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Conserved domains on  [gi|1844060643|ref|WP_171458202|]
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phospholipase D family protein [Acinetobacter towneri]

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 ...
 291-520 1.02e-84

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: 261.39  E-value: 1.02e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 291 VKDAPSKIKDRASKEEHLNFQLLTHLEKPSSSVDIISAYFVPEQSGAEKLKDLADDGVQVRVLTNSFKANDVPVVHAFYA 370
Cdd:cd09113     1 LSDPPEKALKEAGPEPVLAYQLAELLKNAKREVLIVSPYFVPGDEGVALLAELARRGVRVRILTNSLAATDVPAVHSGYA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 371 KYREDLLANNVQLYEFLARPEMenlnththeisKKAKVSMKGLSRSSLHAKLMALDEKQVFIGSFNFDPRSAYLNTEIGV 450
Cdd:cd09113    81 RYRKRLLKAGVELYELKPDAAK-----------RKRLRGLFGSSRASLHAKSFVIDDRLVFVGSFNLDPRSAYLNTEMGL 149

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 451 ILNSPPLARAVHHTMDVNLSKYAYKLVLDAQQNIQWHMKnPQGETQILKKEPGMKWYQRAAMKITSWLPI 520
Cdd:cd09113   150 VIDSPELAAQLRAAMEEDLAPSAYWVLLLDDGGLVWETE-EDGKEKEYDSEPETSFWRRLGAWLLSLLPI 218
PLDc_ymdC_like_1 cd09111
Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and ...
 65-224 5.20e-83

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: 254.77  E-value: 5.20e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643  65 DPLEALAARIYLINKAEKSLDLQYYIWDNDKIGALALHAIIRAADRGVKVRLLVDDNNAKKMEGIYLALDQHVNIDIKLY 144
Cdd:cd09111     3 DGLDALAARLALIRSAERSIDLQYYIWHDDESGRLLLGELLEAADRGVRVRLLLDDLGTSGRDRLLAALDAHPNIEVRLF 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 145 NPYRFRHYRAMDMILDLKRINRRMHNKSFIADNQISLIGGRNMSNQYYNVSDNYQFSDVDVMLVGSASDEIIHSFDEYWN 224
Cdd:cd09111    83 NPFRNRGGRLLEFLTDFSRLNRRMHNKLFIVDGAVAIVGGRNIGDEYFGASPEVNFRDLDVLAVGPVVRQLSESFDTYWN 162
 
Name Accession Description Interval E-value
PLDc_ymdC_like_2 cd09113
Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and ...
 291-520 1.02e-84

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: 261.39  E-value: 1.02e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 291 VKDAPSKIKDRASKEEHLNFQLLTHLEKPSSSVDIISAYFVPEQSGAEKLKDLADDGVQVRVLTNSFKANDVPVVHAFYA 370
Cdd:cd09113     1 LSDPPEKALKEAGPEPVLAYQLAELLKNAKREVLIVSPYFVPGDEGVALLAELARRGVRVRILTNSLAATDVPAVHSGYA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 371 KYREDLLANNVQLYEFLARPEMenlnththeisKKAKVSMKGLSRSSLHAKLMALDEKQVFIGSFNFDPRSAYLNTEIGV 450
Cdd:cd09113    81 RYRKRLLKAGVELYELKPDAAK-----------RKRLRGLFGSSRASLHAKSFVIDDRLVFVGSFNLDPRSAYLNTEMGL 149

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 451 ILNSPPLARAVHHTMDVNLSKYAYKLVLDAQQNIQWHMKnPQGETQILKKEPGMKWYQRAAMKITSWLPI 520
Cdd:cd09113   150 VIDSPELAAQLRAAMEEDLAPSAYWVLLLDDGGLVWETE-EDGKEKEYDSEPETSFWRRLGAWLLSLLPI 218
PLDc_ymdC_like_1 cd09111
Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and ...
 65-224 5.20e-83

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: 254.77  E-value: 5.20e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643  65 DPLEALAARIYLINKAEKSLDLQYYIWDNDKIGALALHAIIRAADRGVKVRLLVDDNNAKKMEGIYLALDQHVNIDIKLY 144
Cdd:cd09111     3 DGLDALAARLALIRSAERSIDLQYYIWHDDESGRLLLGELLEAADRGVRVRLLLDDLGTSGRDRLLAALDAHPNIEVRLF 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 145 NPYRFRHYRAMDMILDLKRINRRMHNKSFIADNQISLIGGRNMSNQYYNVSDNYQFSDVDVMLVGSASDEIIHSFDEYWN 224
Cdd:cd09111    83 NPFRNRGGRLLEFLTDFSRLNRRMHNKLFIVDGAVAIVGGRNIGDEYFGASPEVNFRDLDVLAVGPVVRQLSESFDTYWN 162
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 49-487 2.89e-80

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: 255.25  E-value: 2.89e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643  49 PLREKYPQLTG--YHVLYDPLEALAARIYLINKAEKSLDLQYYIWDNDKIGALALHAIIRAADRGVKVRLLVDDNNAKKM 126
Cdd:COG1502     4 PLAAGLPLVGGnrVTLLVDGDEAFAALLEAIEAARRSIDLEYYIFDDDEVGRRLADALIAAARRGVKVRVLLDGIGSRAL 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 127 EGIYLALDQHVNIDIKLYNPYRFRhyramdmildLKRINRRMHNKSFIADNQISLIGGRNMSNQYYNVSDNY-QFSDVDV 205
Cdd:COG1502    84 NRDFLRRLRAAGVEVRLFNPVRLL----------FRRLNGRNHRKIVVIDGRVAFVGGANITDEYLGRDPGFgPWRDTHV 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 206 MLVGSASDEIIHSFDEYWNDDyaySVKQLVNPQHytlryeslkqqleqhdqeatvqnyldlvtrskaieqwmthsikFDW 285
Cdd:COG1502   154 RIEGPAVADLQAVFAEDWNFA---TGEALPFPEP-------------------------------------------AGD 187

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 286 VSAEVVKDAPskikdrASKEEHLNFQLLTHLEKPSSSVDIISAYFVPEQSGAEKLKDLADDGVQVRVLTNSfkANDVPVV 365
Cdd:COG1502   188 VRVQVVPSGP------DSPRETIERALLAAIASARRRIYIETPYFVPDRSLLRALIAAARRGVDVRILLPA--KSDHPLV 259

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 366 HAFYAKYREDLLANNVQLYEFlarpemenlnththeiskkakvsmkglSRSSLHAKLMALDEKQVFIGSFNFDPRSAYLN 445
Cdd:COG1502   260 HWASRSYYEELLEAGVRIYEY---------------------------EPGFLHAKVMVVDDEWALVGSANLDPRSLRLN 312

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|..
gi 1844060643 446 TEIGVILNSPPLARAVHHTMDVNLSKyAYKLVLDAQQNIQWH 487
Cdd:COG1502   313 FEVNLVIYDPEFAAQLRARFEEDLAH-SREVTLEEWRKRPLR 353
PLDc_2 pfam13091
PLD-like domain;
312-458 3.61e-21

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 89.27  E-value: 3.61e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 312 LLTHLEKPSSSVDIISAYFVPEQSGAEKLKDLADDGVQVRVLTNSFKANDVPVVHAFYAKYREdLLANNVQLYEFLARPe 391
Cdd:pfam13091   1 LIDLINSAKKSIDIATYYFVPDREIIDALIAAAKRGVDVRIILDSNKDDAGGPKKASLKELRS-LLRAGVEIREYQSFL- 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1844060643 392 menlnththeiskkakvsmkglsrSSLHAKLMALDEKQVFIGSFNFDPRSAYLNTEIGVILNSPPLA 458
Cdd:pfam13091  79 ------------------------RSMHAKFYIIDGKTVIVGSANLTRRALRLNLENNVVIKDPELA 121
cls PRK01642
cardiolipin synthetase; Reviewed
 61-463 3.84e-21

cardiolipin synthetase; Reviewed


Pssm-ID: 234967 [Multi-domain]  Cd Length: 483  Bit Score: 96.39  E-value: 3.84e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643  61 HVLYDPLEALAARIYLINKAEKSLDLQYYIWDNDKIGALALHAIIRAADRGVKVRLLVDD---------NNAKKME--GI 129
Cdd:PRK01642  119 RLLTNGDETFQAIIRDIELARHYILMEFYIWRPDGLGDQVAEALIAAAKRGVRVRLLYDSigsfaffrsPYPEELRnaGV 198

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 130 YLALDQHVNidiklynpyRFRhyramdmiLDLKRINRRMHNKSFIADNQISLIGGRNMSNQYY-----NVSdnyQFSDVD 204
Cdd:PRK01642  199 EVVEFLKVN---------LGR--------VFRRRLDLRNHRKIVVIDGYIAYTGSMNVVDPEYfkqdpGVG---QWRDTH 258

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 205 VMLVGSASDE--IIHSFDEYWnddyaysvkqlvnpqhytlryeslkqqleqhdqeATVQNYLDLVTRSKAIEQWMThsik 282
Cdd:PRK01642  259 VRIEGPVVTAlqLIFAEDWEW----------------------------------ETGERILPPPPDVLIMPFEEA---- 300

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 283 fDWVSAEVVKDAPskikdrASKEE--HLNFQLLTHLEKpsSSVDIISAYFVPEQSGAEKLKDLADDGVQVRVLTNSFkaN 360
Cdd:PRK01642  301 -SGHTVQVIASGP------GDPEEtiHQFLLTAIYSAR--ERLWITTPYFVPDEDLLAALKTAALRGVDVRIIIPSK--N 369

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 361 DVPVV-HAFYAKYREdLLANNVQLYEFLarpemenlnththeiskkakvsmKGLsrssLHAKLMALDEKQVFIGSFNFDP 439
Cdd:PRK01642  370 DSLLVfWASRAFFTE-LLEAGVKIYRYE-----------------------GGL----LHTKSVLVDDELALVGTVNLDM 421

                         410       420
                  ....*....|....*....|....
gi 1844060643 440 RSAYLNTEIGVILNSPPLARAVHH 463
Cdd:PRK01642  422 RSFWLNFEITLVIDDTGFAADLAA 445
PLDc_2 pfam13091
PLD-like domain;
74-223 2.17e-12

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 64.24  E-value: 2.17e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643  74 IYLINKAEKSLDLQ-YYIWDNDKIgalaLHAIIRAADRGVKVRLLVDDNNA------KKMEGIYLALDQHvNIDIKLYNP 146
Cdd:pfam13091   2 IDLINSAKKSIDIAtYYFVPDREI----IDALIAAAKRGVDVRIILDSNKDdaggpkKASLKELRSLLRA-GVEIREYQS 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1844060643 147 YrfrhyramdmildlkriNRRMHNKSFIADNQISLIGGRNMSNQ--YYNVSDNYQFSDVDVMlvgsasDEIIHSFDEYW 223
Cdd:pfam13091  77 F-----------------LRSMHAKFYIIDGKTVIVGSANLTRRalRLNLENNVVIKDPELA------QELEKEFDRLW 132
PRK13912 PRK13912
nuclease NucT; Provisional
 46-199 1.37e-06

nuclease NucT; Provisional


Pssm-ID: 184389 [Multi-domain]  Cd Length: 177  Bit Score: 48.62  E-value: 1.37e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643  46 IVLPLREKYPQLTGYHVLYDPLEALAARIYLINKAEKSLDLQYYIWDNDKIGalalHAIIRAADRGVKVRLLVDDNNAKK 125
Cdd:PRK13912   11 LVGCLGVLQAKSSLYFLPYEQKDALNKLVSLISNARSSIKIAIYSFTHKDIA----KALKSAAKRGVKISIIYDYESNHN 86

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1844060643 126 MEGIYLA-LDQHVNIDIKLYNpyrfrhyramdmilDLKRINRR----MHNKSFIADNQISLIGGRNMSNQYYnvSDNYQ 199
Cdd:PRK13912   87 NDQSTIGyLDKYPNIKVCLLK--------------GLKAKNGKyygiMHQKVAIIDDKIVVLGSANWSKNAF--ENNYE 149
PLDc smart00155
Phospholipase D. Active site motifs; Phosphatidylcholine-hydrolyzing phospholipase D (PLD) ...
 418-441 1.03e-04

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


Pssm-ID: 197546 [Multi-domain]  Cd Length: 28  Bit Score: 39.30  E-value: 1.03e-04
                           10        20
                   ....*....|....*....|....
gi 1844060643  418 LHAKLMALDEKQVFIGSFNFDPRS 441
Cdd:smart00155   5 LHTKLMIVDDEIAYIGSANLDGRS 28
YrhO COG1378
Sugar-specific transcriptional regulator TrmB [Transcription];
68-225 1.11e-03

Sugar-specific transcriptional regulator TrmB [Transcription];


Pssm-ID: 440988 [Multi-domain]  Cd Length: 238  Bit Score: 40.77  E-value: 1.11e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643  68 EALAARIY-LINKAEKSLDLqyYIWDNDKIGALALHAIIRAADRGVKVRLLVDDNNAKKMEGIYLALDQhvnidiklynp 146
Cdd:COG1378   116 EAILERLReLIASAEEEILI--VLSPPELLLEELEEALEEALERGVKVRVLVSPEVLEVPERLEEEGEE----------- 182

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 147 yrfrhyramdmildlKRINRRMHNKSFIADNQISLIGGRNMSNQYY-NVSDNYQFSDVdvmlvgsasdeIIHSFDEYWND 225
Cdd:COG1378   183 ---------------VRVLPGLPGRLLIVDDKEALISVSEPDGEETaIWIEDPELAAL-----------LRELFETLWEK 236
 
Name Accession Description Interval E-value
PLDc_ymdC_like_2 cd09113
Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and ...
 291-520 1.02e-84

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: 261.39  E-value: 1.02e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 291 VKDAPSKIKDRASKEEHLNFQLLTHLEKPSSSVDIISAYFVPEQSGAEKLKDLADDGVQVRVLTNSFKANDVPVVHAFYA 370
Cdd:cd09113     1 LSDPPEKALKEAGPEPVLAYQLAELLKNAKREVLIVSPYFVPGDEGVALLAELARRGVRVRILTNSLAATDVPAVHSGYA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 371 KYREDLLANNVQLYEFLARPEMenlnththeisKKAKVSMKGLSRSSLHAKLMALDEKQVFIGSFNFDPRSAYLNTEIGV 450
Cdd:cd09113    81 RYRKRLLKAGVELYELKPDAAK-----------RKRLRGLFGSSRASLHAKSFVIDDRLVFVGSFNLDPRSAYLNTEMGL 149

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 451 ILNSPPLARAVHHTMDVNLSKYAYKLVLDAQQNIQWHMKnPQGETQILKKEPGMKWYQRAAMKITSWLPI 520
Cdd:cd09113   150 VIDSPELAAQLRAAMEEDLAPSAYWVLLLDDGGLVWETE-EDGKEKEYDSEPETSFWRRLGAWLLSLLPI 218
PLDc_ymdC_like_1 cd09111
Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and ...
 65-224 5.20e-83

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: 254.77  E-value: 5.20e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643  65 DPLEALAARIYLINKAEKSLDLQYYIWDNDKIGALALHAIIRAADRGVKVRLLVDDNNAKKMEGIYLALDQHVNIDIKLY 144
Cdd:cd09111     3 DGLDALAARLALIRSAERSIDLQYYIWHDDESGRLLLGELLEAADRGVRVRLLLDDLGTSGRDRLLAALDAHPNIEVRLF 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 145 NPYRFRHYRAMDMILDLKRINRRMHNKSFIADNQISLIGGRNMSNQYYNVSDNYQFSDVDVMLVGSASDEIIHSFDEYWN 224
Cdd:cd09111    83 NPFRNRGGRLLEFLTDFSRLNRRMHNKLFIVDGAVAIVGGRNIGDEYFGASPEVNFRDLDVLAVGPVVRQLSESFDTYWN 162
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 49-487 2.89e-80

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: 255.25  E-value: 2.89e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643  49 PLREKYPQLTG--YHVLYDPLEALAARIYLINKAEKSLDLQYYIWDNDKIGALALHAIIRAADRGVKVRLLVDDNNAKKM 126
Cdd:COG1502     4 PLAAGLPLVGGnrVTLLVDGDEAFAALLEAIEAARRSIDLEYYIFDDDEVGRRLADALIAAARRGVKVRVLLDGIGSRAL 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 127 EGIYLALDQHVNIDIKLYNPYRFRhyramdmildLKRINRRMHNKSFIADNQISLIGGRNMSNQYYNVSDNY-QFSDVDV 205
Cdd:COG1502    84 NRDFLRRLRAAGVEVRLFNPVRLL----------FRRLNGRNHRKIVVIDGRVAFVGGANITDEYLGRDPGFgPWRDTHV 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 206 MLVGSASDEIIHSFDEYWNDDyaySVKQLVNPQHytlryeslkqqleqhdqeatvqnyldlvtrskaieqwmthsikFDW 285
Cdd:COG1502   154 RIEGPAVADLQAVFAEDWNFA---TGEALPFPEP-------------------------------------------AGD 187

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 286 VSAEVVKDAPskikdrASKEEHLNFQLLTHLEKPSSSVDIISAYFVPEQSGAEKLKDLADDGVQVRVLTNSfkANDVPVV 365
Cdd:COG1502   188 VRVQVVPSGP------DSPRETIERALLAAIASARRRIYIETPYFVPDRSLLRALIAAARRGVDVRILLPA--KSDHPLV 259

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 366 HAFYAKYREDLLANNVQLYEFlarpemenlnththeiskkakvsmkglSRSSLHAKLMALDEKQVFIGSFNFDPRSAYLN 445
Cdd:COG1502   260 HWASRSYYEELLEAGVRIYEY---------------------------EPGFLHAKVMVVDDEWALVGSANLDPRSLRLN 312

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|..
gi 1844060643 446 TEIGVILNSPPLARAVHHTMDVNLSKyAYKLVLDAQQNIQWH 487
Cdd:COG1502   313 FEVNLVIYDPEFAAQLRARFEEDLAH-SREVTLEEWRKRPLR 353
PLDc_CLS_1 cd09110
Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Catalytic ...
 68-224 5.21e-30

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: 114.88  E-value: 5.21e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643  68 EALAARIYLINKAEKSLDLQYYIWDNDKIGALALHAIIRAADRGVKVRLLVDDNNAKKMEGIYL-ALDQHvNIDIKLYNP 146
Cdd:cd09110     5 EFFPALLEAIRAARHSIHLEYYIFRDDEIGRRFRDALIEKARRGVEVRLLYDGFGSLGLSRRFLrELREA-GVEVRAFNP 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1844060643 147 YRFRhyramdmiLDLKRINRRMHNKSFIADNQISLIGGRNMSNQYYNVSDNYQ-FSDVDVMLVGSASDEIIHSFDEYWN 224
Cdd:cd09110    84 LSFP--------LFLLRLNYRNHRKILVIDGKIAFVGGFNIGDEYLGKDPGFGpWRDTHVRIEGPAVADLQAAFLEDWY 154
PLDc_ybhO_like_2 cd09159
Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; ...
 312-461 9.33e-22

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: 92.22  E-value: 9.33e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 312 LLTHLEKPSSSVDIISAYFVPEQSGAEKLKDLADDGVQVRVLTNSfKANDVPVVHAFYAKYReDLLANNVQLYEFLARPe 391
Cdd:cd09159    16 YLVAIAAARRRIWIANAYFVPDRRLRRALIEAARRGVDVRLLLPG-KSDDPLTVAASRALYG-KLLRAGVRIFEYQPSM- 92

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 392 menlnththeiskkakvsmkglsrssLHAKLMALDEKQVFIGSFNFDPRSAYLNTEIGVILNSPPLARAV 461
Cdd:cd09159    93 --------------------------LHAKTAVIDGDWATVGSSNLDPRSLRLNLEANLVVEDPAFAAQL 136
PLDc_2 pfam13091
PLD-like domain;
312-458 3.61e-21

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 89.27  E-value: 3.61e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 312 LLTHLEKPSSSVDIISAYFVPEQSGAEKLKDLADDGVQVRVLTNSFKANDVPVVHAFYAKYREdLLANNVQLYEFLARPe 391
Cdd:pfam13091   1 LIDLINSAKKSIDIATYYFVPDREIIDALIAAAKRGVDVRIILDSNKDDAGGPKKASLKELRS-LLRAGVEIREYQSFL- 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1844060643 392 menlnththeiskkakvsmkglsrSSLHAKLMALDEKQVFIGSFNFDPRSAYLNTEIGVILNSPPLA 458
Cdd:pfam13091  79 ------------------------RSMHAKFYIIDGKTVIVGSANLTRRALRLNLENNVVIKDPELA 121
cls PRK01642
cardiolipin synthetase; Reviewed
 61-463 3.84e-21

cardiolipin synthetase; Reviewed


Pssm-ID: 234967 [Multi-domain]  Cd Length: 483  Bit Score: 96.39  E-value: 3.84e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643  61 HVLYDPLEALAARIYLINKAEKSLDLQYYIWDNDKIGALALHAIIRAADRGVKVRLLVDD---------NNAKKME--GI 129
Cdd:PRK01642  119 RLLTNGDETFQAIIRDIELARHYILMEFYIWRPDGLGDQVAEALIAAAKRGVRVRLLYDSigsfaffrsPYPEELRnaGV 198

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 130 YLALDQHVNidiklynpyRFRhyramdmiLDLKRINRRMHNKSFIADNQISLIGGRNMSNQYY-----NVSdnyQFSDVD 204
Cdd:PRK01642  199 EVVEFLKVN---------LGR--------VFRRRLDLRNHRKIVVIDGYIAYTGSMNVVDPEYfkqdpGVG---QWRDTH 258

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 205 VMLVGSASDE--IIHSFDEYWnddyaysvkqlvnpqhytlryeslkqqleqhdqeATVQNYLDLVTRSKAIEQWMThsik 282
Cdd:PRK01642  259 VRIEGPVVTAlqLIFAEDWEW----------------------------------ETGERILPPPPDVLIMPFEEA---- 300

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 283 fDWVSAEVVKDAPskikdrASKEE--HLNFQLLTHLEKpsSSVDIISAYFVPEQSGAEKLKDLADDGVQVRVLTNSFkaN 360
Cdd:PRK01642  301 -SGHTVQVIASGP------GDPEEtiHQFLLTAIYSAR--ERLWITTPYFVPDEDLLAALKTAALRGVDVRIIIPSK--N 369

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 361 DVPVV-HAFYAKYREdLLANNVQLYEFLarpemenlnththeiskkakvsmKGLsrssLHAKLMALDEKQVFIGSFNFDP 439
Cdd:PRK01642  370 DSLLVfWASRAFFTE-LLEAGVKIYRYE-----------------------GGL----LHTKSVLVDDELALVGTVNLDM 421

                         410       420
                  ....*....|....*....|....
gi 1844060643 440 RSAYLNTEIGVILNSPPLARAVHH 463
Cdd:PRK01642  422 RSFWLNFEITLVIDDTGFAADLAA 445
PLDc_CLS_2 cd09112
catalytic domain repeat 2 of bacterial cardiolipin synthase and similar proteins; This CD ...
 322-459 6.67e-16

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


Pssm-ID: 197211 [Multi-domain]  Cd Length: 174  Bit Score: 75.59  E-value: 6.67e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 322 SVDIISAYFVPEQSGAEKLKDLADDGVQVRVLTNsfKANDVPVVHAFYAKYREDLLANNVQLYEFlarpemenlnththe 401
Cdd:cd09112    26 SIYIQTPYFIPDESLLEALKTAALSGVDVRIMIP--GKPDHKLVYWASRSYFEELLKAGVKIYEY--------------- 88

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1844060643 402 iskkakvsmkglSRSSLHAKLMALDEKQVFIGSFNFDPRSAYLNTEIGVILNSPPLAR 459
Cdd:cd09112    89 ------------NKGFLHSKTLIVDDEIASVGTANLDIRSFELNFEVNAVIYDKEVAK 134
PLDc_EcCLS_like_1 cd09152
Catalytic domain, repeat 1, of Escherichia coli cardiolipin synthase and similar proteins; ...
 61-207 4.07e-15

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: 73.01  E-value: 4.07e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643  61 HVLYDPLEALAARIYLINKAEKSLDLQYYIWDNDKIGALALHAIIRAADRGVKVRLLVDDNNAKKM-EGIYLALDQHVNI 139
Cdd:cd09152     5 ELLTDYDAVIDRLIADIDAAKHHVHLLFYIWADDGTGDRVAEALERAAKRGVTCRLLLDAVGSRAFfRSSLWKRLREAGV 84

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 140 DIKLYNPYRF--RHYRAMDMildlkrinrRMHNKSFIADNQISLIGGRNMSNQYYNVSDNYQFSdVDVML 207
Cdd:cd09152    85 EVVEALPLRLfrRRLARFDL---------RNHRKIAVIDGRIAYTGSQNIIDPEFFKKAGGGPW-VDLMV 144
PLDc_CLS_unchar1_1 cd09156
Putative catalytic domain, repeat 1, of uncharacterized proteins similar to bacterial ...
 65-224 6.88e-15

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


Pssm-ID: 197253 [Multi-domain]  Cd Length: 154  Bit Score: 71.91  E-value: 6.88e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643  65 DPLEALAARIYLINKAEKSLDLQYYIWDNDKIGALALHAIIRAADRGVKVRLLVDDNNAKKMEGIYLALDQHVNIDIKLY 144
Cdd:cd09156     2 DGVEAYQALIQLIESAKHSIDVCTFILGDDATGRRVIDALARKAREGVEVRLLLDALGSFFLSRRALKKLRAAGGKVAFF 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 145 NP-YRFRhYRAmdmildlkRINRRMHNKSFIADNQISLIGGRNMSNQYYnvSDNYQ---FSDVDVMLVGSASDEIIHSFD 220
Cdd:cd09156    82 MPvFRLP-FRG--------RTNLRNHRKIAIADGSTAISGGMNLANEYM--GPEPDdgrWVDLSFLIEGPAVAQYQEVFR 150


                  ....
gi 1844060643 221 EYWN 224
Cdd:cd09156   151 SDWA 154
PRK12452 PRK12452
cardiolipin synthase;
76-448 1.02e-14

cardiolipin synthase;


Pssm-ID: 171510 [Multi-domain]  Cd Length: 509  Bit Score: 76.50  E-value: 1.02e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643  76 LINKAEKSLDLQYYIWDNDKIGALALHAIIRAADRGVKVRLLVDDNNAKKMEGIYLALDQHVNIDIKLYNPyrfrhyraM 155
Cdd:PRK12452  158 AIEQAKHHIHIQYYIYKSDEIGTKVRDALIKKAKDGVIVRFLYDGLGSNTLRRRFLQPMKEAGIEIVEFDP--------I 229

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 156 DMILDLKRINRRMHNKSFIADNQISLIGGRNMSNQYYNVSDNYQF-SDVDVMLVGSASDEIIHSFDEYW----NDDYAYS 230
Cdd:PRK12452  230 FSAWLLETVNYRNHRKIVIVDGEIGFTGGLNVGDEYLGRSKKFPVwRDSHLKVEGKALYKLQAIFLEDWlyasSGLNTYS 309

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 231 VKQLVNPQHYTLRyeslkqqlEQHDQEATVQnyldlvtrskaieqwmthsikfdwvsaeVVKDAPSkikdraSKEEHLNF 310
Cdd:PRK12452  310 WDPFMNRQYFPGK--------EISNAEGAVQ----------------------------IVASGPS------SDDKSIRN 347

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 311 QLLTHLEKPSSSVDIISAYFVPEQSGAEKLKDLADDGVQVRVLTNSfkANDVPVVHAFYAKYREDLLANNVQLYEFlarp 390
Cdd:PRK12452  348 TLLAVMGSAKKSIWIATPYFIPDQETLTLLRLSAISGIDVRILYPG--KSDSIISDQASQSYFTPLLKAGASIYSY---- 421

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1844060643 391 emenlnththeiskkakvsmkglSRSSLHAKLMALDEKQVFIGSFNFDPRSAYLNTEI 448
Cdd:PRK12452  422 -----------------------KDGFMHAKIVLVDDKIATIGTANMDVRSFELNYEI 456
PLDc_CLS_unchar2_1 cd09157
Putative catalytic domain, repeat 1, of uncharacterized proteins similar to bacterial ...
 68-191 4.22e-14

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: 69.90  E-value: 4.22e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643  68 EALAARIYLINKAEKSLDLQYYIWDNDKIGALALHAIIRAADRGVKVRLLVDDNNAKKMEG-IYLALdQHVNIDIKLYNP 146
Cdd:cd09157     5 EAYPAMLEAIDAARHSIALSSYIFDNDGVGREFVDALAEAVARGVDVRVLIDGVGARYSRPsIRRRL-RRAGVPVARFLP 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1844060643 147 YRfrhyramdMILDLKRINRRMHNKSFIADNQISLIGGRNMSNQY 191
Cdd:cd09157    84 PR--------LPPRLPFINLRNHRKILVVDGRTGFTGGMNIRDGH 120
PLDc_2 pfam13091
PLD-like domain;
74-223 2.17e-12

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 64.24  E-value: 2.17e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643  74 IYLINKAEKSLDLQ-YYIWDNDKIgalaLHAIIRAADRGVKVRLLVDDNNA------KKMEGIYLALDQHvNIDIKLYNP 146
Cdd:pfam13091   2 IDLINSAKKSIDIAtYYFVPDREI----IDALIAAAKRGVDVRIILDSNKDdaggpkKASLKELRSLLRA-GVEIREYQS 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1844060643 147 YrfrhyramdmildlkriNRRMHNKSFIADNQISLIGGRNMSNQ--YYNVSDNYQFSDVDVMlvgsasDEIIHSFDEYW 223
Cdd:pfam13091  77 F-----------------LRSMHAKFYIIDGKTVIVGSANLTRRalRLNLENNVVIKDPELA------QELEKEFDRLW 132
PLDc_EcCLS_like_2 cd09158
Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase and similar proteins; ...
 320-471 4.36e-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: 4.36e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 320 SSSVDIISAYFVPEQSGAEKLKDLADDGVQVRVLTnSFKaNDVPVVHAFYAKYREDLLANNVQLYEFlaRPEMenlntht 399
Cdd:cd09158    24 RRRVVITTPYFVPDESLLQALCTAALRGVEVTLIL-PAK-NDSFLVGAASRSYYEELLEAGVKIYLY--RGGL------- 92

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1844060643 400 heiskkakvsmkglsrssLHAKLMALDEKQVFIGSFNFDPRSAYLNTEIGVILNSPPLARAVHHTMDVNLSK 471
Cdd:cd09158    93 ------------------LHAKTVTVDDEVALVGSSNFDIRSFALNFEISLILYDKEFTAQLRAIQERYLAR 146
PRK11263 PRK11263
cardiolipin synthase ClsB;
77-466 1.68e-11

cardiolipin synthase ClsB;


Pssm-ID: 236888 [Multi-domain]  Cd Length: 411  Bit Score: 66.12  E-value: 1.68e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643  77 INKAEKSLDLQYYIWDNDKIGaLALH-AIIRAADRGVKVRLLVDDNNAKKMEGIYLALDQHVNIDIKLYNPyrfrHYRAM 155
Cdd:PRK11263   27 IAAAQEEILLETFILFEDKVG-KQLHaALLAAAQRGVKVEVLVDGYGSPDLSDEFVNELTAAGVRFRYFDP----RPRLL 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 156 DMildlkRIN--RRMHNKSFIADNQISLIGGRNMSNQYYNVSDNYQFSDVDVMLVGSASDEiIHSFdeywnddyaysVKQ 233
Cdd:PRK11263  102 GM-----RTNlfRRMHRKIVVIDGRIAFVGGINYSADHLSDYGPEAKQDYAVEVEGPVVAD-IHQF-----------ELE 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 234 LVNPQHYTLRYESLKQQLEQHDQEATVQnyLDLVTR-----SKAIEQWMTHSIkfdwvsaevvkdapskikdRASKEEhl 308
Cdd:PRK11263  165 ALPGQSAARRWWRRHHRAEENRQPGEAQ--ALLVWRdneehRDDIERHYLKAL-------------------RQARRE-- 221

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 309 nfqllthlekpsssVDIISAYFVPeqsGAEKLKDL---ADDGVQVRVLTNSfkANDVPVVHAFYAKYREDLLANNVQLYE 385
Cdd:PRK11263  222 --------------VIIANAYFFP---GYRLLRALrnaARRGVRVRLILQG--EPDMPIVRVGARLLYNYLLKGGVQIYE 282

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 386 FLARPemenlnththeiskkakvsmkglsrssLHAKLMALDEKQVFIGSFNFDPRSAYLNTEIGVILNSPPLARAVHHTM 465
Cdd:PRK11263  283 YCRRP---------------------------LHGKVALMDDHWATVGSSNLDPLSLSLNLEANLIIRDRAFNQTLRDNL 335


                  .
gi 1844060643 466 D 466
Cdd:PRK11263  336 N 336
PLDc_PaCLS_like_1 cd09155
Putative catalytic domain, repeat 1, of Pseudomonas aeruginosa cardiolipin synthase and ...
 77-224 2.34e-11

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: 61.87  E-value: 2.34e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643  77 INKAEKSLDLQYYIWDNDKIGALALHAIIRAADRGVKVRLLVDDNNAKKMEGIYLALDQHVNIDIKLYNPYRFRHYRAmd 156
Cdd:cd09155    14 IASAEEYILVQFYIIRDDDLGRELKDALIARAQAGVRVYLLYDEIGSHSLSRSYIERLRKAGVEVSAFNTTRGWGNRF-- 91

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1844060643 157 mildlkRINRRMHNKSFIADNQISLIGGRNMSNQYYNVSDNY-QFSDVDVMLVGSASDEIIHSFDEYWN 224
Cdd:cd09155    92 ------QLNFRNHRKIVVVDGQTAFVGGHNVGDEYLGRDPRLgPWRDTHVKLEGPAVQQLQLSFAEDWY 154
PLDc_CLS_unchar1_2 cd09162
Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial ...
 304-462 4.99e-11

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: 61.51  E-value: 4.99e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 304 KEEHLNFQLLTHLEKPSSSVDIISAYFVPEQSGAEKLKDLADDGVQVRVLTNSfKANDVPVVHAFYAkYREDLLANNVQL 383
Cdd:cd09162     8 PGDPLYEALLSAIFEAEHRIWIVTPYFVPDEVLLRALRLAARRGVDVRLIVPK-RSNHRIADLARGS-YLRDLQEAGAEI 85

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1844060643 384 YefLARPEMenlnththeiskkakvsmkglsrssLHAKLMALDEKQVFIGSFNFDPRSAYLNTEIGVILNSPPLARAVH 462
Cdd:cd09162    86 Y--LYQPGM-------------------------LHAKAVVVDDKLALVGSANLDMRSLFLNYEVAVFFYSPADIKELS 137
PLDc_Nuc_like cd09116
Catalytic domain of EDTA-resistant nuclease Nuc, vertebrate phospholipase D6, and similar ...
 62-224 8.84e-11

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


Pssm-ID: 197215 [Multi-domain]  Cd Length: 138  Bit Score: 60.00  E-value: 8.84e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643  62 VLYDPLEALAARIY-LINKAEKSLDLQYYIWDNDKIGAlalhAIIRAADRGVKVRLLVD-DNNAKKMEGIYLALDQHVNI 139
Cdd:cd09116     2 FLPRPQDNLERLIVaLIANAKSSIDVAMYALTDPEIAE----ALKRAAKRGVRVRIILDkDSLADNLSITLLALLSNLGI 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 140 DIKlynpyrfrhyramdmildLKRINRRMHNKSFIADNQISLIGGRNMSNQYYNVSDNyqfsdvdvMLVGSASDEIIHSF 219
Cdd:cd09116    78 PVR------------------TDSGSKLMHHKFIIIDGKIVITGSANWTKSGFHRNDE--------NLLIIDDPKLAASF 131


                  ....*
gi 1844060643 220 DEYWN 224
Cdd:cd09116   132 EEEFN 136
PLDc_unchar1_1 cd09127
Putative catalytic domain, repeat 1, of uncharacterized phospholipase D-like proteins; ...
 76-192 1.02e-10

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: 59.58  E-value: 1.02e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643  76 LINKAEKSLDLQYYIWDNDKIgalaLHAIIRAADRGVKVRLLVDDNNAKKM---EGIYLALDQHvNIDIKLYNP-YRFRH 151
Cdd:cd09127    16 AIASAKRSILLKMYEFTDPAL----EKALAAAAKRGVRVRVLLEGGPVGGIsraEKLLDYLNEA-GVEVRWTNGtARYRY 90

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1844060643 152 YramdmildlkrinrrmHNKSFIADNQISLIGGRNMSNQYY 192
Cdd:cd09127    91 T----------------HAKYIVVDDERALVLTENFKPSGF 115
PLDc_SF cd00138
Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D ...
 311-452 2.40e-10

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: 57.91  E-value: 2.40e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 311 QLLTHLEKPS-SSVDIISAYFVPEQSG--AEKLKDLADDGVQVRVLTNsfKANDVPVVHAfyAKYREDLLANNVQLYEFL 387
Cdd:cd00138     1 EALLELLKNAkESIFIATPNFSFNSADrlLKALLAAAERGVDVRLIID--KPPNAAGSLS--AALLEALLRAGVNVRSYV 76

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1844060643 388 ARPEMEnlnththeiskkakvsmkglsrSSLHAKLMALDEKQVFIGSFNFDPRSAYLNTEIGVIL 452
Cdd:cd00138    77 TPPHFF----------------------ERLHAKVVVIDGEVAYVGSANLSTASAAQNREAGVLV 119
PLDc_unchar1_2 cd09128
Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins; ...
 322-458 2.65e-10

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


Pssm-ID: 197226 [Multi-domain]  Cd Length: 142  Bit Score: 58.44  E-value: 2.65e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 322 SVDIISAYFVPEQSGAEKLKDLADDGVQVRVLTNSfkandvpvvhafyAKYREDLLANNVQLYEFLArpemenlnththe 401
Cdd:cd09128    25 SLLIQNEEMGDDAPILDALVDAAKRGVDVRVLLPS-------------AWSAEDERQARLRALEGAG------------- 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1844060643 402 iskkAKVSMKGLSRSSLHAKLMALDEKQVFIGSFNFDPRSAYLNTEIGVILNSPPLA 458
Cdd:cd09128    79 ----VPVRLLKDKFLKIHAKGIVVDGKTALVGSENWSANSLDRNREVGLIFDDPEVA 131
PLDc_SF cd00138
Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D ...
 76-190 3.56e-09

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


Pssm-ID: 197200 [Multi-domain]  Cd Length: 119  Bit Score: 54.83  E-value: 3.56e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643  76 LINKAEKSLDLQYYIWDNDKIGALaLHAIIRAADRGVKVRLLVDDNNAKK--MEGIYLALDQHVNIDIKLYNpyrfrhyr 153
Cdd:cd00138     6 LLKNAKESIFIATPNFSFNSADRL-LKALLAAAERGVDVRLIIDKPPNAAgsLSAALLEALLRAGVNVRSYV-------- 76

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1844060643 154 amdmilDLKRINRRMHNKSFIADNQISLIGGRNMSNQ 190
Cdd:cd00138    77 ------TPPHFFERLHAKVVVIDGEVAYVGSANLSTA 107
PLDc_CLS_unchar2_2 cd09163
Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial ...
 303-459 5.54e-09

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: 55.64  E-value: 5.54e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 303 SKEEHLNFQLLTHLEKPSSSVDIISAYFVPEQSGAEKLKDLADDGVQVRVLTNsfKANDVPVVH-AFYAKYREdLLANNV 381
Cdd:cd09163     7 EDLDKLRWTLLGAISAARHSIRIMTPYFLPDRTLITALQAAALRGVEVDIVLP--ERNNLPLVDwAMRANLWE-LLEHGV 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1844060643 382 QLYefLARPEMEnlnththeiskkakvsmkglsrsslHAKLMALDEKQVFIGSFNFDPRSAYLNTEIGVILNSPPLAR 459
Cdd:cd09163    84 RIY--LQPPPFD-------------------------HSKLMVVDGAWALIGSANWDPRSLRLNFELNLEVYDTALAG 134
PLDc_SMU_988_like_1 cd09154
Putative catalytic domain, repeat 1, of Streptococcus mutans uncharacterized protein SMU_988 ...
 77-224 3.26e-08

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: 52.92  E-value: 3.26e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643  77 INKAEKSLDLQYYI------WDndKIgalaLHAIIRAADRGVKVRLLVDD---------NNAKKMEgiylaldqhvNIDI 141
Cdd:cd09154    15 LKKAEKFIFMEYFIieegymWD--SI----LEILKEKAKEGVEVRIMYDDfgsittlpkDYPKELE----------KIGI 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 142 KLYnpyRFRHYRAMDMIldlkRINRRMHNKSFIADNQISLIGGRNMSNQYYNVSDNY-QFSDVDVMLVGSASDEIIHSFD 220
Cdd:cd09154    79 KCR---VFNPFKPILSL----YMNNRDHRKITVIDGKVAFTGGINLADEYINKIERFgYWKDTGIRLEGEAVWSLTVMFL 151


                  ....
gi 1844060643 221 EYWN 224
Cdd:cd09154   152 EMWN 155
PLDc_unchar1_2 cd09128
Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins; ...
 68-188 3.03e-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: 49.58  E-value: 3.03e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643  68 EALAAriyLINKAEKSLDLQY-YIWDNDKIgalaLHAIIRAADRGVKVRLLVDDNnakkmegiYLALDQHVNIDIKLYNp 146
Cdd:cd09128    13 EALLA---LIDSAEESLLIQNeEMGDDAPI----LDALVDAAKRGVDVRVLLPSA--------WSAEDERQARLRALEG- 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1844060643 147 yRFRHYRAMDMILDlkrinrRMHNKSFIADNQISLIGGRNMS 188
Cdd:cd09128    77 -AGVPVRLLKDKFL------KIHAKGIVVDGKTALVGSENWS 111
PLDc_vPLD6_like cd09171
Catalytic domain of vertebrate phospholipase D6 and similar proteins; Catalytic domain of ...
 77-190 5.61e-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: 48.76  E-value: 5.61e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643  77 INKAEKSLDLQYYIWDNDKIGAlalhAIIRAADRGVKVRLLVDDNNAkKMEGIYlaLDQHVNIDIKLynpyRFRHYRAMd 156
Cdd:cd09171    17 LLSARKSLDVCVFTITCDDLAD----AILDLHRRGVRVRIITDDDQM-EDKGSD--IGKLRKAGIPV----RTDLSSGH- 84

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1844060643 157 mildlkrinrrMHNKSFIADNQISLIGGRNMSNQ 190
Cdd:cd09171    85 -----------MHHKFAVIDGKILITGSFNWTRQ 107
PLDc_PaCLS_like_2 cd09161
Putative catalytic domain, repeat 2, of Pseudomonas aeruginosa cardiolipin synthase and ...
 325-463 7.61e-07

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


Pssm-ID: 197258 [Multi-domain]  Cd Length: 176  Bit Score: 49.21  E-value: 7.61e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 325 IISAYFVPEQSGAEKLKDLADDGVQVRVLTNSfKANDVPVVHAFYAkYREDLLANNVQLYEFLarpemenlnththeisk 404
Cdd:cd09161    29 IASPYFVPDEGVLAALQLAALRGVDVRILIPE-RPDHLLVYLASFS-YLPELIRAGVKVYRYQ----------------- 89

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1844060643 405 kakvsmKGLsrssLHAKLMALDEKQVFIGSFNFDPRSAYLNTEIGVILNSPPLARAVHH 463
Cdd:cd09161    90 ------PGF----LHQKVVLVDDELAAVGTANLDNRSFRLNFEITALVADPGFAQEVEA 138
PLDc_Nuc cd09170
Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar ...
 69-179 7.93e-07

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


Pssm-ID: 197267 [Multi-domain]  Cd Length: 142  Bit Score: 48.67  E-value: 7.93e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643  69 ALAARIYLINKAEKSLDLQYYIWDNDKIGAlalhAIIRAADRGVKVRLLVDdnnAKKMEGIYLALD--QHVNIDIKLYNp 146
Cdd:cd09170    12 ARELILDVIDSARRSIDVAAYSFTSPPIAR----ALIAAKKRGVDVRVVLD---KSQAGGKYSALNylANAGIPVRIDD- 83

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1844060643 147 yrfrHYRAmdmildlkrinrrMHNKSFIADNQI 179
Cdd:cd09170    84 ----NYAI-------------MHNKVMVIDGKT 99
PLDc_vPLD4_1 cd09145
Putative catalytic domain, repeat 1, of vertebrate phospholipase PLD4; Putative catalytic ...
 374-464 8.96e-07

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: 49.14  E-value: 8.96e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 374 EDLLANNVQLYEFLARPEMENLNTHTHEISKKA----KVSMKGLSRSSLHAKLMALDEKQVFIGSFNFDPRSAYLNTEIG 449
Cdd:cd09145    68 AELLSRNVSVRAAASIPTLAANSTDLKILRQKGahvrKVNFGRLTGGVLHSKFWIIDKKHIYVGSANMDWRSLTQVKELG 147

                          90
                  ....*....|....*.
gi 1844060643 450 -VILNSPPLARAVHHT 464
Cdd:cd09145   148 aVIYNCSSLAKDLHKT 163
PRK13912 PRK13912
nuclease NucT; Provisional
 46-199 1.37e-06

nuclease NucT; Provisional


Pssm-ID: 184389 [Multi-domain]  Cd Length: 177  Bit Score: 48.62  E-value: 1.37e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643  46 IVLPLREKYPQLTGYHVLYDPLEALAARIYLINKAEKSLDLQYYIWDNDKIGalalHAIIRAADRGVKVRLLVDDNNAKK 125
Cdd:PRK13912   11 LVGCLGVLQAKSSLYFLPYEQKDALNKLVSLISNARSSIKIAIYSFTHKDIA----KALKSAAKRGVKISIIYDYESNHN 86

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1844060643 126 MEGIYLA-LDQHVNIDIKLYNpyrfrhyramdmilDLKRINRR----MHNKSFIADNQISLIGGRNMSNQYYnvSDNYQ 199
Cdd:PRK13912   87 NDQSTIGyLDKYPNIKVCLLK--------------GLKAKNGKyygiMHQKVAIIDDKIVVLGSANWSKNAF--ENNYE 149
PLDc_vPLD3_4_5_like_1 cd09106
Putative catalytic domain, repeat 1, of vertebrate phospholipases, PLD3, PLD4 and PLD5, viral ...
 338-451 3.92e-06

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: 46.86  E-value: 3.92e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 338 EKLKDLADDGVQVRVLTNSfkandvPVVHAFYAKYREDLLANNVQLYeflarpemenlnththeiskkaKVSM-KGLSRS 416
Cdd:cd09106    63 NALLEAAKRGVKIRILQDK------PSKDKPDEDDLELAALGGAEVR----------------------SLDFtKLIGGG 114

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1844060643 417 SLHAKLMALDEKQVFIGSFNFDPRSayLNT--EIGVI 451
Cdd:cd09106   115 VLHTKFWIVDGKHFYLGSANLDWRS--LTQvkELGVY 149
PLDc_vPLD3_4_5_like_1 cd09106
Putative catalytic domain, repeat 1, of vertebrate phospholipases, PLD3, PLD4 and PLD5, viral ...
 55-188 2.67e-05

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


Pssm-ID: 197205 [Multi-domain]  Cd Length: 153  Bit Score: 44.54  E-value: 2.67e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643  55 PQLTGYHVLYDPLEALAARIYLINKAEKSLDLQYYIW------DNDKI----GALALHAIIRAADRGVKVRLLVDDNNAK 124
Cdd:cd09106     6 PEGLTFLSSSSHLSTFEAWMELISSAKKSIDIASFYWnlrgtdTNPDSsaqeGEDIFNALLEAAKRGVKIRILQDKPSKD 85

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1844060643 125 KMEGIYLALDQHVNIdiklynpyrfrHYRAMDMilDLKRINRRMHNKSFIADNQISLIGGRNMS 188
Cdd:cd09106    86 KPDEDDLELAALGGA-----------EVRSLDF--TKLIGGGVLHTKFWIVDGKHFYLGSANLD 136
PLDc_vPLD3_4_5_like_2 cd09107
Putative catalytic domain, repeat 2, of vertebrate phospholipases, PLD3, PLD4 and PLD5, viral ...
 55-224 3.70e-05

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: 44.55  E-value: 3.70e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643  55 PQLTGYHVLYDpLEALaarIYLINKAEKSLDLQ--------------YYIWDNDKigalalhAIIRAA-DRGVKVRLLV- 118
Cdd:cd09107     7 PELCPPGRTDD-LDAL---LSTIDSAKKFIDISvmdyvplsryadprKYWPVIDN-------ALRRAAvDRGVKVRLLVs 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 119 DDNNAKKMEGIYLALDQ-------HVNIDIKLYN-PyrfrhyRAMDMILDLKRINrrmHNKSFIADNqISLIGGRNMSNQ 190
Cdd:cd09107    76 NWKHTDPSMDAFLKSLQllksgvgNGDIEVKIFTvP------GDQSTKIPFARVN---HAKYMVTDE-RAYIGTSNWSGD 145

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1844060643 191 YYNVSDNYQFSDVDVMLVgSASDEIihsFDEYWN 224
Cdd:cd09107   146 YFYNTAGVSLVINDPAIV-QQLKDV---FERDWN 175
cls PRK01642
cardiolipin synthetase; Reviewed
 54-189 4.08e-05

cardiolipin synthetase; Reviewed


Pssm-ID: 234967 [Multi-domain]  Cd Length: 483  Bit Score: 45.93  E-value: 4.08e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643  54 YPQLTGYHVLydpLEAlaariylINKAEKSLDLQ--YYIWDNDkigalALHAIIRAADRGVKVRLLVDDNNAKKMegIYL 131
Cdd:PRK01642  314 DPEETIHQFL---LTA-------IYSARERLWITtpYFVPDED-----LLAALKTAALRGVDVRIIIPSKNDSLL--VFW 376

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1844060643 132 A--------LDQHVNIdiklynpYRFRHyramdmilDLkrinrrMHNKSFIADNQISLIGGRNMSN 189
Cdd:PRK01642  377 AsrafftelLEAGVKI-------YRYEG--------GL------LHTKSVLVDDELALVGTVNLDM 421
PLDc_SMU_988_like_2 cd09160
Putative catalytic domain, repeat 2, of Streptococcus mutans uncharacterized protein SMU_988 ...
 323-452 8.85e-05

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: 43.25  E-value: 8.85e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 323 VDIISAYFVPEQSGAEKLKDLADDGVQVRVLTNSFKanDVPVVHAFYAKYREDLLANNVQLYEFlarpemenlnththei 402
Cdd:cd09160    27 VYITTPYLILDDEMLDALCLAAKRGVDVRIITPHIP--DKKYVFLVTRSNYPELLEAGVKIYEY---------------- 88

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1844060643 403 skkakvsMKGLsrssLHAKLMALDEKQVFIGSFNFDPRSAYLNTEIGVIL 452
Cdd:cd09160    89 -------TPGF----IHAKTFVSDDKAAVVGTINLDYRSLYLHFECGVYM 127
PLDc_CLS_2 cd09112
catalytic domain repeat 2 of bacterial cardiolipin synthase and similar proteins; This CD ...
 74-187 9.24e-05

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: 43.24  E-value: 9.24e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643  74 IYLINKAEKSLDLQ--YYIWDNDkigalALHAIIRAADRGVKVRLLVDDNNAKKMegIYLALDQHVN------IDIKLYN 145
Cdd:cd09112    17 LKAINSAKKSIYIQtpYFIPDES-----LLEALKTAALSGVDVRIMIPGKPDHKL--VYWASRSYFEellkagVKIYEYN 89

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1844060643 146 PyRFrhyramdmildlkrinrrMHNKSFIADNQISLIGGRNM 187
Cdd:cd09112    90 K-GF------------------LHSKTLIVDDEIASVGTANL 112
PLDc smart00155
Phospholipase D. Active site motifs; Phosphatidylcholine-hydrolyzing phospholipase D (PLD) ...
 418-441 1.03e-04

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


Pssm-ID: 197546 [Multi-domain]  Cd Length: 28  Bit Score: 39.30  E-value: 1.03e-04
                           10        20
                   ....*....|....*....|....
gi 1844060643  418 LHAKLMALDEKQVFIGSFNFDPRS 441
Cdd:smart00155   5 LHTKLMIVDDEIAYIGSANLDGRS 28
PLDc_unchar1_1 cd09127
Putative catalytic domain, repeat 1, of uncharacterized phospholipase D-like proteins; ...
 337-461 1.11e-04

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: 42.25  E-value: 1.11e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 337 AEKLKDLADDGVQVRVLTNSFKANDVPVVHAFYAkyreDLLANNVQlyeflarpemenlnthTHEISKKAKvsmkglsRS 416
Cdd:cd09127    37 EKALAAAAKRGVRVRVLLEGGPVGGISRAEKLLD----YLNEAGVE----------------VRWTNGTAR-------YR 89

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1844060643 417 SLHAKLMALDEKQVFIGSFNFDPRSAYLNTEIGVILNSPPLARAV 461
Cdd:cd09127    90 YTHAKYIVVDDERALVLTENFKPSGFTGTRGFGVVTDDPAVVAEI 134
PLDc_Nuc_like cd09116
Catalytic domain of EDTA-resistant nuclease Nuc, vertebrate phospholipase D6, and similar ...
 316-460 4.15e-04

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


Pssm-ID: 197215 [Multi-domain]  Cd Length: 138  Bit Score: 40.74  E-value: 4.15e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 316 LEKPSSSVDIiSAYFVPEQSGAEKLKDLADDGVQVRVLTNSfkandvpvvhafyaKYREDLLANNvqlyeflarpemenl 395
Cdd:cd09116    18 IANAKSSIDV-AMYALTDPEIAEALKRAAKRGVRVRIILDK--------------DSLADNLSIT--------------- 67

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1844060643 396 nthTHEISKKAKVSMKGLSRSS-LHAKLMALDEKQVFIGSFNFDPRSAYLNTEIGVILNSPPLARA 460
Cdd:cd09116    68 ---LLALLSNLGIPVRTDSGSKlMHHKFIIIDGKIVITGSANWTKSGFHRNDENLLIIDDPKLAAS 130
PLDc_unchar2_2 cd09130
Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins; ...
 77-224 4.47e-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: 40.69  E-value: 4.47e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643  77 INKAEK--SLDL-QYYIWDNDKIGALalhaiIRAADRGVKVRLLVDDN-NAKKME--GI-------YLALDQHVNIDIKL 143
Cdd:cd09130    14 INSARAgdKIWIgMFYLADRDVIKAL-----IDAANRGVDVRLILDPNkDAFGREknGIpnrpvaaELMKKTKGKIQIRW 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 144 YNpyrfrhyramdmildlkRINRRMHNK-SFIADN-QISLIGG------RNMSNqyYNVsdnyqfsDVDVMLVGSASDEI 215
Cdd:cd09130    89 YN-----------------TGGEQFHTKlLLIKKKgQAIIIGGsanftrRNLRD--YNL-------ETDLKILAPNDSPV 142

                         170
                  ....*....|...
gi 1844060643 216 IHSFDEY----WN 224
Cdd:cd09130   143 SKDVDAYfdrlWN 155
PLDc_CLS_unchar1_2 cd09162
Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial ...
 65-189 6.64e-04

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: 40.71  E-value: 6.64e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643  65 DPLEALAarIYLINKAEKSLDL--QYYIWDndkigALALHAIIRAADRGVKVRLLVDDNNAKKM----EGIYLALDQHVN 138
Cdd:cd09162    10 DPLYEAL--LSAIFEAEHRIWIvtPYFVPD-----EVLLRALRLAARRGVDVRLIVPKRSNHRIadlaRGSYLRDLQEAG 82

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1844060643 139 IDIKLYNPyrfrhyrAMdmildlkrinrrMHNKSFIADNQISLIGGRNMSN 189
Cdd:cd09162    83 AEIYLYQP-------GM------------LHAKAVVVDDKLALVGSANLDM 114
PLDc_unchar3 cd09131
Putative catalytic domain of uncharacterized phospholipase D-like proteins; Putative catalytic ...
 414-458 8.92e-04

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: 39.63  E-value: 8.92e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1844060643 414 SRSSLHAKLMALDEKQVFIGSFNFDPRSAYLNTEIGVILNSPPLA 458
Cdd:cd09131    89 PSVTTHTKLVVIDGRTVYVGSHNWTYSALDYNHEASVLIESPEVA 133
YrhO COG1378
Sugar-specific transcriptional regulator TrmB [Transcription];
68-225 1.11e-03

Sugar-specific transcriptional regulator TrmB [Transcription];


Pssm-ID: 440988 [Multi-domain]  Cd Length: 238  Bit Score: 40.77  E-value: 1.11e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643  68 EALAARIY-LINKAEKSLDLqyYIWDNDKIGALALHAIIRAADRGVKVRLLVDDNNAKKMEGIYLALDQhvnidiklynp 146
Cdd:COG1378   116 EAILERLReLIASAEEEILI--VLSPPELLLEELEEALEEALERGVKVRVLVSPEVLEVPERLEEEGEE----------- 182

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 147 yrfrhyramdmildlKRINRRMHNKSFIADNQISLIGGRNMSNQYY-NVSDNYQFSDVdvmlvgsasdeIIHSFDEYWND 225
Cdd:COG1378   183 ---------------VRVLPGLPGRLLIVDDKEALISVSEPDGEETaIWIEDPELAAL-----------LRELFETLWEK 236
PLDc_Nuc_like_unchar1_1 cd09172
Putative catalytic domain, repeat 1, of uncharacterized hypothetical proteins similar to Nuc, ...
 67-177 1.51e-03

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: 39.26  E-value: 1.51e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643  67 LEALAARIYLINKAEKSLDLQYYIWDNDKIgalaLHAIIRAADRGVKVRLLVDDN--NAKKMEGIYLALDQHVNIDIKly 144
Cdd:cd09172     8 REALLAFLDEARSAGSSIRLAIYELDDPEI----IDALKAAKDRGVRVRIILDDSsvTGDPTEESAAATLSKGPGALV-- 81

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1844060643 145 npyRFRHYRAMdmildlkrinrrMHNKSFIADN 177
Cdd:cd09172    82 ---KRRHSSGL------------MHNKFLVVDR 99
PLDc_Nuc_like_unchar1_2 cd09173
Putative catalytic domain, repeat 2, of uncharacterized hypothetical proteins similar to Nuc, ...
 330-458 2.29e-03

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


Pssm-ID: 197270 [Multi-domain]  Cd Length: 159  Bit Score: 38.87  E-value: 2.29e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 330 FVP-EQSGAEKLKDLADDGVQVR-VLTNSFkandvpvvhaFYAKYREDLLANNVQLYEFLARPEMENLNTHTHEISKkak 407
Cdd:cd09173    30 FDFsDGALLDALLAAADAGLFVRgLVDKRF----------GGRYYSAAADMGGIDPVYPAALAPDEPEKFVGEPLLG--- 96

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1844060643 408 VSMKglsrssLHAKLMALD----EKQVFIGSFNFDPRSAYLNTEIGVILNSPPLA 458
Cdd:cd09173    97 VGDK------LHHKFMVIDpfgdDPVVITGSHNFSGAANDNNDENLLVIRDPAIA 145
PLDc_Nuc_like_unchar1_1 cd09172
Putative catalytic domain, repeat 1, of uncharacterized hypothetical proteins similar to Nuc, ...
 311-460 2.35e-03

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: 38.49  E-value: 2.35e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 311 QLLTHLEKPSSSVDIiSAYFVPEQSGAEKLKDLADDGVQVRVLTnsfkanDVPVVHAFYAKYREdllannvqlyeFLARP 390
Cdd:cd09172    13 AFLDEARSAGSSIRL-AIYELDDPEIIDALKAAKDRGVRVRIIL------DDSSVTGDPTEESA-----------AATLS 74

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1844060643 391 EMENLNTHTHEiskkakvsmkglSRSSLHAKLMALDEKQ----VFIGSFNFDPRSAYLNTEIGVILNSPPLARA 460
Cdd:cd09172    75 KGPGALVKRRH------------SSGLMHNKFLVVDRKDgpnrVLTGSTNFTTSGLYGQSNNVLIFRNPAFAAA 136
PLDc_ybhO_like_2 cd09159
Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; ...
 71-118 4.18e-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: 4.18e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1844060643  71 AARIYL--INKAEKSLDLQ--YYIWDNdkigaLALHAIIRAADRGVKVRLLV 118
Cdd:cd09159    12 IRRAYLvaIAAARRRIWIAnaYFVPDR-----RLRRALIEAARRGVDVRLLL 58
PLDc_unchar3 cd09131
Putative catalytic domain of uncharacterized phospholipase D-like proteins; Putative catalytic ...
 63-191 4.59e-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: 37.71  E-value: 4.59e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643  63 LYDPLealaarIYLINKAEKSLDLQYYIW-DNDKIGALA---LHAIIRAADRGVKVRLLVDDNNAKKmegiylaldqhvn 138
Cdd:cd09131     4 YYPAL------LDLINNAKRSIYIAMYMFkYYENPGNGVntlLEALIDAHKRGVDVKVVLEDSIDDD------------- 64

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1844060643 139 iDIKLYNPYRFRHYRAMDMILDLKRINRRMHNKSFIADNQISLIGGRNMSNQY 191
Cdd:cd09131    65 -EVTEENDNTYRYLKDNGVEVRFDSPSVTTHTKLVVIDGRTVYVGSHNWTYSA 116
PLDc pfam00614
Phospholipase D Active site motif; Phosphatidylcholine-hydrolysing phospholipase D (PLD) ...
 417-441 5.42e-03

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


Pssm-ID: 395489 [Multi-domain]  Cd Length: 28  Bit Score: 34.32  E-value: 5.42e-03
                          10        20
                  ....*....|....*....|....*
gi 1844060643 417 SLHAKLMALDEKQVFIGSFNFDPRS 441
Cdd:pfam00614   4 RLHRKIVVVDDELAYIGGANLDGRS 28
PLDc_Nuc cd09170
Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar ...
 419-460 5.48e-03

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


Pssm-ID: 197267 [Multi-domain]  Cd Length: 142  Bit Score: 37.50  E-value: 5.48e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1844060643 419 HAKLMALDEKQVFIGSFNFDPRSAYLNTEIGVIL-NSPPLARA 460
Cdd:cd09170    89 HNKVMVIDGKTVITGSFNFTASAEKRNAENLLVIrNPPELAQQ 131
PLDc_Bfil_DEXD_like cd09117
Catalytic domain of type II restriction endonucleases BfiI and NgoFVII, and uncharacterized ...
 311-452 7.98e-03

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


Pssm-ID: 197216 [Multi-domain]  Cd Length: 117  Bit Score: 36.60  E-value: 7.98e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844060643 311 QLLTHLEKPSSSVDIISAYFvpEQSGAEKLKDLADDGVQVRVLTNSFKANDVPVVHAFYAKYRedllANNVQLYEFLARP 390
Cdd:cd09117     5 ELLTRLIERADTIRIAVAFA--SAGGAIKLLDKFREGKKIRLIVGLDFGGTSPADFALKLLLA----LGNLNVRIFDAGP 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1844060643 391 emenlnththeiskkakvsmkglsrsSLHAKLMAL---DEKQVFIGSFNFDPRSAYLNTEIGVIL 452
Cdd:cd09117    79 --------------------------LLHAKLYLFendDPTRAIVGSANLTQGGLSGNIEAAVVI 117
PLDc_vPLD3_1 cd09144
Putative catalytic domain, repeat 1, of vertebrate phospholipase PLD3; Putative catalytic ...
 408-459 8.67e-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: 37.24  E-value: 8.67e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1844060643 408 VSMKGLSRSSLHAKLMALDEKQVFIGSFNFDPRSAYLNTEIG-VILNSPPLAR 459
Cdd:cd09144   107 VDMRKLTTGVLHTKFWVVDKKHFYIGSANMDWRSLTQVKELGaVVYNCSCLAE 159
 
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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