 GYHLLNDPLEALAARLRLIDKAEKTLDLQY-YIWDNDKVgalaLHAIIRAADRGVKVRLLIDD--NNAKKMEGVLLALSQ 154
Cdd:cd09128    1 SVQLLLSPDNAREALLALIDSAEESLLIQNeEMGDDAPI----LDALVDAAKRGVDVRVLLPSawSAEDERQARLRALEG 76

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 446001333 155 HKNievklfnpyrfrKYRAMDMILDlkrinrRMHNKSFIADNQVALIGGRNMT 207
Cdd:cd09128   77 AGV------------PVRLLKDKFL------KIHAKGIVVDGKTALVGSENWS 111
PLDc_unchar1_2 cd09128
Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins; ...
 331-484 1.47e-07

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


Pssm-ID: 197226 [Multi-domain]  Cd Length: 142  Bit Score: 50.74  E-value: 1.47e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 331 LINHLEKPesnVDLISAYFIPEKQGAKILSTLAKEGVEVRVLTNSFKANDVAVVhafygKYRKELLKNGVQLYEFLPTPD 410
Cdd:cd09128   18 LIDSAEES---LLIQNEEMGDDAPILDALVDAAKRGVDVRVLLPSAWSAEDERQ-----ARLRALEGAGVPVRLLKDKFL 89

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446001333 411 KrdlnkntdelatkakvnmkglsrssLHTKLMALD-EQVFIGSFNFDPRSAYLNTEIGVILDSPSLAKTIHHTMD 484
Cdd:cd09128   90 K-------------------------IHAKGIVVDgKTALVGSENWSANSLDRNREVGLIFDDPEVAAYLQAVFE 139
PLDc_vPLD6_like cd09171
Catalytic domain of vertebrate phospholipase D6 and similar proteins; Catalytic domain of ...
 93-209 2.29e-07

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: 49.92  E-value: 2.29e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333  93 LRLIDKAEKTLDLQYYIWDNDKVGAlalhAIIRAADRGVKVRLLIDDNNAKKMEGVLLALSQHKnIEVKlfnpyrfrkyr 172
Cdd:cd09171   14 LRYLLSARKSLDVCVFTITCDDLAD----AILDLHRRGVRVRIITDDDQMEDKGSDIGKLRKAG-IPVR----------- 77

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 446001333 173 aMDMILDLkrinrrMHNKSFIADNQVALIGGRNMTNQ 209
Cdd:cd09171   78 -TDLSSGH------MHHKFAVIDGKILITGSFNWTRQ 107
PLDc_CLS_unchar1_2 cd09162
Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial ...
 345-485 7.86e-07

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: 49.18  E-value: 7.86e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 345 ISAYFIPEKQGAKILSTLAKEGVEVRVLTNsfKANDVAVVHAFYGKYRKELLKNGVQLYEFLPtpdkrdlnkntdelatk 424
Cdd:cd09162   30 VTPYFVPDEVLLRALRLAARRGVDVRLIVP--KRSNHRIADLARGSYLRDLQEAGAEIYLYQP----------------- 90

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446001333 425 akvNMkglsrssLHTKLMALDEQV-FIGSFNFDPRSAYLNTEIGVILDSPSLAKTIHHTMDE 485
Cdd:cd09162   91 ---GM-------LHAKAVVVDDKLaLVGSANLDMRSLFLNYEVAVFFYSPADIKELSDWIES 142
PLDc_Nuc cd09170
Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar ...
 88-212 1.16e-06

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


Pssm-ID: 197267 [Multi-domain]  Cd Length: 142  Bit Score: 48.28  E-value: 1.16e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333  88 ALAARLRLIDKAEKTLDLQYYIWDNDKVGAlalhAIIRAADRGVKVRLLIDDNNAKKmEGVLLALSQHKNIEVKL-FNPY 166
Cdd:cd09170   12 ARELILDVIDSARRSIDVAAYSFTSPPIAR----ALIAAKKRGVDVRVVLDKSQAGG-KYSALNYLANAGIPVRIdDNYA 86

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 446001333 167 rfrkyramdmildlkrinrRMHNKSFIADNQVALIGGRNMTN--QYYN 212
Cdd:cd09170   87 -------------------IMHNKVMVIDGKTVITGSFNFTAsaEKRN 115
PRK13912 PRK13912
nuclease NucT; Provisional
 79-207 2.31e-06

nuclease NucT; Provisional


Pssm-ID: 184389 [Multi-domain]  Cd Length: 177  Bit Score: 47.85  E-value: 2.31e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333  79 YHLLNDPLEALAARLRLIDKAEKTLDLQYYIWDNDKVGalalHAIIRAADRGVKVRLLID-DNNAKKMEGVLLALSQHKN 157
Cdd:PRK13912  25 YFLPYEQKDALNKLVSLISNARSSIKIAIYSFTHKDIA----KALKSAAKRGVKISIIYDyESNHNNDQSTIGYLDKYPN 100

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 446001333 158 IEVKLFNPYRFRKyramdmildlKRINRRMHNKSFIADNQVALIGGRNMT 207
Cdd:PRK13912 101 IKVCLLKGLKAKN----------GKYYGIMHQKVAIIDDKIVVLGSANWS 140
PLDc_Nuc_like_unchar1_1 cd09172
Putative catalytic domain, repeat 1, of uncharacterized hypothetical proteins similar to Nuc, ...
 81-243 3.06e-06

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: 46.97  E-value: 3.06e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333  81 LLNDPLEALAARLRLIDKAEKTLDLQYYIWDNDKVgalaLHAIIRAADRGVKVRLLIDD---NNAKKMEGVLLALSQHKN 157
Cdd:cd09172    3 LSRELREALLAFLDEARSAGSSIRLAIYELDDPEI----IDALKAAKDRGVRVRIILDDssvTGDPTEESAAATLSKGPG 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 158 IEVKlfnpyrfrkyramdmildlKRINRR-MHNKSFIADN----QVALIGGRNMTnqyynVSDSYQFSDVDVMLVGAAVD 232
Cdd:cd09172   79 ALVK-------------------RRHSSGlMHNKFLVVDRkdgpNRVLTGSTNFT-----TSGLYGQSNNVLIFRNPAFA 134

                        170
                 ....*....|.
gi 446001333 233 DIvnsFDDYWN 243
Cdd:cd09172  135 AA---YLAYWN 142
PLDc_CLS_1 cd09110
Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Catalytic ...
 348-454 3.24e-06

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: 47.09  E-value: 3.24e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 348 YFI--PEKQGAKILSTL---AKEGVEVRVLT---NSFKANDvavvhafygKYRKELLKNGVQLYEFLPTPDKRDLNKNtd 419
Cdd:cd09110   25 YYIfrDDEIGRRFRDALiekARRGVEVRLLYdgfGSLGLSR---------RFLRELREAGVEVRAFNPLSFPLFLLRL-- 93

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 446001333 420 elatkakvnmkgLSRssLHTKLMALDEQV-FIGSFN 454
Cdd:cd09110   94 ------------NYR--NHRKILVIDGKIaFVGGFN 115
YrhO COG1378
Sugar-specific transcriptional regulator TrmB [Transcription];
50-211 2.73e-05

Sugar-specific transcriptional regulator TrmB [Transcription];


Pssm-ID: 440988 [Multi-domain]  Cd Length: 238  Bit Score: 45.78  E-value: 2.73e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333  50 QYARDIDTSQTSLSKIITPLREKNP----NLTGYhllndplEALAARLR-LIDKAEKTLDLqyYIWDNDKVGALALHAII 124
Cdd:COG1378   82 EREEELEELREELEELYEELREPEEelvwVVKGR-------EAILERLReLIASAEEEILI--VLSPPELLLEELEEALE 152

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 125 RAADRGVKVRLLIDDNNAKKMEGVllalsQHKNIEVklfnpyrfrkyramdmildlkRINRRMHNKSFIADNQVALIGGR 204
Cdd:COG1378  153 EALERGVKVRVLVSPEVLEVPERL-----EEEGEEV---------------------RVLPGLPGRLLIVDDKEALISVS 206


                 ....*..
gi 446001333 205 NMTNQYY 211
Cdd:COG1378  207 EPDGEET 213
PLDc_unchar2_2 cd09130
Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins; ...
 93-245 1.48e-04

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: 42.23  E-value: 1.48e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333  93 LRLIDKAEK--TLDL-QYYIWDNDKVGALalhaiIRAADRGVKVRLLIDDN-NAKKME--GV--------LLALSqHKNI 158
Cdd:cd09130   11 LKEINSARAgdKIWIgMFYLADRDVIKAL-----IDAANRGVDVRLILDPNkDAFGREknGIpnrpvaaeLMKKT-KGKI 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 159 EVKLFNpyrfrkyramdmildlkRINRRMHNK-SFIADN-QVALIGG------RNMTNqyYNVsdsyqfsDVDVMLVGAA 230
Cdd:cd09130   85 QIRWYN-----------------TGGEQFHTKlLLIKKKgQAIIIGGsanftrRNLRD--YNL-------ETDLKILAPN 138

                        170
                 ....*....|....*....
gi 446001333 231 ----VDDIVNSFDDYWNHE 245
Cdd:cd09130  139 dspvSKDVDAYFDRLWNNE 157
PLDc_vPLD3_4_5_like_1 cd09106
Putative catalytic domain, repeat 1, of vertebrate phospholipases, PLD3, PLD4 and PLD5, viral ...
 354-471 3.16e-04

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


Pssm-ID: 197205 [Multi-domain]  Cd Length: 153  Bit Score: 41.46  E-value: 3.16e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 354 QGAKILSTL---AKEGVEVRVLTNSfkandvavvhafygkyrkellkngvqlyeflPTPDKRDlnKNTDELATKA----- 425
Cdd:cd09106   57 EGEDIFNALleaAKRGVKIRILQDK-------------------------------PSKDKPD--EDDLELAALGgaevr 103

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 446001333 426 KVNM-KGLSRSSLHTKLMALDEQ-VFIGSFNFDPRSayLNT--EIGVILD 471
Cdd:cd09106  104 SLDFtKLIGGGVLHTKFWIVDGKhFYLGSANLDWRS--LTQvkELGVYIY 151
PLDc_vPLD4_1 cd09145
Putative catalytic domain, repeat 1, of vertebrate phospholipase PLD4; Putative catalytic ...
 393-482 6.12e-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: 40.66  E-value: 6.12e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 393 KELLKNGVQLYEFLPTPDKRDLNKNTDELATKA----KVNMKGLSRSSLHTKLMALD-EQVFIGSFNFDPRSAYLNTEIG 467
Cdd:cd09145   68 AELLSRNVSVRAAASIPTLAANSTDLKILRQKGahvrKVNFGRLTGGVLHSKFWIIDkKHIYVGSANMDWRSLTQVKELG 147

                         90
                 ....*....|....*.
gi 446001333 468 -VILDSPSLAKTIHHT 482
Cdd:cd09145  148 aVIYNCSSLAKDLHKT 163
PLDc_vPLD3_2 cd09147
Putative catalytic domain, repeat 2, of vertebrate phospholipase PLD3; Putative catalytic ...
 125-211 6.94e-04

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: 40.72  E-value: 6.94e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 125 RAA-DRGVKVRLLID--DNNAKKMEGVLLALS------QHKNIEVKLFN-PYRFRKYRamdmiLDLKRINrrmHNKSFIA 194
Cdd:cd09147   61 RATyERGVKVRLLIScwGHSEPSMFAFLRSLAalrdntTHSDIQVKIFVvPADEAQKK-----IPYARVN---HNKYMVT 132

                         90
                 ....*....|....*..
gi 446001333 195 DnQVALIGGRNMTNQYY 211
Cdd:cd09147  133 D-RVAYIGTSNWSGDYF 148
PLDc_unchar3 cd09131
Putative catalytic domain of uncharacterized phospholipase D-like proteins; Putative catalytic ...
 91-210 1.22e-03

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


Pssm-ID: 197229 [Multi-domain]  Cd Length: 143  Bit Score: 39.25  E-value: 1.22e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333  91 ARLRLIDKAEKTL-----DLQYYIWDNDKVGALaLHAIIRAADRGVKVRLLIDDNNAKKMEGV----LLALSQHKNIEVK 161
Cdd:cd09131    7 ALLDLINNAKRSIyiamyMFKYYENPGNGVNTL-LEALIDAHKRGVDVKVVLEDSIDDDEVTEendnTYRYLKDNGVEVR 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 446001333 162 LFNPyrfrkyramdmildlkriNRRMHNKSFIADNQVALIGGRNMTNQY 210
Cdd:cd09131   86 FDSP------------------SVTTHTKLVVIDGRTVYVGSHNWTYSA 116
PLDc_EcCLS_like_1 cd09152
Catalytic domain, repeat 1, of Escherichia coli cardiolipin synthase and similar proteins; ...
 330-458 1.22e-03

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


Pssm-ID: 197250 [Multi-domain]  Cd Length: 163  Bit Score: 39.88  E-value: 1.22e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 330 QLINHLEKPESNVDLISAYFIPEKQGAKILSTL---AKEGVEVRVLTNSFKANDVavvhaFYGKYRKELLKNGVQLYEFL 406
Cdd:cd09152   16 RLIADIDAAKHHVHLLFYIWADDGTGDRVAEALeraAKRGVTCRLLLDAVGSRAF-----FRSSLWKRLREAGVEVVEAL 90

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 446001333 407 PtpdkrdlnkntdelatkAKVNMKGLSRSSL--HTKLMALDEQV-FIGSFNF-DPR 458
Cdd:cd09152   91 P-----------------LRLFRRRLARFDLrnHRKIAVIDGRIaYTGSQNIiDPE 129
PLDc_unchar3 cd09131
Putative catalytic domain of uncharacterized phospholipase D-like proteins; Putative catalytic ...
 433-477 1.23e-03

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


Pssm-ID: 197229 [Multi-domain]  Cd Length: 143  Bit Score: 39.25  E-value: 1.23e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 446001333 433 SRSSLHTKLMALDEQ-VFIGSFNFDPRSAYLNTEIGVILDSPSLAK 477
Cdd:cd09131   89 PSVTTHTKLVVIDGRtVYVGSHNWTYSALDYNHEASVLIESPEVAD 134
PHA03003 PHA03003
palmytilated EEV membrane glycoprotein; Provisional
 96-250 1.38e-03

palmytilated EEV membrane glycoprotein; Provisional


Pssm-ID: 177506 [Multi-domain]  Cd Length: 369  Bit Score: 41.19  E-value: 1.38e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333  96 IDKAEKTLDLQY------YIWDNDKVGALALH-AIIRAA-DRGVKVRLLI---DDNNAKKMEGV--LLALSQHKNIEVKL 162
Cdd:PHA03003 225 IKSAKKSIDLELlslvpvIREDDKTTYWPDIYnALIRAAiNRGVKVRLLVgswKKNDVYSMASVksLQALCVGNDLSVKV 304

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 163 FnpyrfrkyramdmildlkRINRrmHNKSFIADNQVALIGGRNMTNQYYNVSDSYQFSDVDVMLVGAavddIVNSFDDYW 242
Cdd:PHA03003 305 F------------------RIPN--NTKLLIVDDEFAHITSANFDGTHYLHHAFVSFNTIDKELVKE----LSAIFERDW 360


                 ....*...
gi 446001333 243 NHEYAYSV 250
Cdd:PHA03003 361 TSSYSKPL 368
PLDc smart00155
Phospholipase D. Active site motifs; Phosphatidylcholine-hydrolyzing phospholipase D (PLD) ...
 437-459 2.07e-03

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: 35.83  E-value: 2.07e-03
                           10        20
                   ....*....|....*....|....
gi 446001333   437 LHTKLMALD-EQVFIGSFNFDPRS 459
Cdd:smart00155   5 LHTKLMIVDdEIAYIGSANLDGRS 28
PLDc_Nuc_like_unchar2 cd09174
Putative catalytic domain of uncharacterized hypothetical proteins closely related to Nuc, , ...
 122-208 2.52e-03

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: 38.45  E-value: 2.52e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 122 AIIRAADRGVKVRLLIDDNNAKKMEGVLLALSQHKNIEVKLFNPYRfrkyramdmildlkriNRRMHNKSFIADNQVALI 201
Cdd:cd09174   38 ALKNKKKEGVNIQIIINDDDINKKDVLILDEDSFEIYKLPGNGSRY----------------GNLMHNKFCVIDFKTVIT 101


                 ....*..
gi 446001333 202 GGRNMTN 208
Cdd:cd09174  102 GSYNWTK 108
PLDc_ybhO_like_2 cd09159
Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; ...
 93-137 4.60e-03

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


Pssm-ID: 197256 [Multi-domain]  Cd Length: 170  Bit Score: 38.29  E-value: 4.60e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 446001333  93 LRLIDKAEKTLDLQ--YYIWDNdkvgaLALHAIIRAADRGVKVRLLI 137
Cdd:cd09159   17 LVAIAAARRRIWIAnaYFVPDR-----RLRRALIEAARRGVDVRLLL 58
COG3886 COG3886
HKD family nuclease [Replication, recombination and repair];
122-245 5.48e-03

HKD family nuclease [Replication, recombination and repair];


Pssm-ID: 443094 [Multi-domain]  Cd Length: 941  Bit Score: 39.58  E-value: 5.48e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 122 AIIRAADRGVKVRLLI-DDNNAKKMEgVLLALSQHKNIEVKLFNpyrfrkyramdmildlkRINRRMHNKSFI---ADNQ 197
Cdd:COG3886   63 ALKELLERGVKGRILTsTYLGFTEPK-ALRELLDLPNIEVRVSY-----------------DRKTRFHAKAYIferTGYG 124

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 446001333 198 VALIGGRNMTNQ--YYNVSDSYQFSDVDVmlvGAAVDDIVNSFDDYWNHE 245
Cdd:COG3886  125 TAIIGSSNLTRSalTDNLEWNVKLSSAED---PDLIEKFRAEFESLWEDS 171
PLDc_vPLD3_1 cd09144
Putative catalytic domain, repeat 1, of vertebrate phospholipase PLD3; Putative catalytic ...
 407-477 5.81e-03

Putative catalytic domain, repeat 1, of vertebrate phospholipase PLD3; Putative catalytic domain, repeat 1, 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: 197242 [Multi-domain]  Cd Length: 172  Bit Score: 38.01  E-value: 5.81e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446001333 407 PTPDKrDLNKNTDELATKAKVNMKGLSRSSLHTKLMALD-EQVFIGSFNFDPRSAYLNTEIG-VILDSPSLAK 477
Cdd:cd09144   88 PKPME-DINALSSYGADVRMVDMRKLTTGVLHTKFWVVDkKHFYIGSANMDWRSLTQVKELGaVVYNCSCLAE 159
PHA02820 PHA02820
phospholipase-D-like protein; Provisional
 93-242 6.10e-03

phospholipase-D-like protein; Provisional


Pssm-ID: 222934 [Multi-domain]  Cd Length: 424  Bit Score: 39.21  E-value: 6.10e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333  93 LRLIDKAEKTLDLQYYIW-----DNDKVGALALHAIIRAADRGVKVRLLIDDNNaKKMEGVLLalsqhknievklfnpyr 167
Cdd:PHA02820  32 REILSNTTKTLDISSFYWslsdeVGTNFGTMILNEIIQLPKRGVRVRIAVNKSN-KPLKDVEL----------------- 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333 168 FRKYRAMDMILDLKRI-NRRMHNKSFIADNQVALIGGRNMtnqyynvsDSYQFSDVDVMLVG-----AAVDDIVNSFDDY 241
Cdd:PHA02820  94 LQMAGVEVRYIDITNIlGGVLHTKFWISDNTHIYLGSANM--------DWRSLTQVKELGIAifnnsNLAADLTQIFEVY 165


                 .
gi 446001333 242 W 242
Cdd:PHA02820 166 W 166
PLDc_CLS_2 cd09112
catalytic domain repeat 2 of bacterial cardiolipin synthase and similar proteins; This CD ...
 93-206 9.99e-03

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: 37.07  E-value: 9.99e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446001333  93 LRLIDKAEKTLDLQ--YYIWDNDkvgalALHAIIRAADRGVKVRLLIDDNNAKKmegVLLALSQH-------KNIEVKLF 163
Cdd:cd09112   17 LKAINSAKKSIYIQtpYFIPDES-----LLEALKTAALSGVDVRIMIPGKPDHK---LVYWASRSyfeellkAGVKIYEY 88

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 446001333 164 NPyRFrkyramdmildlkrinrrMHNKSFIADNQVALIGGRNM 206
Cdd:cd09112   89 NK-GF------------------LHSKTLIVDDEIASVGTANL 112
 
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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