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Conserved domains on  [gi|446572968|ref|WP_000650314|]
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MULTISPECIES: cardiolipin synthase ClsB [Enterobacteriaceae]

Protein Classification

cardiolipin synthase B( domain architecture ID 11485287)

cardiolipin synthase B catalyzes the formation of cardiolipin, but its substrates have not been definitively established

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK11263 PRK11263
cardiolipin synthase ClsB;
2-412 0e+00

cardiolipin synthase ClsB;


:

Pssm-ID: 236888 [Multi-domain]  Cd Length: 411  Bit Score: 814.18  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968   2 KCSWREGNKIELLENGEQYYPAVFKAIGEAQERIILETFIWFEDDVGKQLHAALLAAAQRGVKAEVLLDGYGSPDLSDEF 81
Cdd:PRK11263   1 KCSWREGNRIQLLENGEQYYPRVFEAIAAAQEEILLETFILFEDKVGKQLHAALLAAAQRGVKVEVLVDGYGSPDLSDEF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968  82 VNELTAAGVVFRYYDPRPRLFGMRTNVFRRMHRKIVVIDARIAFIGGLNYSAEHMSSYGPEAKQDYAVRLEGPIVEDILQ 161
Cdd:PRK11263  81 VNELTAAGVRFRYFDPRPRLLGMRTNLFRRMHRKIVVIDGRIAFVGGINYSADHLSDYGPEAKQDYAVEVEGPVVADIHQ 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 162 FELENLPGQSAARRWWRRHHKAEENRQPGEAQVLLVWRDNEEHRDDIERHYLKMLTQAQREVIIANAYFFPGYRFLHALR 241
Cdd:PRK11263 161 FELEALPGQSAARRWWRRHHRAEENRQPGEAQALLVWRDNEEHRDDIERHYLKALRQARREVIIANAYFFPGYRLLRALR 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 242 KAARRGVRIKLIIQGEPDMPIVRVGARLLYNYLVKGGVQVFEYRRRPLHGKVALMDDHWATVGSSNLDPLSLSLNLEANV 321
Cdd:PRK11263 241 NAARRGVRVRLILQGEPDMPIVRVGARLLYNYLLKGGVQIYEYCRRPLHGKVALMDDHWATVGSSNLDPLSLSLNLEANL 320

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 322 IIHDRHFNQTLRDNLNGIIAADCQQVDETMLPKRTWWNLTKSVLAFHFLRHFPALVGWLPAHTPRLTQVDPPAQPTMETQ 401
Cdd:PRK11263 321 IIRDRAFNQTLRDNLNGLIAADCQQVDETMLPKRTWWRLTKSVLAFHFLRHFPALAGWLPAHTPRLAQVDPPAQPTMETQ 400

                        410
                 ....*....|.
gi 446572968 402 DRVETENTGVK 412
Cdd:PRK11263 401 DRVETENTGVK 411
 
Name Accession Description Interval E-value
PRK11263 PRK11263
cardiolipin synthase ClsB;
2-412 0e+00

cardiolipin synthase ClsB;


Pssm-ID: 236888 [Multi-domain]  Cd Length: 411  Bit Score: 814.18  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968   2 KCSWREGNKIELLENGEQYYPAVFKAIGEAQERIILETFIWFEDDVGKQLHAALLAAAQRGVKAEVLLDGYGSPDLSDEF 81
Cdd:PRK11263   1 KCSWREGNRIQLLENGEQYYPRVFEAIAAAQEEILLETFILFEDKVGKQLHAALLAAAQRGVKVEVLVDGYGSPDLSDEF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968  82 VNELTAAGVVFRYYDPRPRLFGMRTNVFRRMHRKIVVIDARIAFIGGLNYSAEHMSSYGPEAKQDYAVRLEGPIVEDILQ 161
Cdd:PRK11263  81 VNELTAAGVRFRYFDPRPRLLGMRTNLFRRMHRKIVVIDGRIAFVGGINYSADHLSDYGPEAKQDYAVEVEGPVVADIHQ 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 162 FELENLPGQSAARRWWRRHHKAEENRQPGEAQVLLVWRDNEEHRDDIERHYLKMLTQAQREVIIANAYFFPGYRFLHALR 241
Cdd:PRK11263 161 FELEALPGQSAARRWWRRHHRAEENRQPGEAQALLVWRDNEEHRDDIERHYLKALRQARREVIIANAYFFPGYRLLRALR 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 242 KAARRGVRIKLIIQGEPDMPIVRVGARLLYNYLVKGGVQVFEYRRRPLHGKVALMDDHWATVGSSNLDPLSLSLNLEANV 321
Cdd:PRK11263 241 NAARRGVRVRLILQGEPDMPIVRVGARLLYNYLLKGGVQIYEYCRRPLHGKVALMDDHWATVGSSNLDPLSLSLNLEANL 320

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 322 IIHDRHFNQTLRDNLNGIIAADCQQVDETMLPKRTWWNLTKSVLAFHFLRHFPALVGWLPAHTPRLTQVDPPAQPTMETQ 401
Cdd:PRK11263 321 IIRDRAFNQTLRDNLNGLIAADCQQVDETMLPKRTWWRLTKSVLAFHFLRHFPALAGWLPAHTPRLAQVDPPAQPTMETQ 400

                        410
                 ....*....|.
gi 446572968 402 DRVETENTGVK 412
Cdd:PRK11263 401 DRVETENTGVK 411
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 5-367 1.70e-113

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: 336.53  E-value: 1.70e-113
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968   5 WREGNKIELLENGEQYYPAVFKAIGEAQERIILETFIWFEDDVGKQLHAALLAAAQRGVKAEVLLDGYGSPDLSDEFVNE 84
Cdd:COG1502   11 LVGGNRVTLLVDGDEAFAALLEAIEAARRSIDLEYYIFDDDEVGRRLADALIAAARRGVKVRVLLDGIGSRALNRDFLRR 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968  85 LTAAGVVFRYYDPRPRLFGmrtNVFRRMHRKIVVIDARIAFIGGLNYSAEHMSSY-GPEAKQDYAVRLEGPIVEDILQFe 163
Cdd:COG1502   91 LRAAGVEVRLFNPVRLLFR---RLNGRNHRKIVVIDGRVAFVGGANITDEYLGRDpGFGPWRDTHVRIEGPAVADLQAV- 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 164 lenlpgqsAARRW-WRRHHKAEENRQPGEAQVLLVWRDNEEHRDDIERHYLKMLTQAQREVIIANAYFFPGYRFLHALRK 242
Cdd:COG1502  167 --------FAEDWnFATGEALPFPEPAGDVRVQVVPSGPDSPRETIERALLAAIASARRRIYIETPYFVPDRSLLRALIA 238

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 243 AARRGVRIKLIIQGEPDMPIVRVGARLLYNYLVKGGVQVFEYRRRPLHGKVALMDDHWATVGSSNLDPLSLSLNLEANVI 322
Cdd:COG1502  239 AARRGVDVRILLPAKSDHPLVHWASRSYYEELLEAGVRIYEYEPGFLHAKVMVVDDEWALVGSANLDPRSLRLNFEVNLV 318

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....*
gi 446572968 323 IHDRHFNQTLRDNLNGIIaADCQQVDETMLPKRTWWNLTKSVLAF 367
Cdd:COG1502  319 IYDPEFAAQLRARFEEDL-AHSREVTLEEWRKRPLRRLRERLARL 362
PLDc_ybhO_like_2 cd09159
Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; ...
 197-366 2.15e-65

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: 206.24  E-value: 2.15e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 197 VWRDNEEHRDDIERHYLKMLTQAQREVIIANAYFFPGYRFLHALRKAARRGVRIKLIIQGEPDMPIVRVGARLLYNYLVK 276
Cdd:cd09159    1 VVSDPRRRRSSIRRAYLVAIAAARRRIWIANAYFVPDRRLRRALIEAARRGVDVRLLLPGKSDDPLTVAASRALYGKLLR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 277 GGVQVFEYRRRPLHGKVALMDDHWATVGSSNLDPLSLSLNLEANVIIHDRHFNQTLRDNLNGIIAADCQQVDETMLPKRT 356
Cdd:cd09159   81 AGVRIFEYQPSMLHAKTAVIDGDWATVGSSNLDPRSLRLNLEANLVVEDPAFAAQLEELFEEDLARSREITLEEWRRRPL 160

                        170
                 ....*....|
gi 446572968 357 WWNLTKSVLA 366
Cdd:cd09159  161 WQRLLEWLAY 170
bac_cardiolipin TIGR04265
cardiolipin synthase; This model is based on experimentally characterized bacterial ...
 7-358 2.48e-49

cardiolipin synthase; This model is based on experimentally characterized bacterial cardiolipin synthases (cls) from E. coli, Staphylococcus aureus (two), and Bacillus pseudofirmus OF4. This model describes just one of several homologous but non-orthologous forms of cls. The cutoff score is set arbitrarily high to avoid false-positives. Note that there are two enzymatic activites called cardiolipin synthase. This model represents type 1, which does not rely on a CDP-linked donor, but instead does a reversible transfer of a phosphatidyl group from one phosphatidylglycerol molecule to another.


Pssm-ID: 211988 [Multi-domain]  Cd Length: 483  Bit Score: 173.82  E-value: 2.48e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968    7 EGNKIELLENGEQYYPAVFKAIGEAQERIILETFIWFEDDVGKQLHAALLAAAQRGVKAEVLLDGYGSPDLSDEFVNELT 86
Cdd:TIGR04265 117 EGNQLKLMTDGDDVYDALIQDIKNARHYIHLEYYIWQPDGLGDQILESLMAKAKQGVHVRILYDDVGSVALFKSWPELFR 196

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968   87 AAGVVFRYYDPR--PRLFgMRTNVfrRMHRKIVVIDARIAFIGGLNYSAEHMssyGPEAK----QDYAVRLEGPIVEDI- 159
Cdd:TIGR04265 197 NAGGEVVAFFPVklPLLN-LRMNN--RNHRKIIVIDGQIGYVGGFNIGDEYL---GKDAKfgywRDTHLRIEGDAVTALq 270

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968  160 LQFELEnlpgqsaarrWWRRHHK----------AEENRQPGEAQVLLVWRDNEEHRDDIERHYLKMLTQAQREVIIANAY 229
Cdd:TIGR04265 271 LIFILD----------WNSQTGRriipydpdyfPMPNEQAGGHGIQIIASGPDFPWEQIKYGYLKMIYSAKKSIYIQSPY 340

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968  230 FFPGYRFLHALRKAARRGVRIKLIIQGEPDMPIVRVGARLLYNYLVKGGVQVFEYRRRPLHGKVALMDDHWATVGSSNLD 309
Cdd:TIGR04265 341 FIPDDDLLHAIKIAALSGVDVSIMIPNKPDHPLVFWASRSNFTELLAAGVKIYQYENGFLHSKSVLVDDEIASVGTANMD 420

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*....
gi 446572968  310 PLSLSLNLEANVIIHDRHFNQTLRDNLNGIIAADcQQVDETMLPKRTWW 358
Cdd:TIGR04265 421 MRSFWLNFEVNAFIYDKGFAKDLAAAYDDDISRS-RQLTKRLYAKRPLW 468
PLDc_2 pfam13091
PLD-like domain;
212-337 5.02e-31

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 115.47  E-value: 5.02e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968  212 YLKMLTQAQREVIIANAYFFPGYRFLHALRKAARRGVRIKLIIQG-EPDMPIVRVGARLLYNYLVKGGVQVFEYRR--RP 288
Cdd:pfam13091   1 LIDLINSAKKSIDIATYYFVPDREIIDALIAAAKRGVDVRIILDSnKDDAGGPKKASLKELRSLLRAGVEIREYQSflRS 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 446572968  289 LHGKVALMDDHWATVGSSNLDPLSLSLNLEANVIIHDRHFNQTLRDNLN 337
Cdd:pfam13091  81 MHAKFYIIDGKTVIVGSANLTRRALRLNLENNVVIKDPELAQELEKEFD 129
PLDc smart00155
Phospholipase D. Active site motifs; Phosphatidylcholine-hydrolyzing phospholipase D (PLD) ...
 108-135 6.00e-06

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: 42.38  E-value: 6.00e-06
                           10        20
                   ....*....|....*....|....*...
gi 446572968   108 VFRRMHRKIVVIDARIAFIGGLNYSAEH 135
Cdd:smart00155   1 YDGVLHTKLMIVDDEIAYIGSANLDGRS 28
 
Name Accession Description Interval E-value
PRK11263 PRK11263
cardiolipin synthase ClsB;
2-412 0e+00

cardiolipin synthase ClsB;


Pssm-ID: 236888 [Multi-domain]  Cd Length: 411  Bit Score: 814.18  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968   2 KCSWREGNKIELLENGEQYYPAVFKAIGEAQERIILETFIWFEDDVGKQLHAALLAAAQRGVKAEVLLDGYGSPDLSDEF 81
Cdd:PRK11263   1 KCSWREGNRIQLLENGEQYYPRVFEAIAAAQEEILLETFILFEDKVGKQLHAALLAAAQRGVKVEVLVDGYGSPDLSDEF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968  82 VNELTAAGVVFRYYDPRPRLFGMRTNVFRRMHRKIVVIDARIAFIGGLNYSAEHMSSYGPEAKQDYAVRLEGPIVEDILQ 161
Cdd:PRK11263  81 VNELTAAGVRFRYFDPRPRLLGMRTNLFRRMHRKIVVIDGRIAFVGGINYSADHLSDYGPEAKQDYAVEVEGPVVADIHQ 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 162 FELENLPGQSAARRWWRRHHKAEENRQPGEAQVLLVWRDNEEHRDDIERHYLKMLTQAQREVIIANAYFFPGYRFLHALR 241
Cdd:PRK11263 161 FELEALPGQSAARRWWRRHHRAEENRQPGEAQALLVWRDNEEHRDDIERHYLKALRQARREVIIANAYFFPGYRLLRALR 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 242 KAARRGVRIKLIIQGEPDMPIVRVGARLLYNYLVKGGVQVFEYRRRPLHGKVALMDDHWATVGSSNLDPLSLSLNLEANV 321
Cdd:PRK11263 241 NAARRGVRVRLILQGEPDMPIVRVGARLLYNYLLKGGVQIYEYCRRPLHGKVALMDDHWATVGSSNLDPLSLSLNLEANL 320

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 322 IIHDRHFNQTLRDNLNGIIAADCQQVDETMLPKRTWWNLTKSVLAFHFLRHFPALVGWLPAHTPRLTQVDPPAQPTMETQ 401
Cdd:PRK11263 321 IIRDRAFNQTLRDNLNGLIAADCQQVDETMLPKRTWWRLTKSVLAFHFLRHFPALAGWLPAHTPRLAQVDPPAQPTMETQ 400

                        410
                 ....*....|.
gi 446572968 402 DRVETENTGVK 412
Cdd:PRK11263 401 DRVETENTGVK 411
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 5-367 1.70e-113

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: 336.53  E-value: 1.70e-113
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968   5 WREGNKIELLENGEQYYPAVFKAIGEAQERIILETFIWFEDDVGKQLHAALLAAAQRGVKAEVLLDGYGSPDLSDEFVNE 84
Cdd:COG1502   11 LVGGNRVTLLVDGDEAFAALLEAIEAARRSIDLEYYIFDDDEVGRRLADALIAAARRGVKVRVLLDGIGSRALNRDFLRR 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968  85 LTAAGVVFRYYDPRPRLFGmrtNVFRRMHRKIVVIDARIAFIGGLNYSAEHMSSY-GPEAKQDYAVRLEGPIVEDILQFe 163
Cdd:COG1502   91 LRAAGVEVRLFNPVRLLFR---RLNGRNHRKIVVIDGRVAFVGGANITDEYLGRDpGFGPWRDTHVRIEGPAVADLQAV- 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 164 lenlpgqsAARRW-WRRHHKAEENRQPGEAQVLLVWRDNEEHRDDIERHYLKMLTQAQREVIIANAYFFPGYRFLHALRK 242
Cdd:COG1502  167 --------FAEDWnFATGEALPFPEPAGDVRVQVVPSGPDSPRETIERALLAAIASARRRIYIETPYFVPDRSLLRALIA 238

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 243 AARRGVRIKLIIQGEPDMPIVRVGARLLYNYLVKGGVQVFEYRRRPLHGKVALMDDHWATVGSSNLDPLSLSLNLEANVI 322
Cdd:COG1502  239 AARRGVDVRILLPAKSDHPLVHWASRSYYEELLEAGVRIYEYEPGFLHAKVMVVDDEWALVGSANLDPRSLRLNFEVNLV 318

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....*
gi 446572968 323 IHDRHFNQTLRDNLNGIIaADCQQVDETMLPKRTWWNLTKSVLAF 367
Cdd:COG1502  319 IYDPEFAAQLRARFEEDL-AHSREVTLEEWRKRPLRRLRERLARL 362
PLDc_ybhO_like_2 cd09159
Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; ...
 197-366 2.15e-65

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: 206.24  E-value: 2.15e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 197 VWRDNEEHRDDIERHYLKMLTQAQREVIIANAYFFPGYRFLHALRKAARRGVRIKLIIQGEPDMPIVRVGARLLYNYLVK 276
Cdd:cd09159    1 VVSDPRRRRSSIRRAYLVAIAAARRRIWIANAYFVPDRRLRRALIEAARRGVDVRLLLPGKSDDPLTVAASRALYGKLLR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 277 GGVQVFEYRRRPLHGKVALMDDHWATVGSSNLDPLSLSLNLEANVIIHDRHFNQTLRDNLNGIIAADCQQVDETMLPKRT 356
Cdd:cd09159   81 AGVRIFEYQPSMLHAKTAVIDGDWATVGSSNLDPRSLRLNLEANLVVEDPAFAAQLEELFEEDLARSREITLEEWRRRPL 160

                        170
                 ....*....|
gi 446572968 357 WWNLTKSVLA 366
Cdd:cd09159  161 WQRLLEWLAY 170
cls PRK01642
cardiolipin synthetase; Reviewed
 8-359 2.40e-57

cardiolipin synthetase; Reviewed


Pssm-ID: 234967 [Multi-domain]  Cd Length: 483  Bit Score: 195.38  E-value: 2.40e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968   8 GNKIELLENGEQYYPAVFKAIGEAQERIILETFIWFEDDVGKQLHAALLAAAQRGVKAEVLLDGYGSPDLSD-EFVNELT 86
Cdd:PRK01642 115 GNQLRLLTNGDETFQAIIRDIELARHYILMEFYIWRPDGLGDQVAEALIAAAKRGVRVRLLYDSIGSFAFFRsPYPEELR 194

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968  87 AAGVVFRYYDPRPRLfgmRTNVFR---RMHRKIVVIDARIAFIGGLNYS-AEHMssygpeaKQ--------DYAVRLEGP 154
Cdd:PRK01642 195 NAGVEVVEFLKVNLG---RVFRRRldlRNHRKIVVIDGYIAYTGSMNVVdPEYF-------KQdpgvgqwrDTHVRIEGP 264

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 155 IVEDiLQF------ELENlpGQSAARRWWRRHHKAEENRQPGEAQVLLVWRDNEEhrDDIERHYLKMLTQAQREVIIANA 228
Cdd:PRK01642 265 VVTA-LQLifaedwEWET--GERILPPPPDVLIMPFEEASGHTVQVIASGPGDPE--ETIHQFLLTAIYSARERLWITTP 339

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 229 YFFPGYRFLHALRKAARRGVRIKLIIQGEPDMPIVRVGARLLYNYLVKGGVQVFEYRRRPLHGKVALMDDHWATVGSSNL 308
Cdd:PRK01642 340 YFVPDEDLLAALKTAALRGVDVRIIIPSKNDSLLVFWASRAFFTELLEAGVKIYRYEGGLLHTKSVLVDDELALVGTVNL 419

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|.
gi 446572968 309 DPLSLSLNLEANVIIHDRHFNQTLRDNLNGIIaADCQQVDETMLPKRTWWN 359
Cdd:PRK01642 420 DMRSFWLNFEITLVIDDTGFAADLAAMQEDYF-ARSRELDLEEWRKRPLWQ 469
PLDc_CLS_2 cd09112
catalytic domain repeat 2 of bacterial cardiolipin synthase and similar proteins; This CD ...
 197-362 1.16e-55

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: 181.52  E-value: 1.16e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 197 VWRDNEEHRDDIERHYLKMLTQAQREVIIANAYFFPGYRFLHALRKAARRGVRIKLIIQGEPDMPIVRVGARLLYNYLVK 276
Cdd:cd09112    1 VSSGPDSDWSSIEQAYLKAINSAKKSIYIQTPYFIPDESLLEALKTAALSGVDVRIMIPGKPDHKLVYWASRSYFEELLK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 277 GGVQVFEYRRRPLHGKVALMDDHWATVGSSNLDPLSLSLNLEANVIIHDRHFNQTLRDNLNGIIaADCQQVDETMLPKRT 356
Cdd:cd09112   81 AGVKIYEYNKGFLHSKTLIVDDEIASVGTANLDIRSFELNFEVNAVIYDKEVAKKLEEIFEEDL-KDSELLTLEEWRKRS 159


                 ....*.
gi 446572968 357 WWNLTK 362
Cdd:cd09112  160 LWKRFK 165
bac_cardiolipin TIGR04265
cardiolipin synthase; This model is based on experimentally characterized bacterial ...
 7-358 2.48e-49

cardiolipin synthase; This model is based on experimentally characterized bacterial cardiolipin synthases (cls) from E. coli, Staphylococcus aureus (two), and Bacillus pseudofirmus OF4. This model describes just one of several homologous but non-orthologous forms of cls. The cutoff score is set arbitrarily high to avoid false-positives. Note that there are two enzymatic activites called cardiolipin synthase. This model represents type 1, which does not rely on a CDP-linked donor, but instead does a reversible transfer of a phosphatidyl group from one phosphatidylglycerol molecule to another.


Pssm-ID: 211988 [Multi-domain]  Cd Length: 483  Bit Score: 173.82  E-value: 2.48e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968    7 EGNKIELLENGEQYYPAVFKAIGEAQERIILETFIWFEDDVGKQLHAALLAAAQRGVKAEVLLDGYGSPDLSDEFVNELT 86
Cdd:TIGR04265 117 EGNQLKLMTDGDDVYDALIQDIKNARHYIHLEYYIWQPDGLGDQILESLMAKAKQGVHVRILYDDVGSVALFKSWPELFR 196

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968   87 AAGVVFRYYDPR--PRLFgMRTNVfrRMHRKIVVIDARIAFIGGLNYSAEHMssyGPEAK----QDYAVRLEGPIVEDI- 159
Cdd:TIGR04265 197 NAGGEVVAFFPVklPLLN-LRMNN--RNHRKIIVIDGQIGYVGGFNIGDEYL---GKDAKfgywRDTHLRIEGDAVTALq 270

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968  160 LQFELEnlpgqsaarrWWRRHHK----------AEENRQPGEAQVLLVWRDNEEHRDDIERHYLKMLTQAQREVIIANAY 229
Cdd:TIGR04265 271 LIFILD----------WNSQTGRriipydpdyfPMPNEQAGGHGIQIIASGPDFPWEQIKYGYLKMIYSAKKSIYIQSPY 340

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968  230 FFPGYRFLHALRKAARRGVRIKLIIQGEPDMPIVRVGARLLYNYLVKGGVQVFEYRRRPLHGKVALMDDHWATVGSSNLD 309
Cdd:TIGR04265 341 FIPDDDLLHAIKIAALSGVDVSIMIPNKPDHPLVFWASRSNFTELLAAGVKIYQYENGFLHSKSVLVDDEIASVGTANMD 420

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*....
gi 446572968  310 PLSLSLNLEANVIIHDRHFNQTLRDNLNGIIAADcQQVDETMLPKRTWW 358
Cdd:TIGR04265 421 MRSFWLNFEVNAFIYDKGFAKDLAAAYDDDISRS-RQLTKRLYAKRPLW 468
PLDc_CLS_1 cd09110
Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Catalytic ...
 16-167 4.97e-49

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: 163.42  E-value: 4.97e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968  16 NGEQYYPAVFKAIGEAQERIILETFIWFEDDVGKQLHAALLAAAQRGVKAEVLLDGYGSPDLSDEFVNELTAAGVVFRYY 95
Cdd:cd09110    2 DGEEFFPALLEAIRAARHSIHLEYYIFRDDEIGRRFRDALIEKARRGVEVRLLYDGFGSLGLSRRFLRELREAGVEVRAF 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446572968  96 DPRPRLFgMRTNVFRRMHRKIVVIDARIAFIGGLNYSAEHMSS-YGPEAKQDYAVRLEGPIVEDILQFELENL 167
Cdd:cd09110   82 NPLSFPL-FLLRLNYRNHRKILVIDGKIAFVGGFNIGDEYLGKdPGFGPWRDTHVRIEGPAVADLQAAFLEDW 153
PRK12452 PRK12452
cardiolipin synthase;
12-325 1.02e-35

cardiolipin synthase;


Pssm-ID: 171510 [Multi-domain]  Cd Length: 509  Bit Score: 137.36  E-value: 1.02e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968  12 ELLENGEQYYPAVFKAIGEAQERIILETFIWFEDDVGKQLHAALLAAAQRGVKAEVLLDGYGSPDLSDEFVNELTAAGVV 91
Cdd:PRK12452 143 KLLTNGDQTFSEILQAIEQAKHHIHIQYYIYKSDEIGTKVRDALIKKAKDGVIVRFLYDGLGSNTLRRRFLQPMKEAGIE 222

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968  92 FRYYDPRPRLFGMRTNVFRRmHRKIVVIDARIAFIGGLNYSAEHMssyGPEAK----QDYAVRLEGPIVEDILQFELENL 167
Cdd:PRK12452 223 IVEFDPIFSAWLLETVNYRN-HRKIVIVDGEIGFTGGLNVGDEYL---GRSKKfpvwRDSHLKVEGKALYKLQAIFLEDW 298

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 168 PGQSAARRWWRRHHKAEENRQPG------EAQVLLVWRDNEEHRDDIERHYLKMLTQAQREVIIANAYFFPGYRFLHALR 241
Cdd:PRK12452 299 LYASSGLNTYSWDPFMNRQYFPGkeisnaEGAVQIVASGPSSDDKSIRNTLLAVMGSAKKSIWIATPYFIPDQETLTLLR 378

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 242 KAARRGVRIKLIIQGEPDMPIVRVGARLLYNYLVKGGVQVFEYRRRPLHGKVALMDDHWATVGSSNLDPLSLSLNLEANV 321
Cdd:PRK12452 379 LSAISGIDVRILYPGKSDSIISDQASQSYFTPLLKAGASIYSYKDGFMHAKIVLVDDKIATIGTANMDVRSFELNYEIIS 458


                 ....
gi 446572968 322 IIHD 325
Cdd:PRK12452 459 VLYE 462
PLDc_2 pfam13091
PLD-like domain;
212-337 5.02e-31

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 115.47  E-value: 5.02e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968  212 YLKMLTQAQREVIIANAYFFPGYRFLHALRKAARRGVRIKLIIQG-EPDMPIVRVGARLLYNYLVKGGVQVFEYRR--RP 288
Cdd:pfam13091   1 LIDLINSAKKSIDIATYYFVPDREIIDALIAAAKRGVDVRIILDSnKDDAGGPKKASLKELRSLLRAGVEIREYQSflRS 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 446572968  289 LHGKVALMDDHWATVGSSNLDPLSLSLNLEANVIIHDRHFNQTLRDNLN 337
Cdd:pfam13091  81 MHAKFYIIDGKTVIVGSANLTRRALRLNLENNVVIKDPELAQELEKEFD 129
PLDc_EcCLS_like_2 cd09158
Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase and similar proteins; ...
 205-362 1.59e-30

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: 115.37  E-value: 1.59e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 205 RDDIERHYLKMLTQAQREVIIANAYFFPGYRFLHALRKAARRGVRIKLIIQGEPDMPIVRVGARLLYNYLVKGGVQVFEY 284
Cdd:cd09158    9 TENIPQLLLSAIHAARRRVVITTPYFVPDESLLQALCTAALRGVEVTLILPAKNDSFLVGAASRSYYEELLEAGVKIYLY 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 285 RRRPLHGKVALMDDHWATVGSSNLDPLSLSLNLEANVIIHDRHFNQTLRDNLNGIIAA----DCQQVDETMLPKRTWWNL 360
Cdd:cd09158   89 RGGLLHAKTVTVDDEVALVGSSNFDIRSFALNFEISLILYDKEFTAQLRAIQERYLARsdplTLEEWKKRPLWRRLLENL 168


                 ..
gi 446572968 361 TK 362
Cdd:cd09158  169 AR 170
PLDc_CLS_unchar2_2 cd09163
Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial ...
 202-355 2.10e-29

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: 112.26  E-value: 2.10e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 202 EEHRDDIERHYLKMLTQAQREVIIANAYFFPGYRFLHALRKAARRGVRIKLIIQGEPDMPIVRVGARLLYNYLVKGGVQV 281
Cdd:cd09163    6 DEDLDKLRWTLLGAISAARHSIRIMTPYFLPDRTLITALQAAALRGVEVDIVLPERNNLPLVDWAMRANLWELLEHGVRI 85

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446572968 282 FeYRRRPL-HGKVALMDDHWATVGSSNLDPLSLSLNLEANVIIHDRHFNQTLRDNLNGIIAA----DCQQVDETMLPKR 355
Cdd:cd09163   86 Y-LQPPPFdHSKLMVVDGAWALIGSANWDPRSLRLNFELNLEVYDTALAGQLDALFDSKIAKsrevTLEELDARPLPIR 163
PLDc_PaCLS_like_2 cd09161
Putative catalytic domain, repeat 2, of Pseudomonas aeruginosa cardiolipin synthase and ...
 206-358 5.00e-26

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: 103.14  E-value: 5.00e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 206 DDIER---HYLKMLTQAQREVIIANAYFFPGYRFLHALRKAARRGVRIKLIIQGEPDMPIVRVGARLLYNYLVKGGVQVF 282
Cdd:cd09161    7 DRIETcslFFVQAINAAQKRLWIASPYFVPDEGVLAALQLAALRGVDVRILIPERPDHLLVYLASFSYLPELIRAGVKVY 86

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446572968 283 EYRRRPLHGKVALMDDHWATVGSSNLDPLSLSLNLEANVIIHDRHFNQTLRDNLNGIIAAdCQQVDETMLPKRTWW 358
Cdd:cd09161   87 RYQPGFLHQKVVLVDDELAAVGTANLDNRSFRLNFEITALVADPGFAQEVEAMLEADFAA-SREVTAAELANRPLW 161
PLDc_PaCLS_like_1 cd09155
Putative catalytic domain, repeat 1, of Pseudomonas aeruginosa cardiolipin synthase and ...
 16-156 1.25e-25

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: 101.55  E-value: 1.25e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968  16 NGEQYYPAVFKAIGEAQERIILETFIWFEDDVGKQLHAALLAAAQRGVKAEVLLDGYGSPDLSDEFVNELTAAGVVFRYY 95
Cdd:cd09155    2 DGEATFAAIFEAIASAEEYILVQFYIIRDDDLGRELKDALIARAQAGVRVYLLYDEIGSHSLSRSYIERLRKAGVEVSAF 81

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446572968  96 DPRPRlfgmRTNVFR---RMHRKIVVIDARIAFIGGLNYSAEHM---SSYGPEakQDYAVRLEGPIV 156
Cdd:cd09155   82 NTTRG----WGNRFQlnfRNHRKIVVVDGQTAFVGGHNVGDEYLgrdPRLGPW--RDTHVKLEGPAV 142
PLDc_SMU_988_like_2 cd09160
Putative catalytic domain, repeat 2, of Streptococcus mutans uncharacterized protein SMU_988 ...
 212-358 3.21e-25

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: 101.03  E-value: 3.21e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 212 YLKMLTQAQREVIIANAYFFPGYRFLHALRKAARRGVRIKLIIQGEPDMPIVRVGARLLYNYLVKGGVQVFEYRRRPLHG 291
Cdd:cd09160   16 YLDLINQAKDYVYITTPYLILDDEMLDALCLAAKRGVDVRIITPHIPDKKYVFLVTRSNYPELLEAGVKIYEYTPGFIHA 95

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446572968 292 KVALMDDHWATVGSSNLDPLSLSLNLEANVIIHDRHFNQTLRDNLNGIIaADCQQVDETMLPKRTWW 358
Cdd:cd09160   96 KTFVSDDKAAVVGTINLDYRSLYLHFECGVYMYDTPVISDIKEDFEETL-AQSQEITLEECRKRSLV 161
PLDc_CLS_unchar1_1 cd09156
Putative catalytic domain, repeat 1, of uncharacterized proteins similar to bacterial ...
 17-161 1.89e-24

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: 98.10  E-value: 1.89e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968  17 GEQYYPAVFKAIGEAQERIILETFIWFEDDVGKQLHAALLAAAQRGVKAEVLLDGYGSPDLSDEFVNELTAAGVVFRYYD 96
Cdd:cd09156    3 GVEAYQALIQLIESAKHSIDVCTFILGDDATGRRVIDALARKAREGVEVRLLLDALGSFFLSRRALKKLRAAGGKVAFFM 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446572968  97 P--RPRLFGmRTNVfrRMHRKIVVIDARIAFIGGLNYSAEHMssyGPEAKQ----DYAVRLEGPIVEDILQ 161
Cdd:cd09156   83 PvfRLPFRG-RTNL--RNHRKIAIADGSTAISGGMNLANEYM---GPEPDDgrwvDLSFLIEGPAVAQYQE 147
PLDc_CLS_unchar2_1 cd09157
Putative catalytic domain, repeat 1, of uncharacterized proteins similar to bacterial ...
 15-161 2.59e-24

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: 98.02  E-value: 2.59e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968  15 ENGEQYYPAVFKAIGEAQERIILETFIWFEDDVGKQLHAALLAAAQRGVKAEVLLDGYGS----PDLsdefVNELTAAGV 90
Cdd:cd09157    1 VNGDEAYPAMLEAIDAARHSIALSSYIFDNDGVGREFVDALAEAVARGVDVRVLIDGVGArysrPSI----RRRLRRAGV 76

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446572968  91 VFRYYDPrPRLFGMRTNVFRRMHRKIVVIDARIAFIGGLNYSAEHMSSYGPEAK-QDYAVRLEGPIVEDILQ 161
Cdd:cd09157   77 PVARFLP-PRLPPRLPFINLRNHRKILVVDGRTGFTGGMNIRDGHLVADDPKNPvQDLHFRVEGPVVAQLQE 147
PLDc_EcCLS_like_1 cd09152
Catalytic domain, repeat 1, of Escherichia coli cardiolipin synthase and similar proteins; ...
 8-156 6.42e-21

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: 88.80  E-value: 6.42e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968   8 GNKIELLENGEQYYPAVFKAIGEAQERIILETFIWFEDDVGKQLHAALLAAAQRGVKAEVLLDGYGSPDLS-DEFVNELT 86
Cdd:cd09152    1 GNRVELLTDYDAVIDRLIADIDAAKHHVHLLFYIWADDGTGDRVAEALERAAKRGVTCRLLLDAVGSRAFFrSSLWKRLR 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446572968  87 AAGVVFRYYDPRpRLFGMRtnvFRRM----HRKIVVIDARIAFIGGLN-YSAEHMSSYGPEAKQDYAVRLEGPIV 156
Cdd:cd09152   81 EAGVEVVEALPL-RLFRRR---LARFdlrnHRKIAVIDGRIAYTGSQNiIDPEFFKKAGGGPWVDLMVRVEGPVV 151
PLDc_ymdC_like_2 cd09113
Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and ...
 213-381 1.28e-20

Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and similar proteins; Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and similar proteins. In Escherichia coli, there are two genes, f413 (ybhO) and o493 (ymdC), which are homologous to gene cls that encodes the Escherichia coli cardiolipin (CL) synthase. The prototype of this subfamily is an uncharacterized protein ymdC specified by the o493 (ymdC) gene. Although the functional characterization of ymdC and similar proteins remains unknown, members of this subfamily show high sequence homology to bacterial CL synthases, which catalyze the reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form CL and glycerol. Moreover, ymdC and its similar proteins contain two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characteriszes the phospholipase D (PLD) superfamily. The two motifs may be part of the active site and may be involved in phosphatidyl group transfer.


Pssm-ID: 197212 [Multi-domain]  Cd Length: 218  Bit Score: 89.59  E-value: 1.28e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 213 LKMLTQAQREVIIANAYFFPGYRFLHALRKAARRGVRIKLIIQGEP--DMPIVRVGARLLYNYLVKGGVQVFEYRRRP-- 288
Cdd:cd09113   23 AELLKNAKREVLIVSPYFVPGDEGVALLAELARRGVRVRILTNSLAatDVPAVHSGYARYRKRLLKAGVELYELKPDAak 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 289 --------------LHGKVALMDDHWATVGSSNLDPLSLSLNLEANVIIHDRHFNQTLRDNLNGIIAADCQQVDETMLPK 354
Cdd:cd09113  103 rkrlrglfgssrasLHAKSFVIDDRLVFVGSFNLDPRSAYLNTEMGLVIDSPELAAQLRAAMEEDLAPSAYWVLLLDDGG 182

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 446572968 355 RTWWNLTKSVLAFH-------FLRHFPA-LVGWLP 381
Cdd:cd09113  183 LVWETEEDGKEKEYdsepetsFWRRLGAwLLSLLP 217
PLDc_CLS_unchar1_2 cd09162
Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial ...
 204-364 5.98e-17

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: 78.07  E-value: 5.98e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 204 HRDDIERHYLKMLTQAQREVIIANAYFFPGYRFLHALRKAARRGVRIKLIIQGEPDMPIVRVGARLLYNYLVKGGVQVFE 283
Cdd:cd09162    8 PGDPLYEALLSAIFEAEHRIWIVTPYFVPDEVLLRALRLAARRGVDVRLIVPKRSNHRIADLARGSYLRDLQEAGAEIYL 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 284 YRRRPLHGKVALMDDHWATVGSSNLDPLSLSLNLEANVIIHDRHFNQTLRDNLNGIIAADCQQVDETMLPKRTWWNLTKS 363
Cdd:cd09162   88 YQPGMLHAKAVVVDDKLALVGSANLDMRSLFLNYEVAVFFYSPADIKELSDWIESLISQCTEGAPPPSALRDIAEGLMRL 167


                 .
gi 446572968 364 V 364
Cdd:cd09162  168 L 168
PLDc_SF cd00138
Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D ...
 211-323 1.19e-16

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: 75.63  E-value: 1.19e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 211 HYLKMLTQAQREVIIANAYFFPGY--RFLHALRKAARRGVRIKLIIQGEPDMPIVRVGARLLYnyLVKGGVQVFEYRRRP 288
Cdd:cd00138    2 ALLELLKNAKESIFIATPNFSFNSadRLLKALLAAAERGVDVRLIIDKPPNAAGSLSAALLEA--LLRAGVNVRSYVTPP 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 446572968 289 -----LHGKVALMDDHWATVGSSNLDPLSLSLNLEANVII 323
Cdd:cd00138   80 hfferLHAKVVVIDGEVAYVGSANLSTASAAQNREAGVLV 119
PLDc_ymdC_like_1 cd09111
Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and ...
 14-161 7.36e-15

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: 71.80  E-value: 7.36e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968  14 LENGEQYYPAVFKAIGEAQERIILETFIWFEDDVGKQLHAALLAAAQRGVKAEVLLDGYGSPDLSDEFVNELTAAGVVFR 93
Cdd:cd09111    1 LEDGLDALAARLALIRSAERSIDLQYYIWHDDESGRLLLGELLEAADRGVRVRLLLDDLGTSGRDRLLAALDAHPNIEVR 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446572968  94 YYDP----RPRLFGMRTNVFR---RMHRKIVVIDARIAFIGGLNYSAEHMsSYGPEAK-QDYAVRLEGPIVEDILQ 161
Cdd:cd09111   81 LFNPfrnrGGRLLEFLTDFSRlnrRMHNKLFIVDGAVAIVGGRNIGDEYF-GASPEVNfRDLDVLAVGPVVRQLSE 155
PLDc_vPLD1_2_like_2 cd09105
Catalytic domain, repeat 2, of vertebrate phospholipases, PLD1 and PLD2, and similar proteins; ...
 208-325 1.06e-14

Catalytic domain, repeat 2, of vertebrate phospholipases, PLD1 and PLD2, and similar proteins; Catalytic domain, repeat 2, of phospholipase D (PLD, EC 3.1.4.4) found in yeast, plants, and vertebrates, and their bacterial homologs. PLDs are involved in signal transduction, vesicle formation, protein transport, and mitosis by participating in phospholipid metabolism. They hydrolyze the terminal phosphodiester bond of phospholipids resulting in the formation of phosphatidic acid and alcohols. Phosphatidic acid is an essential compound involved in signal transduction. PLDs also catalyze the transphosphatidylation of phospholipids to acceptor alcohols, by which various phospholipids can be synthesized. Both prokaryotic and eukaryotic PLDs have two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. PLDs are active as bi-lobed monomers. Each monomer contains two domains, each of which carries one copy of the HKD motif. Two HKD motifs from two domains form a single active site. PLDs utilize a common two-step ping-pong catalytic mechanism involving an enzyme-substrate intermediate to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine residue from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group.


Pssm-ID: 197204 [Multi-domain]  Cd Length: 146  Bit Score: 70.79  E-value: 1.06e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 208 IERHYLKMLTQAQREVIIANAYFFPgYRFLHALRKA--ARRGVRIKLIIQGEPDMPIVRVGARLLYNYLVK--------- 276
Cdd:cd09105    9 IADAYLKAIRNARRYIYIEDQYLWS-PELLDALAEAlkANPGLRVVLVLPALPDAVAFGADDGLDALALLAlllladaap 87

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 446572968 277 GGVQVF--------EYRRRPL--HGKVALMDDHWATVGSSNLDPLSLSLNLEANVIIHD 325
Cdd:cd09105   88 DRVAVFslathrrgLLGGPPIyvHSKVVIVDDEWATVGSANLNRRSMTWDTELNLAVVD 146
PLDc_unchar1_2 cd09128
Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins; ...
 206-334 4.55e-14

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: 68.84  E-value: 4.55e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 206 DDIERHYLKMLTQAQREVIIANAYFFPGYRFLHALRKAARRGVRIKLIIqgePDMPIVRVGARLLYNYLVKGGVQVfEYR 285
Cdd:cd09128    9 DNAREALLALIDSAEESLLIQNEEMGDDAPILDALVDAAKRGVDVRVLL---PSAWSAEDERQARLRALEGAGVPV-RLL 84

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 446572968 286 RRP---LHGKVALMDDHWATVGSSNLDPLSLSLNLEANVIIHDRHFNQTLRD 334
Cdd:cd09128   85 KDKflkIHAKGIVVDGKTALVGSENWSANSLDRNREVGLIFDDPEVAAYLQA 136
PLDc_unchar3 cd09131
Putative catalytic domain of uncharacterized phospholipase D-like proteins; Putative catalytic ...
 211-323 5.91e-13

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: 65.83  E-value: 5.91e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 211 HYLKMLTQAQREVIIA-------NAYFFPGYRFLHALRKAARRGVRIKLIIQGEPDMPIVRVGARLLYNYLVKGGVQV-F 282
Cdd:cd09131    7 ALLDLINNAKRSIYIAmymfkyyENPGNGVNTLLEALIDAHKRGVDVKVVLEDSIDDDEVTEENDNTYRYLKDNGVEVrF 86

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 446572968 283 EYRRRPLHGKVALMDDHWATVGSSNLDPLSLSLNLEANVII 323
Cdd:cd09131   87 DSPSVTTHTKLVVIDGRTVYVGSHNWTYSALDYNHEASVLI 127
PLDc_SMU_988_like_1 cd09154
Putative catalytic domain, repeat 1, of Streptococcus mutans uncharacterized protein SMU_988 ...
 16-156 7.21e-12

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: 62.93  E-value: 7.21e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968  16 NGEQYYPAVFKAIGEAQERIILETFIWFEDDVGKQLHAALLAAAQRGVKAEVLLDGYGS-PDLSDEFVNELTAAGVVFRY 94
Cdd:cd09154    3 LGEDMFEDMLEDLKKAEKFIFMEYFIIEEGYMWDSILEILKEKAKEGVEVRIMYDDFGSiTTLPKDYPKELEKIGIKCRV 82

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446572968  95 YDPRPRLFGMRTNvfRRMHRKIVVIDARIAFIGGLNYSAEHMSSYGPEAK-QDYAVRLEGPIV 156
Cdd:cd09154   83 FNPFKPILSLYMN--NRDHRKITVIDGKVAFTGGINLADEYINKIERFGYwKDTGIRLEGEAV 143
PLDc_unchar1_1 cd09127
Putative catalytic domain, repeat 1, of uncharacterized phospholipase D-like proteins; ...
 218-328 1.74e-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: 58.81  E-value: 1.74e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 218 QAQREVIIaNAYFFPGYRFLHALRKAARRGVRIKLIIQGEPDMPIVRvgARLLYNYLVKGGVQVFEY----RRRPLHGKV 293
Cdd:cd09127   19 SAKRSILL-KMYEFTDPALEKALAAAAKRGVRVRVLLEGGPVGGISR--AEKLLDYLNEAGVEVRWTngtaRYRYTHAKY 95

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 446572968 294 ALMDDHWATVGSSNLDPLSLSLNLEANVIIHDRHF 328
Cdd:cd09127   96 IVVDDERALVLTENFKPSGFTGTRGFGVVTDDPAV 130
PLDc_unchar3 cd09131
Putative catalytic domain of uncharacterized phospholipase D-like proteins; Putative catalytic ...
 20-132 1.79e-10

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: 58.89  E-value: 1.79e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968  20 YYPAVFKAIGEAQERI--ILETFIWFEDDVGK--QLHAALLAAAQRGVKAEVLLDGYGSPDLSDEF----VNELTAAGVV 91
Cdd:cd09131    4 YYPALLDLINNAKRSIyiAMYMFKYYENPGNGvnTLLEALIDAHKRGVDVKVVLEDSIDDDEVTEEndntYRYLKDNGVE 83

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 446572968  92 FRYYDPRprlfgmrtnvfRRMHRKIVVIDARIAFIGGLNYS 132
Cdd:cd09131   84 VRFDSPS-----------VTTHTKLVVIDGRTVYVGSHNWT 113
PLDc_Nuc_like cd09116
Catalytic domain of EDTA-resistant nuclease Nuc, vertebrate phospholipase D6, and similar ...
 199-326 3.77e-10

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: 57.69  E-value: 3.77e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 199 RDNEEHRDDIERHYLKMLTQAQREVIIAnAYFFPGYRFLHALRKAARRGVRIKLIIQgepDMPIVRVGARLLYNYLVKGG 278
Cdd:cd09116    1 YFLPRPQDNLERLIVALIANAKSSIDVA-MYALTDPEIAEALKRAAKRGVRVRIILD---KDSLADNLSITLLALLSNLG 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 446572968 279 VQVFEYRRRP-LHGKVALMDDHWATVGSSNLDPLSLSLNLEANVIIHDR 326
Cdd:cd09116   77 IPVRTDSGSKlMHHKFIIIDGKIVITGSANWTKSGFHRNDENLLIIDDP 125
PLDc_N_Snf2_like cd09178
N-terminal putative catalytic domain of uncharacterized HKD family nucleases fused to putative ...
 199-326 1.23e-09

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


Pssm-ID: 197275 [Multi-domain]  Cd Length: 134  Bit Score: 56.02  E-value: 1.23e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 199 RDNEEHRD--DIERHYLKmltqAQREVIIANAYFFP-GYRflhALRKAARRGVRIKLIIqGEPDmpivrvgarllynyLV 275
Cdd:cd09178    2 IDNREGKTlaDALKELLK----DSDRLDIAVGYFYLsGFR---LLKEELENFEKLRILI-GIEL--------------IK 59

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 446572968 276 KGGVQVFEYRRRPLHGKVALMD-------DHWATVGSSNLDPLSLSLNLEANVIIHDR 326
Cdd:cd09178   60 EGKVEIRVYTKGFLHAKAYLFDgpdndngPGTAIVGSSNFTKAGLTGNLELNVEVKDR 117
PLDc_2 pfam13091
PLD-like domain;
27-132 1.65e-09

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 55.76  E-value: 1.65e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968   27 AIGEAQERIILETFIWFEDdvgKQLHAALLAAAQRGVKAEVLLDG-----YGSPDLSDEFVNELTAAGVVFRYYDPRprl 101
Cdd:pfam13091   4 LINSAKKSIDIATYYFVPD---REIIDALIAAAKRGVDVRIILDSnkddaGGPKKASLKELRSLLRAGVEIREYQSF--- 77

                          90       100       110
                  ....*....|....*....|....*....|.
gi 446572968  102 fgmrtnvFRRMHRKIVVIDARIAFIGGLNYS 132
Cdd:pfam13091  78 -------LRSMHAKFYIIDGKTVIVGSANLT 101
PLDc_unchar1_1 cd09127
Putative catalytic domain, repeat 1, of uncharacterized phospholipase D-like proteins; ...
 24-156 1.35e-08

Putative catalytic domain, repeat 1, of uncharacterized phospholipase D-like proteins; Putative catalytic domain, repeat 1, of uncharacterized phospholipase D (PLD, EC 3.1.4.4)-like proteins. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze transphosphatidylation of phospholipids to acceptor alcohols. Members of this subfamily contain two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the PLD superfamily. The two motifs may be part of the active site and may be involved in phosphatidyl group transfer.


Pssm-ID: 197225 [Multi-domain]  Cd Length: 141  Bit Score: 53.42  E-value: 1.35e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968  24 VFKAIGEAQERIILETFIWFEDDVGKQLhaalLAAAQRGVKAEVLLDGY---GSPDLsDEFVNELTAAGVVFRYYDPRPR 100
Cdd:cd09127   13 VVDAIASAKRSILLKMYEFTDPALEKAL----AAAAKRGVRVRVLLEGGpvgGISRA-EKLLDYLNEAGVEVRWTNGTAR 87

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 446572968 101 lfgmrtnvFRRMHRKIVVIDARIAFIGGLNYSAEhmssyGPEAKQDYAVRLEGPIV 156
Cdd:cd09127   88 --------YRYTHAKYIVVDDERALVLTENFKPS-----GFTGTRGFGVVTDDPAV 130
PLDc_CDP-OH_P_transf_II_2 cd09103
Catalytic domain, repeat 2, of CDP-alcohol phosphatidyltransferase class-II family members; ...
 213-337 4.61e-08

Catalytic domain, repeat 2, of CDP-alcohol phosphatidyltransferase class-II family members; Catalytic domain, repeat 2, of CDP-alcohol phosphatidyltransferase class-II family members, which mainly include gram-negative bacterial phosphatidylserine synthases (PSS; CDP-diacylglycerol--serine O-phosphatidyltransferase, EC 2.7.8.8), yeast phosphatidylglycerophosphate synthase (PGP synthase; CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, EC 2.7.8.5), and metazoan PGP synthase 1. All members in this subfamily have two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterize the phospholipase D (PLD) superfamily. They may utilize a common two-step ping-pong catalytic mechanism, involving a substrate-enzyme intermediate, to cleave phosphodiester bonds. The two motifs are suggested to constitute the active site involving phosphatidyl group transfer. Phosphatidylserine synthases from gram-positive bacteria and eukaryotes, and prokaryotic phosphatidylglycerophosphate synthases are not members of this subfamily.


Pssm-ID: 197202 [Multi-domain]  Cd Length: 184  Bit Score: 52.61  E-value: 4.61e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 213 LKMLTQAQREVIIANAYFFPGYRFLHALRKAARRGVRIKLIIQ--------GEPDMPIVRVGA---------RLLYN--- 272
Cdd:cd09103   21 EQLITSAESKIILCTPYFNLPQALMRDILRLLKRGVKVEIIVGdktandfyIPPEEPFKVIGAlpylyeinlRRFAKrlq 100

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446572968 273 -YLVKGGVQVFEYRR--RPLHGKVALMDDHWATVGSSNLDPLSLSLNLEANVIIHDRhfNQTLRDNLN 337
Cdd:cd09103  101 kYIDQGQLNVRLWKDgdNSFHLKGIWVDDRYTLLTGNNLNPRAWRLDLENGLLIHDP--QKQLQQQLE 166
PLDc_SF cd00138
Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D ...
 26-132 5.36e-08

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


Pssm-ID: 197200 [Multi-domain]  Cd Length: 119  Bit Score: 50.98  E-value: 5.36e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968  26 KAIGEAQERIILETFiWFEDDVGKQLHAALLAAAQRGVKAEVLLDGYGS--PDLSDEFVNELTAAGVVFRYYDPRPrlfg 103
Cdd:cd00138    5 ELLKNAKESIFIATP-NFSFNSADRLLKALLAAAERGVDVRLIIDKPPNaaGSLSAALLEALLRAGVNVRSYVTPP---- 79

                         90       100
                 ....*....|....*....|....*....
gi 446572968 104 mrtNVFRRMHRKIVVIDARIAFIGGLNYS 132
Cdd:cd00138   80 ---HFFERLHAKVVVIDGEVAYVGSANLS 105
PRK13912 PRK13912
nuclease NucT; Provisional
 206-330 2.95e-07

nuclease NucT; Provisional


Pssm-ID: 184389 [Multi-domain]  Cd Length: 177  Bit Score: 50.16  E-value: 2.95e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 206 DDIERHYLKMLTQAQREVIIAnAYFFPGYRFLHALRKAARRGVRIKLIIQGEPDM--PIVRVGARLLYN----YLVKGGV 279
Cdd:PRK13912  32 KDALNKLVSLISNARSSIKIA-IYSFTHKDIAKALKSAAKRGVKISIIYDYESNHnnDQSTIGYLDKYPnikvCLLKGLK 110

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 446572968 280 QVFEYRRRPLHGKVALMDDHWATVGSSNLDPLSLSLNLEANVIIHDRHFNQ 330
Cdd:PRK13912 111 AKNGKYYGIMHQKVAIIDDKIVVLGSANWSKNAFENNYEVLLITDDTETIL 161
PLDc_unchar5 cd09133
Putative catalytic domain of uncharacterized hypothetical proteins with one or two copies of ...
 203-307 3.90e-07

Putative catalytic domain of uncharacterized hypothetical proteins with one or two copies of the HKD motif; Putative catalytic domain of uncharacterized hypothetical proteins with similarity to phospholipase D (PLD, EC 3.1.4.4). PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze transphosphatidylation of phospholipids to acceptor alcohols. Members of this subfamily contain one or two copies of the HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the PLD superfamily.


Pssm-ID: 197231 [Multi-domain]  Cd Length: 127  Bit Score: 48.87  E-value: 3.90e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 203 EHRDdierHYLKMLTQAQREVIIA----NAYFFPgyRFLHALRKAARRGVRIKLI-IQGEPDMPIVRVG----ARLLYNY 273
Cdd:cd09133    1 EHRE----KLLRALREAKRRVIIHspwlGNAVFE--NLLEALEKAAERGVKIDILwGISSDEEKEKKALseiaEKLLADR 74

                         90       100       110
                 ....*....|....*....|....*....|....
gi 446572968 274 LVKGGVQVFEYRRRpLHGKVALMDDHWATVGSSN 307
Cdd:cd09133   75 GLRGGVNVHLRTTG-SHAKFLVCDDWFALVGSCN 107
PLDc_vPLD3_4_5_like_1 cd09106
Putative catalytic domain, repeat 1, of vertebrate phospholipases, PLD3, PLD4 and PLD5, viral ...
 213-325 8.70e-07

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


Pssm-ID: 197205 [Multi-domain]  Cd Length: 153  Bit Score: 48.40  E-value: 8.70e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 213 LKMLTQAQREVIIANAYF-------------FPGYRFLHALRKAARRGVRIKlIIQGEPDMPIVRVGARLL--------- 270
Cdd:cd09106   25 MELISSAKKSIDIASFYWnlrgtdtnpdssaQEGEDIFNALLEAAKRGVKIR-ILQDKPSKDKPDEDDLELaalggaevr 103

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 446572968 271 ---YNYLVKGGVqvfeyrrrpLHGKVALMDD-HWAtVGSSNLDPLSLSLNLEANVIIHD 325
Cdd:cd09106  104 sldFTKLIGGGV---------LHTKFWIVDGkHFY-LGSANLDWRSLTQVKELGVYIYN 152
YrhO COG1378
Sugar-specific transcriptional regulator TrmB [Transcription];
183-337 1.31e-06

Sugar-specific transcriptional regulator TrmB [Transcription];


Pssm-ID: 440988 [Multi-domain]  Cd Length: 238  Bit Score: 49.25  E-value: 1.31e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 183 AEENRQPGEAQVLLVwrdneEHRDDIERHYLKMLTQAQREVII-ANAYFFPGYRFLHALRKAARRGVRIKLIIQGEPDMP 261
Cdd:COG1378   98 YEELREPEEELVWVV-----KGREAILERLRELIASAEEEILIvLSPPELLLEELEEALEEALERGVKVRVLVSPEVLEV 172

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446572968 262 IVRVGARLlynylvkggvqvFEYRRRP-LHGKVALMDDHWATVGSSNLDPlslslNLEAnVIIHDRHFNQTLRDNLN 337
Cdd:COG1378  173 PERLEEEG------------EEVRVLPgLPGRLLIVDDKEALISVSEPDG-----EETA-IWIEDPELAALLRELFE 231
PLDc_Bfil_DEXD_like cd09117
Catalytic domain of type II restriction endonucleases BfiI and NgoFVII, and uncharacterized ...
 207-323 2.18e-06

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: 46.23  E-value: 2.18e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 207 DIERHYLKMLTQAqREVIIANAYFfpGYRFLHALRKAARRGVRIKLIIqgEPDMPIVRVGARLLYNYLVKGGVQVFEY-R 285
Cdd:cd09117    2 SLEELLTRLIERA-DTIRIAVAFA--SAGGAIKLLDKFREGKKIRLIV--GLDFGGTSPADFALKLLLALGNLNVRIFdA 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 446572968 286 RRPLHGKVAL--MDDHW-ATVGSSNLDPLSLSLNLEANVII 323
Cdd:cd09117   77 GPLLHAKLYLfeNDDPTrAIVGSANLTQGGLSGNIEAAVVI 117
PLDc_unchar4 cd09132
Putative catalytic domain of uncharacterized phospholipase D-like proteins; Putative catalytic ...
 212-323 5.08e-06

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


Pssm-ID: 197230 [Multi-domain]  Cd Length: 122  Bit Score: 45.34  E-value: 5.08e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 212 YLKMLTQAQREVIIAnayffpGYRFLH------ALRKAARRGVRIKLII---QGEPDmPIVRVGARLLYNYLVkgGVQVF 282
Cdd:cd09132    4 LLELIEGAERSLLIV------GYSAYKvsellqALAAALERGVQVRVVVessEKAGS-VLSLDEDELMWPKLA--GATLY 74

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 446572968 283 EYRRRP-------LHGKVALMDDHWATVGSSNLDPLSLSLNLEANVII 323
Cdd:cd09132   75 VWPEKKrpgkrasLHAKVIVADRRRLLVTSANLTGAGMERNIEAGVLV 122
PLDc smart00155
Phospholipase D. Active site motifs; Phosphatidylcholine-hydrolyzing phospholipase D (PLD) ...
 108-135 6.00e-06

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: 42.38  E-value: 6.00e-06
                           10        20
                   ....*....|....*....|....*...
gi 446572968   108 VFRRMHRKIVVIDARIAFIGGLNYSAEH 135
Cdd:smart00155   1 YDGVLHTKLMIVDDEIAYIGSANLDGRS 28
PLDc_CLS_1 cd09110
Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Catalytic ...
 200-308 6.11e-06

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


Pssm-ID: 197209 [Multi-domain]  Cd Length: 154  Bit Score: 45.93  E-value: 6.11e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 200 DNEEHRDDIerhyLKMLTQAQREVIIANaYFF----PGYRFLHALRKAARRGVRIKLIIQGepdmpivrVGARLL----Y 271
Cdd:cd09110    2 DGEEFFPAL----LEAIRAARHSIHLEY-YIFrddeIGRRFRDALIEKARRGVEVRLLYDG--------FGSLGLsrrfL 68

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 446572968 272 NYLVKGGVQVFEYRRRPL-----------HGKVALMDDHWATVGSSNL 308
Cdd:cd09110   69 RELREAGVEVRAFNPLSFplfllrlnyrnHRKILVIDGKIAFVGGFNI 116
PLDc_unchar1_2 cd09128
Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins; ...
 23-133 9.99e-06

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: 44.96  E-value: 9.99e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968  23 AVFKAIGEAQERIILET--FIWFEDDVGKQLHAAllaaaQRGVKAEVLLDG-YGSPDLSDEFVNELTAAGVVFRYYDPRp 99
Cdd:cd09128   14 ALLALIDSAEESLLIQNeeMGDDAPILDALVDAA-----KRGVDVRVLLPSaWSAEDERQARLRALEGAGVPVRLLKDK- 87

                         90       100       110
                 ....*....|....*....|....*....|....
gi 446572968 100 rlfgmrtnvFRRMHRKIVVIDARIAFIGGLNYSA 133
Cdd:cd09128   88 ---------FLKIHAKGIVVDGKTALVGSENWSA 112
PLDc pfam00614
Phospholipase D Active site motif; Phosphatidylcholine-hydrolysing phospholipase D (PLD) ...
 108-131 3.36e-05

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: 40.48  E-value: 3.36e-05
                          10        20
                  ....*....|....*....|....
gi 446572968  108 VFRRMHRKIVVIDARIAFIGGLNY 131
Cdd:pfam00614   1 YDGRLHRKIVVVDDELAYIGGANL 24
PLDc_unchar4 cd09132
Putative catalytic domain of uncharacterized phospholipase D-like proteins; Putative catalytic ...
 28-132 3.87e-05

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


Pssm-ID: 197230 [Multi-domain]  Cd Length: 122  Bit Score: 43.03  E-value: 3.87e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968  28 IGEAQERIILETFIWfeDDVgKQLHAALLAAAQRGVKAEVLLDGY-GSPDLSDEFVNELTAAGVVFR--YYDPRPrlfgM 104
Cdd:cd09132    8 IEGAERSLLIVGYSA--YKV-SELLQALAAALERGVQVRVVVESSeKAGSVLSLDEDELMWPKLAGAtlYVWPEK----K 80

                         90       100
                 ....*....|....*....|....*...
gi 446572968 105 RTNVFRRMHRKIVVIDARIAFIGGLNYS 132
Cdd:cd09132   81 RPGKRASLHAKVIVADRRRLLVTSANLT 108
PLDc_Nuc cd09170
Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar ...
 213-307 6.31e-05

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: 42.50  E-value: 6.31e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 213 LKMLTQAQREVIIAnAYFFPGYRFLHALRKAARRGVRIKLIIQGEPdmpivRVGARLLYNYLVKGGVQVFEYRRRPL-HG 291
Cdd:cd09170   17 LDVIDSARRSIDVA-AYSFTSPPIARALIAAKKRGVDVRVVLDKSQ-----AGGKYSALNYLANAGIPVRIDDNYAImHN 90

                         90
                 ....*....|....*.
gi 446572968 292 KVALMDDHWATVGSSN 307
Cdd:cd09170   91 KVMVIDGKTVITGSFN 106
PLDc_like_TrmB_middle cd09124
Middle phospholipase D-like domain of the transcriptional regulator TrmB and similar proteins; ...
 214-324 6.46e-05

Middle phospholipase D-like domain of the transcriptional regulator TrmB and similar proteins; Middle phospholipase D (PLD)-like domain of the transcriptional regulator TrmB and similar proteins. TrmB acts as a bifunctional sugar-sensing transcriptional regulator which controls two operons encoding maltose/trehalose and maltodextrin ABC transporters of Pyrococcus fruiosus. It functions as a dimer. Full length TrmB includes an N-terminal DNA-binding domain, a C-terminal sugar-binding domain and middle region that has been named as a PLD-like domain. The middle domain displays homology to PLD enzymes, which contain one or two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) per chain. The HKD motif characterizes the PLD superfamily. Due to the lack of key residues related to PLD activity in the PLD-like domain, members of this subfamily are unlikely to carry PLD activity.


Pssm-ID: 197223 [Multi-domain]  Cd Length: 126  Bit Score: 42.31  E-value: 6.46e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 214 KMLTQAQREVIIANAYFFPgYRFLHALRKAARRGVRIKLIIQGEPDMPivrvgarllynyLVKGGVQVFEYRRRPLHGKV 293
Cdd:cd09124   17 EMINSAKEEIYISLPSEEL-EELLEELEKAAERGVKVVIIIFGDDDLD------------DLDSPAIEVRVREGGGRPFL 83

                         90       100       110
                 ....*....|....*....|....*....|.
gi 446572968 294 ALMDDHWATVGSSNLDPLSLSLNLEANVIIH 324
Cdd:cd09124   84 LIVDSKEALIGPSSEEEETYALYTENPALVL 114
PLDc_unchar2_1 cd09129
Putative catalytic domain, repeat 1, of uncharacterized phospholipase D-like proteins; ...
 21-164 1.06e-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: 197227  Cd Length: 196  Bit Score: 42.99  E-value: 1.06e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968  21 YPAVFKAIGEAQERIILETFIwFEDDVGKQLHAALLAAAQ------------RGVKAEVLLD----GYGSpdLSDEFVNE 84
Cdd:cd09129    2 FDEILEIIDEAKDFIVLDMFL-FNDYYDKKKGKFPPLSEEltdaliekkkenPDLPIVVITDpintFYGS--HDNPHLKK 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968  85 LTAAGV------VFRYYDPRP------RLF---------GMRTNVFRRM------------------HRKIVVIDARiAF 125
Cdd:cd09129   79 LKEAGIevvetdLDKLRDSNPlysgiwRTFiqwfgnsgkGWLPNPFGKEapkvtlrsylrllnfkanHRKVLVTENT-AL 157

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 446572968 126 IGGLNysaEHMSSYgpeAKQDYAVRLEGPIVEDILQFEL 164
Cdd:cd09129  158 VTSAN---PHDASA---RHSNIAFEVSGPIIGDLLKSEQ 190
PLDc_Nuc cd09170
Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar ...
 22-133 1.97e-04

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: 41.35  E-value: 1.97e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968  22 PAVFKAIGEAQERIILETFIWFEDDVGKQLhaalLAAAQRGVKAEVLLDgYGSPDLSDEFVNELTAAGVVFRyydprprl 101
Cdd:cd09170   14 ELILDVIDSARRSIDVAAYSFTSPPIARAL----IAAKKRGVDVRVVLD-KSQAGGKYSALNYLANAGIPVR-------- 80

                         90       100       110
                 ....*....|....*....|....*....|..
gi 446572968 102 fgmRTNVFRRMHRKIVVIDARIAFIGGLNYSA 133
Cdd:cd09170   81 ---IDDNYAIMHNKVMVIDGKTVITGSFNFTA 109
PLDc_vPLD1_2_like_bac_2 cd09143
Catalytic domain, repeat 2, of uncharacterized bacterial proteins with similarity to ...
 200-323 6.10e-04

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


Pssm-ID: 197241 [Multi-domain]  Cd Length: 142  Bit Score: 39.82  E-value: 6.10e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 200 DNEEHRDDIERHYLKMLTQAQREVIIANAYFfPGYRFLHAL--RKAARRGVRIKLIIQGEPD-------MPIVRVGA-RL 269
Cdd:cd09143    1 RGQPEVREIEALYLDAIAAARRFIYIENQYF-TSRRIAEALaeRLREPDGPEIVIVLPRTSDgwleqltMGVARARLlRR 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446572968 270 LYNYLVKGGVQVF-----EYRRRPL--HGKVALMDDHWATVGSSNLDPLSLSLNLEANVII 323
Cdd:cd09143   80 LREADRHGRLRVYypvtaGGGGRPIyvHSKLMIVDDRLLRVGSANLNNRSMGLDTECDLAI 140
PLDc_C_DEXD_like cd09126
C-terminal putative phospholipase D-like domain of uncharacterized prokaryotic HKD family ...
 204-298 8.54e-04

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


Pssm-ID: 197224 [Multi-domain]  Cd Length: 126  Bit Score: 39.16  E-value: 8.54e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 204 HRDDIERHYLKMLTQAQREVIIANAYFFPGYR--FLHALRKAARRGVRIKLIIQGEPDmpivrvgARLLYNYLVKGGVQV 281
Cdd:cd09126    5 DGNNYEEVFRKDLAQAKKSIIISSPYVSQKRItkLINLLKEAQERGVEVTVVTREPKE-------YKELIEELRSAGVKV 77

                         90
                 ....*....|....*..
gi 446572968 282 feYRRRPLHGKVALMDD 298
Cdd:cd09126   78 --KLKEEIHEKFAIIDK 92
PLDc_Nuc_like cd09116
Catalytic domain of EDTA-resistant nuclease Nuc, vertebrate phospholipase D6, and similar ...
 26-132 2.74e-03

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: 38.05  E-value: 2.74e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968  26 KAIGEAQERIILETFiWFED-DVGKQLHAALlaaaQRGVKAEVLLDG-YGSPDLSDEFVNELTAAGVVFRYYDPRPRlfg 103
Cdd:cd09116   16 ALIANAKSSIDVAMY-ALTDpEIAEALKRAA----KRGVRVRIILDKdSLADNLSITLLALLSNLGIPVRTDSGSKL--- 87

                         90       100
                 ....*....|....*....|....*....
gi 446572968 104 mrtnvfrrMHRKIVVIDARIAFIGGLNYS 132
Cdd:cd09116   88 --------MHHKFIIIDGKIVITGSANWT 108
PLDc_Nuc_like_unchar2 cd09174
Putative catalytic domain of uncharacterized hypothetical proteins closely related to Nuc, , ...
 201-258 2.94e-03

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


Pssm-ID: 197271 [Multi-domain]  Cd Length: 136  Bit Score: 37.68  E-value: 2.94e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 446572968 201 NEEHRDDIERHYLKMLTQAQREVIIANAYFfPGYRFLHALRKAARRGVRIKLIIQGEP 258
Cdd:cd09174    1 TEVLFDDIENRIIEEIKKAKFSIWIAVAWF-TNKDIFNALKNKKKEGVNIQIIINDDD 57
PLDc_CLS_unchar1_2 cd09162
Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial ...
 16-130 3.56e-03

Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial cardiolipin synthase; Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial cardiolipin (CL) synthases, which catalyze the reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form CL and glycerol. Members of this subfamily contain two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. The two motifs may be part of the active site and may be involved in phosphatidyl group transfer.


Pssm-ID: 197259 [Multi-domain]  Cd Length: 172  Bit Score: 38.01  E-value: 3.56e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968  16 NGEQYYPAVFKAIGEAQERIILETFIWFEDDVgkqLHAALLAAAQRGVKAEVLLdgygsPDLSDE---------FVNELT 86
Cdd:cd09162    8 PGDPLYEALLSAIFEAEHRIWIVTPYFVPDEV---LLRALRLAARRGVDVRLIV-----PKRSNHriadlargsYLRDLQ 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 446572968  87 AAGVVFRYYDPrprlfGMrtnvfrrMHRKIVVIDARIAFIGGLN 130
Cdd:cd09162   80 EAGAEIYLYQP-----GM-------LHAKAVVVDDKLALVGSAN 111
PLDc_yjhR_C_like cd09118
C-terminal domain of Escherichia coli uncharacterized protein yjhR and similar proteins; ...
 235-339 6.10e-03

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


Pssm-ID: 197217 [Multi-domain]  Cd Length: 144  Bit Score: 36.91  E-value: 6.10e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968 235 RFLHALRKAARRGVRIKliIQGEPDMPIVRVG-----ARLLYNYLVKGGVQVFEYRRrpLHGKVALMDDHWATVGSSNLd 309
Cdd:cd09118   33 GLLEAIREAVSRGVDVT--IYTDPHLNTGDANdtkanLEDAAEALAEAGIRIHEVNG--VHSKIVIVDNHLLAVGSFNW- 107

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 446572968 310 pLSLS-----LNLEANVIIHDRHFNQ---TLRDNLNGI 339
Cdd:cd09118  108 -LSAVrdgkyARHETSLVYRGEGLEKeinTILDSLNSR 144
PLDc_vPLD1_2_like_1 cd09104
Catalytic domain, repeat 1, of vertebrate phospholipases, PLD1 and PLD2, and similar proteins; ...
 11-130 6.89e-03

Catalytic domain, repeat 1, of vertebrate phospholipases, PLD1 and PLD2, and similar proteins; Catalytic domain, repeat 1, of phospholipase D (PLD, EC 3.1.4.4) found in yeast, plants, and vertebrates, and their bacterial homologs. PLDs are involved in signal transduction, vesicle formation, protein transport, and mitosis by participating in phospholipid metabolism. They hydrolyze the terminal phosphodiester bond of phospholipids resulting in the formation of phosphatidic acid and alcohols. Phosphatidic acid is an essential compound involved in signal transduction. PLDs also catalyze the transphosphatidylation of phospholipids to acceptor alcohols, by which various phospholipids can be synthesized. Both prokaryotic and eukaryotic PLDs have two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. PLDs are active as bi-lobed monomers. Each monomer contains two domains, each of which carries one copy of the HKD motif. Two HKD motifs from two domains form a single active site. PLDs utilize a common two-step ping-pong catalytic mechanism involving an enzyme-substrate intermediate to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine residue from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group.


Pssm-ID: 197203 [Multi-domain]  Cd Length: 147  Bit Score: 36.99  E-value: 6.89e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446572968  11 IELLENGEQYYPAVFKAIGEAQERIILETFiWFEDDVGKQLHAALLAA---------AQRGVKAEVLLdgYGSP------ 75
Cdd:cd09104    1 VEPLIDGEEYFDDLAEALDGARHSVYITGW-QVSADIILAPLLAGPDRlgdtlrtlaARRGVDVRVLL--WDSPllvllg 77

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446572968  76 -DLSDEFV-----NELTAAGVVFRYYDPRPRLFGmrtnvfrrMHRKIVVID-ARIAFIGGLN 130
Cdd:cd09104   78 pDDKDLNLgfptfLRLTTALLVLDLRLRRHTLFS--------HHQKLVVIDsAEVAFVGGID 131
PLDc_vPLD1_2_yPLD_like_1 cd09138
Catalytic domain, repeat 1, of vertebrate phospholipases, PLD1 and PLD2, yeast PLDs, and ...
 113-129 8.98e-03

Catalytic domain, repeat 1, of vertebrate phospholipases, PLD1 and PLD2, yeast PLDs, and similar proteins; Catalytic domain, repeat 1, of vertebrate phospholipases D (PLD1 and PLD2), yeast phospholipase D (PLD SPO14/PLD1), and other similar eukaryotic proteins. These PLD enzymes play a pivotal role in transmembrane signaling and cellular regulation. They hydrolyze the terminal phosphodiester bond of phospholipids resulting in the formation of phosphatidic acid and alcohols. Phosphatidic acid is an essential compound involved in signal transduction. PLDs also catalyze the transphosphatidylation of phospholipids to acceptor alcohols, by which various phospholipids can be synthesized. The vertebrate PLD1 and PLD2 are membrane associated phosphatidylinositol 4,5-bisphosphate (PIP2)-dependent enzymes that selectively hydrolyze phosphatidylcholine (PC). Protein cofactors and calcium may be required for their activation. Yeast SPO14/PLD1 is a calcium-independent PLD, which needs PIP2 for its activity. Instead of the regulatory calcium-dependent phospholipid-binding C2 domain in plants, most mammalian and yeast PLDs have adjacent Phox (PX) and the Pleckstrin homology (PH) domains at the N-terminus, which have been shown to mediate membrane targeting of the protein and are closely linked to polyphosphoinositide signaling. The PX and PH domains are also present in zeta-type PLD from Arabidopsis, which is more closely related to vertebrate PLDs than to other plant PLD types. In addition, this subfamily also includes some related proteins which have either PX-like or PH domains in their N-termini. Like other members of the PLD superfamily, the monomer of mammalian and yeast PLDs consists of two catalytic domains, each containing one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue). Two HKD motifs from the two domains form a single active site. These PLDs utilize a common two-step ping-pong catalytic mechanism involving an enzyme-substrate intermediate to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine residue from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group.


Pssm-ID: 197236 [Multi-domain]  Cd Length: 146  Bit Score: 36.39  E-value: 8.98e-03
                         10
                 ....*....|....*..
gi 446572968 113 HRKIVVIDARIAFIGGL 129
Cdd:cd09138  113 HEKIVVIDQSIAFVGGL 129
 
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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