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Conserved domains on  [gi|166197683|ref|NP_036400|]
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5'-3' exonuclease PLD3 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PHA02820 super family cl33698
phospholipase-D-like protein; Provisional
 77-490 2.45e-145

phospholipase-D-like protein; Provisional


The actual alignment was detected with superfamily member PHA02820:

Pssm-ID: 222934 [Multi-domain]  Cd Length: 424  Bit Score: 422.87  E-value: 2.45e-145
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683  77 CYDPCEAVLVESIPEGLDFPNAstgNPSTSQAWLGLLAGAHSSLDIASFYWTLTNNDthtqepSAQQGEEVLRQLQTLAP 156
Cdd:PHA02820   2 NPDNTIAVITETIPIGMQFDKV---YLSTFNFWREILSNTTKTLDISSFYWSLSDEV------GTNFGTMILNEIIQLPK 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 157 KGVNVRIAVSKPSgpQPQADLQALLQSGAQVRMVDMQKLTHGVLHTKFWVVDQTHFYLGSANMDWRSLTQVKELGVVMYN 236
Cdd:PHA02820  73 RGVRVRIAVNKSN--KPLKDVELLQMAGVEVRYIDITNILGGVLHTKFWISDNTHIYLGSANMDWRSLTQVKELGIAIFN 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 237 CSCLARDLTKIFEAYWFLGQagSSIPSTWPRFYDTRYNQETPMEICLNGTPALAYLASAPPPLCPSGRTPDLKALLNVVD 316
Cdd:PHA02820 151 NSNLAADLTQIFEVYWYLGV--NNLPYNWKNFYPLYYNTDHPLSLNVSGVPHSVFIASAPQQLCTMERTNDLTALLSCIR 228

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 317 NARSFIYVAVMNYLPTLeFSHPHR--FWPAIDDGLRRATYERGVKVRLLISCWGHSEPSMRAFLLSLAALrdNHTHSDIQ 394
Cdd:PHA02820 229 NASKFVYVSVMNFIPII-YSKAGKilFWPYIEDELRRAAIDRKVSVKLLISCWQRSSFIMRNFLRSIAML--KSKNINIE 305

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 395 VKLFVVPadEAQARIPYARVNHNKYMVTERATYIGTSNWSGNYFTETAGTSLLVTQNGRGGLRSQLEAIFLRDWDSPYSH 474
Cdd:PHA02820 306 VKLFIVP--DADPPIPYSRVNHAKYMVTDKTAYIGTSNWTGNYFTDTCGVSINITPDDGLGLRQQLEDIFIRDWNSKYSY 383

                        410
                 ....*....|....*.
gi 166197683 475 DLdtSADSVGNACRLL 490
Cdd:PHA02820 384 EL--YDTSPTKRCRLL 397
 
Name Accession Description Interval E-value
PHA02820 PHA02820
phospholipase-D-like protein; Provisional
 77-490 2.45e-145

phospholipase-D-like protein; Provisional


Pssm-ID: 222934 [Multi-domain]  Cd Length: 424  Bit Score: 422.87  E-value: 2.45e-145
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683  77 CYDPCEAVLVESIPEGLDFPNAstgNPSTSQAWLGLLAGAHSSLDIASFYWTLTNNDthtqepSAQQGEEVLRQLQTLAP 156
Cdd:PHA02820   2 NPDNTIAVITETIPIGMQFDKV---YLSTFNFWREILSNTTKTLDISSFYWSLSDEV------GTNFGTMILNEIIQLPK 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 157 KGVNVRIAVSKPSgpQPQADLQALLQSGAQVRMVDMQKLTHGVLHTKFWVVDQTHFYLGSANMDWRSLTQVKELGVVMYN 236
Cdd:PHA02820  73 RGVRVRIAVNKSN--KPLKDVELLQMAGVEVRYIDITNILGGVLHTKFWISDNTHIYLGSANMDWRSLTQVKELGIAIFN 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 237 CSCLARDLTKIFEAYWFLGQagSSIPSTWPRFYDTRYNQETPMEICLNGTPALAYLASAPPPLCPSGRTPDLKALLNVVD 316
Cdd:PHA02820 151 NSNLAADLTQIFEVYWYLGV--NNLPYNWKNFYPLYYNTDHPLSLNVSGVPHSVFIASAPQQLCTMERTNDLTALLSCIR 228

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 317 NARSFIYVAVMNYLPTLeFSHPHR--FWPAIDDGLRRATYERGVKVRLLISCWGHSEPSMRAFLLSLAALrdNHTHSDIQ 394
Cdd:PHA02820 229 NASKFVYVSVMNFIPII-YSKAGKilFWPYIEDELRRAAIDRKVSVKLLISCWQRSSFIMRNFLRSIAML--KSKNINIE 305

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 395 VKLFVVPadEAQARIPYARVNHNKYMVTERATYIGTSNWSGNYFTETAGTSLLVTQNGRGGLRSQLEAIFLRDWDSPYSH 474
Cdd:PHA02820 306 VKLFIVP--DADPPIPYSRVNHAKYMVTDKTAYIGTSNWTGNYFTDTCGVSINITPDDGLGLRQQLEDIFIRDWNSKYSY 383

                        410
                 ....*....|....*.
gi 166197683 475 DLdtSADSVGNACRLL 490
Cdd:PHA02820 384 EL--YDTSPTKRCRLL 397
PLDc_vPLD3_2 cd09147
Putative catalytic domain, repeat 2, of vertebrate phospholipase PLD3; Putative catalytic ...
 291-473 2.17e-134

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


Pssm-ID: 197245  Cd Length: 186  Bit Score: 385.86  E-value: 2.17e-134
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 291 YLASAPPPLCPSGRTPDLKALLNVVDNARSFIYVAVMNYLPTLEFSHPHRFWPAIDDGLRRATYERGVKVRLLISCWGHS 370
Cdd:cd09147    1 YLSSSPPPLCASGRTPDLQSILNVIDNARSFVYIAVMNYLPTLEFSHPHRYWPAIDDGLRRATYERGVKVRLLISCWGHS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 371 EPSMRAFLLSLAALRDNHTHSDIQVKLFVVPADEAQARIPYARVNHNKYMVTERATYIGTSNWSGNYFTETAGTSLLVTQ 450
Cdd:cd09147   81 EPSMFAFLRSLAALRDNTTHSDIQVKIFVVPADEAQKKIPYARVNHNKYMVTDRVAYIGTSNWSGDYFTNTAGSALVVNQ 160

                        170       180
                 ....*....|....*....|....*.
gi 166197683 451 NGR---GGLRSQLEAIFLRDWDSPYS 473
Cdd:cd09147  161 TGRsasGTLQSQLQAVFERDWDSPYS 186
PLDc_3 pfam13918
PLD-like domain;
223-401 3.22e-39

PLD-like domain;


Pssm-ID: 464040  Cd Length: 180  Bit Score: 140.15  E-value: 3.22e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683  223 SLTQVKELGVVMYNCSCLARDLTKIFEAYWFLgQAGSSIPSTWPRFYDTRYNQETPMEICLNGTPALAYLASAPPPLCPS 302
Cdd:pfam13918   1 SLGQIKELGLVFTNCKCLALDLMNIFALFSSL-IFENKVPFTWSKRLCCAVDNEKALNFHLNESGGGAFFSDSPELFCGF 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683  303 GRTPDLKALLNVVDNARSFIYVAVMNYLPTLEFSHPHRFWPAIDDGLRRATYERGVKVRLLISCWGHSEPSMRAFLLSLA 382
Cdd:pfam13918  80 NRSFDEDAILHRIDDAKLSIDIALLDMLPIIKHAGAREYWPDIDDAILEAAILRGVKVRLIISEWKEADPLSFNAARSLD 159

                         170
                  ....*....|....*....
gi 166197683  383 ALRDNHTHSDIQVKLFVVP 401
Cdd:pfam13918 160 AFCTEIANCDLKVKFFDLE 178
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 107-477 1.31e-19

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: 90.39  E-value: 1.31e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 107 QAWLGLLAGAHSSLDIASFYWTltnNDthtqepsaQQGEEVLRQLQTLAPKGVNVRIAV-SKPSGPQPQADLQALLQSGA 185
Cdd:COG1502   28 AALLEAIEAARRSIDLEYYIFD---DD--------EVGRRLADALIAAARRGVKVRVLLdGIGSRALNRDFLRRLRAAGV 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 186 QVRMVDMQKLT----HGVLHTKFWVVDQTHFYLGSANMDWRSLTQVKELG-----VVMYNCSCLArDLTKIFEAYWFLgQ 256
Cdd:COG1502   97 EVRLFNPVRLLfrrlNGRNHRKIVVIDGRVAFVGGANITDEYLGRDPGFGpwrdtHVRIEGPAVA-DLQAVFAEDWNF-A 174

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 257 AGSSIPstWPRFydtrynqetpmeiclNGTPALAYLASAPpplcPSGRTPDLKALLNVVDNARSFIYVAVMNYLPTlefs 336
Cdd:COG1502  175 TGEALP--FPEP---------------AGDVRVQVVPSGP----DSPRETIERALLAAIASARRRIYIETPYFVPD---- 229

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 337 hphrfwPAIDDGLRRAtYERGVKVRLLISCWGHSEPSMRAFLLSLAALRdnhthsdiqvklfvvpadEAQARI--PYARV 414
Cdd:COG1502  230 ------RSLLRALIAA-ARRGVDVRILLPAKSDHPLVHWASRSYYEELL------------------EAGVRIyeYEPGF 284

                        330       340       350       360       370       380
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 166197683 415 NHNKYMVT-ERATYIGTSNWSGNYF---TETAgtslLVTQNGRggLRSQLEAIFLRDWDSPYSHDLD 477
Cdd:COG1502  285 LHAKVMVVdDEWALVGSANLDPRSLrlnFEVN----LVIYDPE--FAAQLRARFEEDLAHSREVTLE 345
PLDc smart00155
Phospholipase D. Active site motifs; Phosphatidylcholine-hydrolyzing phospholipase D (PLD) ...
 198-223 7.40e-10

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: 53.93  E-value: 7.40e-10
                           10        20
                   ....*....|....*....|....*.
gi 166197683   198 GVLHTKFWVVDQTHFYLGSANMDWRS 223
Cdd:smart00155   3 GVLHTKLMIVDDEIAYIGSANLDGRS 28
bac_cardiolipin TIGR04265
cardiolipin synthase; This model is based on experimentally characterized bacterial ...
 107-251 3.11e-05

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: 46.32  E-value: 3.11e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683  107 QAWLGLLAGAHSSLDIASFYWTltnndthtqePSaqqgEEVLRQLQTLAPKGVNVRIAV-SKPSGP----QPQADLQALL 181
Cdd:TIGR04265 321 YGYLKMIYSAKKSIYIQSPYFI----------PD----DDLLHAIKIAALSGVDVSIMIpNKPDHPlvfwASRSNFTELL 386

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683  182 QSGAQVRMVDmqkltHGVLHTKFWVVDQTHFYLGSANMDWRSLTQVKELGVVMYNCScLARDLTKIFEAY 251
Cdd:TIGR04265 387 AAGVKIYQYE-----NGFLHSKSVLVDDEIASVGTANMDMRSFWLNFEVNAFIYDKG-FAKDLAAAYDDD 450
 
Name Accession Description Interval E-value
PHA02820 PHA02820
phospholipase-D-like protein; Provisional
 77-490 2.45e-145

phospholipase-D-like protein; Provisional


Pssm-ID: 222934 [Multi-domain]  Cd Length: 424  Bit Score: 422.87  E-value: 2.45e-145
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683  77 CYDPCEAVLVESIPEGLDFPNAstgNPSTSQAWLGLLAGAHSSLDIASFYWTLTNNDthtqepSAQQGEEVLRQLQTLAP 156
Cdd:PHA02820   2 NPDNTIAVITETIPIGMQFDKV---YLSTFNFWREILSNTTKTLDISSFYWSLSDEV------GTNFGTMILNEIIQLPK 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 157 KGVNVRIAVSKPSgpQPQADLQALLQSGAQVRMVDMQKLTHGVLHTKFWVVDQTHFYLGSANMDWRSLTQVKELGVVMYN 236
Cdd:PHA02820  73 RGVRVRIAVNKSN--KPLKDVELLQMAGVEVRYIDITNILGGVLHTKFWISDNTHIYLGSANMDWRSLTQVKELGIAIFN 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 237 CSCLARDLTKIFEAYWFLGQagSSIPSTWPRFYDTRYNQETPMEICLNGTPALAYLASAPPPLCPSGRTPDLKALLNVVD 316
Cdd:PHA02820 151 NSNLAADLTQIFEVYWYLGV--NNLPYNWKNFYPLYYNTDHPLSLNVSGVPHSVFIASAPQQLCTMERTNDLTALLSCIR 228

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 317 NARSFIYVAVMNYLPTLeFSHPHR--FWPAIDDGLRRATYERGVKVRLLISCWGHSEPSMRAFLLSLAALrdNHTHSDIQ 394
Cdd:PHA02820 229 NASKFVYVSVMNFIPII-YSKAGKilFWPYIEDELRRAAIDRKVSVKLLISCWQRSSFIMRNFLRSIAML--KSKNINIE 305

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 395 VKLFVVPadEAQARIPYARVNHNKYMVTERATYIGTSNWSGNYFTETAGTSLLVTQNGRGGLRSQLEAIFLRDWDSPYSH 474
Cdd:PHA02820 306 VKLFIVP--DADPPIPYSRVNHAKYMVTDKTAYIGTSNWTGNYFTDTCGVSINITPDDGLGLRQQLEDIFIRDWNSKYSY 383

                        410
                 ....*....|....*.
gi 166197683 475 DLdtSADSVGNACRLL 490
Cdd:PHA02820 384 EL--YDTSPTKRCRLL 397
PLDc_vPLD3_2 cd09147
Putative catalytic domain, repeat 2, of vertebrate phospholipase PLD3; Putative catalytic ...
 291-473 2.17e-134

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


Pssm-ID: 197245  Cd Length: 186  Bit Score: 385.86  E-value: 2.17e-134
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 291 YLASAPPPLCPSGRTPDLKALLNVVDNARSFIYVAVMNYLPTLEFSHPHRFWPAIDDGLRRATYERGVKVRLLISCWGHS 370
Cdd:cd09147    1 YLSSSPPPLCASGRTPDLQSILNVIDNARSFVYIAVMNYLPTLEFSHPHRYWPAIDDGLRRATYERGVKVRLLISCWGHS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 371 EPSMRAFLLSLAALRDNHTHSDIQVKLFVVPADEAQARIPYARVNHNKYMVTERATYIGTSNWSGNYFTETAGTSLLVTQ 450
Cdd:cd09147   81 EPSMFAFLRSLAALRDNTTHSDIQVKIFVVPADEAQKKIPYARVNHNKYMVTDRVAYIGTSNWSGDYFTNTAGSALVVNQ 160

                        170       180
                 ....*....|....*....|....*.
gi 166197683 451 NGR---GGLRSQLEAIFLRDWDSPYS 473
Cdd:cd09147  161 TGRsasGTLQSQLQAVFERDWDSPYS 186
PLDc_vPLD3_1 cd09144
Putative catalytic domain, repeat 1, of vertebrate phospholipase PLD3; Putative catalytic ...
 84-255 6.57e-125

Putative catalytic domain, repeat 1, of vertebrate phospholipase PLD3; Putative catalytic domain, repeat 1, of phospholipase D3 (PLD3, EC 3.1.4.4). The human protein is also known as Hu-K4 or HUK4 and it was identified as a human homolog of the vaccinia virus protein K4, which is encoded by the HindIII K4L gene. PLD3 is found in many human organs with highest expression levels found in the central nervous system. Due to the presence of two copies of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue), PLD3 has been assigned to the PLD superfamily although no catalytic activity has been detected experimentally. PLD3 is a membrane-bound protein that colocalizes with protein disulfide isomerase, an endoplasmic reticulum (ER) protein. Like other homologs of protein K4, PLD3 might alter the lipid content of associated membranes by selectively hydrolyzing phosphatidylcholine (PC) into the corresponding phosphatidic acid, which is thought to be involved in the regulation of lipid movement.


Pssm-ID: 197242 [Multi-domain]  Cd Length: 172  Bit Score: 361.19  E-value: 6.57e-125
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683  84 VLVESIPEGLDFPNASTGNPSTSQAWLGLLAGAHSSLDIASFYWTLTNNDTHTQEPSAQQGEEVLRQLQTLAPKGVNVRI 163
Cdd:cd09144    1 VLVESIPEGLVFNSSSTINPSIYQAWLNLISAAQSSLDIASFYWTLTNSDTHTQEPSANQGEQILKKLGQLSQSGVYVRI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 164 AVSKPSGPQPQADLQALLQSGAQVRMVDMQKLTHGVLHTKFWVVDQTHFYLGSANMDWRSLTQVKELGVVMYNCSCLARD 243
Cdd:cd09144   81 AVDKPADPKPMEDINALSSYGADVRMVDMRKLTTGVLHTKFWVVDKKHFYIGSANMDWRSLTQVKELGAVVYNCSCLAED 160

                        170
                 ....*....|..
gi 166197683 244 LTKIFEAYWFLG 255
Cdd:cd09144  161 LGKIFEAYWYLG 172
PLDc_vPLD3_4_5_like_2 cd09107
Putative catalytic domain, repeat 2, of vertebrate phospholipases, PLD3, PLD4 and PLD5, viral ...
 291-469 7.77e-95

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


Pssm-ID: 197206 [Multi-domain]  Cd Length: 175  Bit Score: 284.53  E-value: 7.77e-95
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 291 YLASAPPPLCPSGRTPDLKALLNVVDNARSFIYVAVMNYLPTLEFSHPHRFWPAIDDGLRRATYERGVKVRLLISCWGHS 370
Cdd:cd09107    1 FLSSSPPELCPPGRTDDLDALLSTIDSAKKFIDISVMDYVPLSRYADPRKYWPVIDNALRRAAVDRGVKVRLLVSNWKHT 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 371 EPSMRAFLLSLAALRDNHTHSDIQVKLFVVPADEAQaRIPYARVNHNKYMVTERATYIGTSNWSGNYFTETAGTSLLVTQ 450
Cdd:cd09107   81 DPSMDAFLKSLQLLKSGVGNGDIEVKIFTVPGDQST-KIPFARVNHAKYMVTDERAYIGTSNWSGDYFYNTAGVSLVIND 159

                        170
                 ....*....|....*....
gi 166197683 451 NgrgGLRSQLEAIFLRDWD 469
Cdd:cd09107  160 P---AIVQQLKDVFERDWN 175
PLDc_vPLD4_2 cd09148
Putative catalytic domain, repeat 2, of vertebrate phospholipase PLD4; Putative catalytic ...
 291-473 5.12e-81

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


Pssm-ID: 197246  Cd Length: 187  Bit Score: 249.76  E-value: 5.12e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 291 YLASAPPPLCPSGRTPDLKALLNVVDNARSFIYVAVMNYLPTLEFSHPHRFWPAIDDGLRRATYERGVKVRLLISCWGHS 370
Cdd:cd09148    1 YLSASPPALCPTGRTSDLQAILSVISQAQEFIYISVMEYFPTCRFCHPKRYWSVLDNALRAAAFDRRVLIRLLISCGRHS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 371 EPSMRAFLLSLAALRDNHTHSDIQVKLFVVPADEaQARIPYARVNHNKYMVTERATYIGTSNWSGNYFTETAGTSLLVTQ 450
Cdd:cd09148   81 DPDMFPFLRSLNALSNPPLSISVHVKLFIVPVGN-QTNIPYSRVNHNKFMVTDKAAYIGTSNWSEDYFLNTAGVGLVILQ 159

                        170       180
                 ....*....|....*....|....*...
gi 166197683 451 ----NGRG-GLRSQLEAIFLRDWDSPYS 473
Cdd:cd09148  160 spgaNEEMlPVQEQLRSLFERDWSSPYA 187
PLDc_vPLD3_4_5_like_1 cd09106
Putative catalytic domain, repeat 1, of vertebrate phospholipases, PLD3, PLD4 and PLD5, viral ...
 85-237 5.61e-74

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: 230.21  E-value: 5.61e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683  85 LVESIPEGLDFPNaSTGNPSTSQAWLGLLAGAHSSLDIASFYWTLTNNDTHTqEPSAQQGEEVLRQLQTLAPKGVNVRIA 164
Cdd:cd09106    1 LVESIPEGLTFLS-SSSHLSTFEAWMELISSAKKSIDIASFYWNLRGTDTNP-DSSAQEGEDIFNALLEAAKRGVKIRIL 78

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 166197683 165 VSKPSGPQPQADLQALLQ-SGAQVRMVDMQKL-THGVLHTKFWVVDQTHFYLGSANMDWRSLTQVKELGVVMYNC 237
Cdd:cd09106   79 QDKPSKDKPDEDDLELAAlGGAEVRSLDFTKLiGGGVLHTKFWIVDGKHFYLGSANLDWRSLTQVKELGVYIYNC 153
PLDc_vPLD4_1 cd09145
Putative catalytic domain, repeat 1, of vertebrate phospholipase PLD4; Putative catalytic ...
 85-254 3.08e-66

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


Pssm-ID: 197243 [Multi-domain]  Cd Length: 170  Bit Score: 210.92  E-value: 3.08e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683  85 LVESIPEGLDFPNASTGNPSTSQAWLGLLAGAHSSLDIASFYWTLTNNDTHTQEPSAQQGEEVLRQLQTLAPKGVNVRIA 164
Cdd:cd09145    1 LVESIPEDLTYEGNSTFALPLQKAWTKLLDMAQEQVHVASYYWSLTGEDIGVNDSSSLPGEDILKELAELLSRNVSVRAA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 165 VSKPSGPQPQADLQALLQSGAQVRMVDMQKLTHGVLHTKFWVVDQTHFYLGSANMDWRSLTQVKELGVVMYNCSCLARDL 244
Cdd:cd09145   81 ASIPTLAANSTDLKILRQKGAHVRKVNFGRLTGGVLHSKFWIIDKKHIYVGSANMDWRSLTQVKELGAVIYNCSSLAKDL 160

                        170
                 ....*....|
gi 166197683 245 TKIFEAYWFL 254
Cdd:cd09145  161 HKTFQTYWVL 170
PHA03003 PHA03003
palmytilated EEV membrane glycoprotein; Provisional
 85-477 6.01e-51

palmytilated EEV membrane glycoprotein; Provisional


Pssm-ID: 177506 [Multi-domain]  Cd Length: 369  Bit Score: 177.55  E-value: 6.01e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683  85 LVESIPEGLDFPnasTGNPSTSQAWLGLLAGAHSSLDIASFYWTLTNNDthtqepsaqQGEEVLRQLQTLAPKGVNVRIA 164
Cdd:PHA03003  15 IVETLPKSLGIA---TQHMSTYECFDEIISQAKKYIYIASFCCNLRSTP---------EGRLILDKLKEAAESGVKVTIL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 165 VSKPSGpqpQADLQALLQSGAQVRMVDMQKLTH-GVLHTKFWVVDQTHFYLGSANMDWRSLTQVKELGVvmYN-CSCLAR 242
Cdd:PHA03003  83 VDEQSG---DKDEEELQSSNINYIKVDIGKLNNvGVLLGSFWVSDDRRCYIGNASLTGGSISTIKTLGV--YStYPPLAT 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 243 DLTKIFEAYWFLGQAGS-----SIPSTWPRfyDTRYNQETPMEIClngtpalaYLASAPPPLCPSGRTPDLKALLNVVDN 317
Cdd:PHA03003 158 DLRRRFDTFKAFNKNKSvfnrlCCACCLPV--STKYHINNPIGGV--------FFSDSPEHLLGYSRTLDADVVLHKIKS 227

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 318 ARSFIYVAVMNYLPTLEFSHPHRFWPAIDDGLRRATYERGVKVRLLISCWGHSEPSMRAFLLSLAALRDNHthsDIQVKL 397
Cdd:PHA03003 228 AKKSIDLELLSLVPVIREDDKTTYWPDIYNALIRAAINRGVKVRLLVGSWKKNDVYSMASVKSLQALCVGN---DLSVKV 304

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 398 FVVPadeaqaripyarvNHNKYM-VTERATYIGTSNWSGNYFTETAGTSLlvtQNGRGGLRSQLEAIFLRDWDSPYSHDL 476
Cdd:PHA03003 305 FRIP-------------NNTKLLiVDDEFAHITSANFDGTHYLHHAFVSF---NTIDKELVKELSAIFERDWTSSYSKPL 368


                 .
gi 166197683 477 D 477
Cdd:PHA03003 369 K 369
PLDc_vPLD5_2 cd09149
Putative catalytic domain, repeat 2, of inactive veterbrate phospholipase PLD5; Putative ...
 291-476 5.72e-49

Putative catalytic domain, repeat 2, of inactive veterbrate phospholipase PLD5; Putative catalytic domain, repeat 2, of inactive veterbrate phospholipases D5 (PLD5, EC 3.1.4.4), homologs of the vaccinia virus protein K4 encoded by the HindIII K4L gene. Vertebrate PLD5 has been assigned to the PLD superfamily, since it shows high sequence similarity to other human homologs of protein K4, which contain two copies of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue). However, due to the lack of functionally important histidine and lysine residues in the HKD motif, vetebrate PLD5 has been characterized as an inactive PLD.


Pssm-ID: 197247  Cd Length: 188  Bit Score: 166.57  E-value: 5.72e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 291 YLASAPPPLCPSGRTPDLKALLNVVDNARSFIYVAVMNYLPTLEFSHPHRFWPAIDDGLRRATYERGVKVRLLISCWGHS 370
Cdd:cd09149    1 YVSTSPKLFCPKHRSNDLEAIYRVIQDAKQFIYISVMDYLPLLSRSYARRYWSRIDSKIREALVLRSVRVRLLISFWRKT 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 371 EPSMRAFLLSLAALRDNHTHSDIQVKLFVVPADEAQAripYARVNHNKYMVTERATYIGTSNWSGNYFTETAGTSLLVTQ 450
Cdd:cd09149   81 DPLTFNFVSSLKSLCTEQANCSLEVKFFDLEEESDCT---SPRLNRNKYMVTDGAAYIGNFDWVGNDFTQNAGVGLVINQ 157

                        170       180       190
                 ....*....|....*....|....*....|.
gi 166197683 451 -----NGRGGLRSQLEAIFLRDWDSPYSHDL 476
Cdd:cd09149  158 adgveENNATIIEQLRAAFERDWYSNYAKSL 188
PLDc_vPLD5_1 cd09146
Putative catalytic domain, repeat 1, of inactive veterbrate phospholipase PLD5; Putative ...
 84-254 1.61e-45

Putative catalytic domain, repeat 1, of inactive veterbrate phospholipase PLD5; Putative catalytic domain, repeat 1, of inactive veterbrate phospholipases D5 (PLD5, EC 3.1.4.4), homologs of the vaccinia virus protein K4 encoded by the HindIII K4L gene. Vertebrate PLD5 has been assigned to the PLD superfamily, since it shows high sequence similarity to other human homologs of protein K4, which contain two copies of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue). However, due to the lack of functionally important histidine and lysine residues in the HKD motif, vetebrate PLD5 has been characterized as an inactive PLD.


Pssm-ID: 197244 [Multi-domain]  Cd Length: 163  Bit Score: 156.56  E-value: 1.61e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683  84 VLVESIPEGLDFPNASTGNPSTSQAWLGLLAGAHSSLDIASFYWTLtnNDTHtqePSAQQGEEVLRQLQTLAPKGVNVRI 163
Cdd:cd09146    1 ALVENIPDGINFSEHAPPHLPLSQGWMNLLDMAVKSVEIVSPLWDL--NASH---PSACQGQRLFERLLGLASRGVELKI 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 164 AvskpSGPQPQADLQALLQS-GAQVRMVDMQKLTHGVLHTKFWVVDQTHFYLGSANMDWRSLTQVKELGVVMYNCSCLAR 242
Cdd:cd09146   76 V----SGITDSTEVLVLLKKkGAEVHYVNMTALTKGRLQSSFWIVDKRHVYIGSASMDWRSLGQRKELGVIVYNCSCLAL 151

                        170
                 ....*....|..
gi 166197683 243 DLTKIFEAYWFL 254
Cdd:cd09146  152 DLHRVFALYWSL 163
PLDc_3 pfam13918
PLD-like domain;
223-401 3.22e-39

PLD-like domain;


Pssm-ID: 464040  Cd Length: 180  Bit Score: 140.15  E-value: 3.22e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683  223 SLTQVKELGVVMYNCSCLARDLTKIFEAYWFLgQAGSSIPSTWPRFYDTRYNQETPMEICLNGTPALAYLASAPPPLCPS 302
Cdd:pfam13918   1 SLGQIKELGLVFTNCKCLALDLMNIFALFSSL-IFENKVPFTWSKRLCCAVDNEKALNFHLNESGGGAFFSDSPELFCGF 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683  303 GRTPDLKALLNVVDNARSFIYVAVMNYLPTLEFSHPHRFWPAIDDGLRRATYERGVKVRLLISCWGHSEPSMRAFLLSLA 382
Cdd:pfam13918  80 NRSFDEDAILHRIDDAKLSIDIALLDMLPIIKHAGAREYWPDIDDAILEAAILRGVKVRLIISEWKEADPLSFNAARSLD 159

                         170
                  ....*....|....*....
gi 166197683  383 ALRDNHTHSDIQVKLFVVP 401
Cdd:pfam13918 160 AFCTEIANCDLKVKFFDLE 178
PLDc_SF cd00138
Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D ...
 107-234 4.93e-21

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: 88.34  E-value: 4.93e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 107 QAWLGLLAGAHSSLDIASFYWtltnndthtqepSAQQGEEVLRQLQTLAPKGVNVRIAVSKPSGPQPQ---ADLQALLQS 183
Cdd:cd00138    1 EALLELLKNAKESIFIATPNF------------SFNSADRLLKALLAAAERGVDVRLIIDKPPNAAGSlsaALLEALLRA 68

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 166197683 184 GAQVRMVDMQKLTHGVLHTKFWVVDQTHFYLGSANMDWRSLTQVKELGVVM 234
Cdd:cd00138   69 GVNVRSYVTPPHFFERLHAKVVVIDGEVAYVGSANLSTASAAQNREAGVLV 119
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 107-477 1.31e-19

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: 90.39  E-value: 1.31e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 107 QAWLGLLAGAHSSLDIASFYWTltnNDthtqepsaQQGEEVLRQLQTLAPKGVNVRIAV-SKPSGPQPQADLQALLQSGA 185
Cdd:COG1502   28 AALLEAIEAARRSIDLEYYIFD---DD--------EVGRRLADALIAAARRGVKVRVLLdGIGSRALNRDFLRRLRAAGV 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 186 QVRMVDMQKLT----HGVLHTKFWVVDQTHFYLGSANMDWRSLTQVKELG-----VVMYNCSCLArDLTKIFEAYWFLgQ 256
Cdd:COG1502   97 EVRLFNPVRLLfrrlNGRNHRKIVVIDGRVAFVGGANITDEYLGRDPGFGpwrdtHVRIEGPAVA-DLQAVFAEDWNF-A 174

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 257 AGSSIPstWPRFydtrynqetpmeiclNGTPALAYLASAPpplcPSGRTPDLKALLNVVDNARSFIYVAVMNYLPTlefs 336
Cdd:COG1502  175 TGEALP--FPEP---------------AGDVRVQVVPSGP----DSPRETIERALLAAIASARRRIYIETPYFVPD---- 229

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 337 hphrfwPAIDDGLRRAtYERGVKVRLLISCWGHSEPSMRAFLLSLAALRdnhthsdiqvklfvvpadEAQARI--PYARV 414
Cdd:COG1502  230 ------RSLLRALIAA-ARRGVDVRILLPAKSDHPLVHWASRSYYEELL------------------EAGVRIyeYEPGF 284

                        330       340       350       360       370       380
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 166197683 415 NHNKYMVT-ERATYIGTSNWSGNYF---TETAgtslLVTQNGRggLRSQLEAIFLRDWDSPYSHDLD 477
Cdd:COG1502  285 LHAKVMVVdDEWALVGSANLDPRSLrlnFEVN----LVIYDPE--FAAQLRARFEEDLAHSREVTLE 345
PLDc_2 pfam13091
PLD-like domain;
112-252 3.44e-16

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 75.02  E-value: 3.44e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683  112 LLAGAHSSLDIASFYWTLtnndthtqepsaqqGEEVLRQLQTLAPKGVNVRIAV----SKPSGPQ--PQADLQALLQSGA 185
Cdd:pfam13091   4 LINSAKKSIDIATYYFVP--------------DREIIDALIAAAKRGVDVRIILdsnkDDAGGPKkaSLKELRSLLRAGV 69

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 166197683  186 QVRMVDMQkltHGVLHTKFWVVDQTHFYLGSANMDWRSLTQVKELGVVMYNcSCLARDLTKIFEAYW 252
Cdd:pfam13091  70 EIREYQSF---LRSMHAKFYIIDGKTVIVGSANLTRRALRLNLENNVVIKD-PELAQELEKEFDRLW 132
PLDc_SF cd00138
Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D ...
 309-438 7.62e-14

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


Pssm-ID: 197200 [Multi-domain]  Cd Length: 119  Bit Score: 67.93  E-value: 7.62e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 309 KALLNVVDNARSFIYVAVmnylptleFSHPHRFWPAIDDGLRRATyERGVKVRLLISCWGHSEPSMRafllslAALRDNH 388
Cdd:cd00138    1 EALLELLKNAKESIFIAT--------PNFSFNSADRLLKALLAAA-ERGVDVRLIIDKPPNAAGSLS------AALLEAL 65

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 166197683 389 THSDIQVKLFVVPADeaqaripYARVNHNKYMVTERAT-YIGTSNWSGNYF 438
Cdd:cd00138   66 LRAGVNVRSYVTPPH-------FFERLHAKVVVIDGEVaYVGSANLSTASA 109
PLDc_CLS_2 cd09112
catalytic domain repeat 2 of bacterial cardiolipin synthase and similar proteins; This CD ...
 103-249 1.01e-10

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: 60.57  E-value: 1.01e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 103 PSTSQAWLGLLAGAHSSLDIASFYWTLTnndthtqepsaqqgEEVLRQLQTLAPKGVNVRIAVSKpsgpqpQAD------ 176
Cdd:cd09112   10 SSIEQAYLKAINSAKKSIYIQTPYFIPD--------------ESLLEALKTAALSGVDVRIMIPG------KPDhklvyw 69

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 166197683 177 -----LQALLQSGAQVRMvdMQKlthGVLHTKFWVVDQTHFYLGSANMDWRSLTQVKELGVVMYNcSCLARDLTKIFE 249
Cdd:cd09112   70 asrsyFEELLKAGVKIYE--YNK---GFLHSKTLIVDDEIASVGTANLDIRSFELNFEVNAVIYD-KEVAKKLEEIFE 141
PLDc_unchar1_2 cd09128
Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins; ...
 106-252 5.29e-10

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


Pssm-ID: 197226 [Multi-domain]  Cd Length: 142  Bit Score: 57.67  E-value: 5.29e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 106 SQAWLGLLAGAHSSLDIasfywtltnndthtQEPSAQQGEEVLRQLQTLAPKGVNVRIAVSKP--SGPQPQADLQALLQS 183
Cdd:cd09128   12 REALLALIDSAEESLLI--------------QNEEMGDDAPILDALVDAAKRGVDVRVLLPSAwsAEDERQARLRALEGA 77

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 166197683 184 GAQVRMVDMQKLThgvLHTKFWVVDQTHFYLGSANMDWRSLTQVKELGVVMYNCSCLARdLTKIFEAYW 252
Cdd:cd09128   78 GVPVRLLKDKFLK---IHAKGIVVDGKTALVGSENWSANSLDRNREVGLIFDDPEVAAY-LQAVFESDW 142
PLDc smart00155
Phospholipase D. Active site motifs; Phosphatidylcholine-hydrolyzing phospholipase D (PLD) ...
 198-223 7.40e-10

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: 53.93  E-value: 7.40e-10
                           10        20
                   ....*....|....*....|....*.
gi 166197683   198 GVLHTKFWVVDQTHFYLGSANMDWRS 223
Cdd:smart00155   3 GVLHTKLMIVDDEIAYIGSANLDGRS 28
PLDc_ybhO_like_2 cd09159
Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; ...
 97-249 4.72e-09

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: 55.62  E-value: 4.72e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683  97 NASTGNPSTSQAWLGLLAGAHSSLDIASFYWTltnndthtqePsaqqGEEVLRQLQTLAPKGVNVRIAVSKPSGPQP--- 173
Cdd:cd09159    4 DPRRRRSSIRRAYLVAIAAARRRIWIANAYFV----------P----DRRLRRALIEAARRGVDVRLLLPGKSDDPLtva 69

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 166197683 174 --QADLQALLQSGAQVRMvdmqkLTHGVLHTKFWVVDQTHFYLGSANMDWRSLTQVKELGVVMYnCSCLARDLTKIFE 249
Cdd:cd09159   70 asRALYGKLLRAGVRIFE-----YQPSMLHAKTAVIDGDWATVGSSNLDPRSLRLNLEANLVVE-DPAFAAQLEELFE 141
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 308-490 8.52e-09

Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and metabolism]; Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase is part of the Pathway/BioSystem: Phospholipid biosynthesis


Pssm-ID: 441111 [Multi-domain]  Cd Length: 367  Bit Score: 57.26  E-value: 8.52e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 308 LKALLNVVDNARSFIYVAvmnylpTLEFSHPHRfWPAIDDGLRRATyERGVKVRLLISCWGHSEPSmRAFLLSLAALRdn 387
Cdd:COG1502   27 FAALLEAIEAARRSIDLE------YYIFDDDEV-GRRLADALIAAA-RRGVKVRVLLDGIGSRALN-RDFLRRLRAAG-- 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 388 hthsdIQVKLFVvPADEAQARIPyaRVNHNKYMVT-ERATYIGTSNWSGNYFTETAG------TSLLVtqngRGGLRSQL 460
Cdd:COG1502   96 -----VEVRLFN-PVRLLFRRLN--GRNHRKIVVIdGRVAFVGGANITDEYLGRDPGfgpwrdTHVRI----EGPAVADL 163

                        170       180       190
                 ....*....|....*....|....*....|
gi 166197683 461 EAIFLRDWDSPYSHDLDTSADSVGNACRLL 490
Cdd:COG1502  164 QAVFAEDWNFATGEALPFPEPAGDVRVQVV 193
PLDc_Nuc_like cd09116
Catalytic domain of EDTA-resistant nuclease Nuc, vertebrate phospholipase D6, and similar ...
 110-252 1.13e-08

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


Pssm-ID: 197215 [Multi-domain]  Cd Length: 138  Bit Score: 53.84  E-value: 1.13e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 110 LGLLAGAHSSLDIASFywTLTNNdthtqepsaqqgeEVLRQLQTLAPKGVNVRIAVSKPSGPQPQADLQALLQSGAQVRM 189
Cdd:cd09116   15 VALIANAKSSIDVAMY--ALTDP-------------EIAEALKRAAKRGVRVRIILDKDSLADNLSITLLALLSNLGIPV 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 166197683 190 VDMQKltHGVLHTKFWVVDQTHFYLGSANMDWRSLTQVKELGVVMYNcsclaRDLTKIFEAYW 252
Cdd:cd09116   80 RTDSG--SKLMHHKFIIIDGKIVITGSANWTKSGFHRNDENLLIIDD-----PKLAASFEEEF 135
PLDc_SMU_988_like_2 cd09160
Putative catalytic domain, repeat 2, of Streptococcus mutans uncharacterized protein SMU_988 ...
 144-249 3.49e-08

Putative catalytic domain, repeat 2, of Streptococcus mutans uncharacterized protein SMU_988 and similar proteins; Putative catalytic domain, repeat 2, of Streptococcus mutans uncharacterized protein SMU_988 and similar proteins. Although SMU_988 and similar proteins have not been functionally characterized, members in this subfamily show high sequence homology to bacterial cardiolipin (CL) synthases, which catalyze the reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form CL and glycerol. Members of this subfamily contain two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. The two motifs may be part of the active site and may be involved in phosphatidyl group transfer.


Pssm-ID: 197257 [Multi-domain]  Cd Length: 176  Bit Score: 53.27  E-value: 3.49e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 144 GEEVLRQLQTLAPKGVNVRIAVskPSGP-------QPQADLQALLQSGaqvrmVDMQKLTHGVLHTKFWVVDQTHFYLGS 216
Cdd:cd09160   37 DDEMLDALCLAAKRGVDVRIIT--PHIPdkkyvflVTRSNYPELLEAG-----VKIYEYTPGFIHAKTFVSDDKAAVVGT 109

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 166197683 217 ANMDWRSLTQVKELGVVMYNCSCLA---RDLTKIFE 249
Cdd:cd09160  110 INLDYRSLYLHFECGVYMYDTPVISdikEDFEETLA 145
PLDc_ymdC_like_2 cd09113
Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and ...
 112-251 5.12e-08

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: 53.38  E-value: 5.12e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 112 LLAGAHSSLDIASFYWTLTNndthtqepsaqQGEEVLRQLqtlAPKGVNVRI-----------AVSkpSGPQPQadLQAL 180
Cdd:cd09113   25 LLKNAKREVLIVSPYFVPGD-----------EGVALLAEL---ARRGVRVRIltnslaatdvpAVH--SGYARY--RKRL 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 181 LQSGAQV-----------RMVDMQKLTHGVLHTKFWVVDQTHFYLGSANMDWRSLTQVKELGVVmYNCSCLARDLTKIFE 249
Cdd:cd09113   87 LKAGVELyelkpdaakrkRLRGLFGSSRASLHAKSFVIDDRLVFVGSFNLDPRSAYLNTEMGLV-IDSPELAAQLRAAME 165


                 ..
gi 166197683 250 AY 251
Cdd:cd09113  166 ED 167
PLDc pfam00614
Phospholipase D Active site motif; Phosphatidylcholine-hydrolysing phospholipase D (PLD) ...
 198-223 5.14e-08

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: 48.57  E-value: 5.14e-08
                          10        20
                  ....*....|....*....|....*.
gi 166197683  198 GVLHTKFWVVDQTHFYLGSANMDWRS 223
Cdd:pfam00614   3 GRLHRKIVVVDDELAYIGGANLDGRS 28
PLDc_2 pfam13091
PLD-like domain;
311-468 6.14e-08

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 51.52  E-value: 6.14e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683  311 LLNVVDNARSFIYVAVMnYLPTLefshphrfwPAIDDGLRRATyERGVKVRLLISCWGHSEPSM----RAFLLSLAAlrd 386
Cdd:pfam13091   1 LIDLINSAKKSIDIATY-YFVPD---------REIIDALIAAA-KRGVDVRIILDSNKDDAGGPkkasLKELRSLLR--- 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683  387 nhthSDIQVKLFVvpadeaqariPYARVNHNKYMVTERAT-YIGTSNWSGNYFTETAGTSLLVTQNgrgGLRSQLEAIFL 465
Cdd:pfam13091  67 ----AGVEIREYQ----------SFLRSMHAKFYIIDGKTvIVGSANLTRRALRLNLENNVVIKDP---ELAQELEKEFD 129


                  ...
gi 166197683  466 RDW 468
Cdd:pfam13091 130 RLW 132
PLDc_CLS_unchar1_2 cd09162
Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial ...
 146-267 9.83e-08

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: 51.88  E-value: 9.83e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 146 EVLRQLQTLAP-KGVNVRIAVSKPSGpQPQAD------LQALLQSGAQVRMvdmqkLTHGVLHTKFWVVDQTHFYLGSAN 218
Cdd:cd09162   38 EVLLRALRLAArRGVDVRLIVPKRSN-HRIADlargsyLRDLQEAGAEIYL-----YQPGMLHAKAVVVDDKLALVGSAN 111

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 166197683 219 MDWRSLTQVKELGVVMYNcsclARDLTKIFEayWFLGQAGSSIPSTWPR 267
Cdd:cd09162  112 LDMRSLFLNYEVAVFFYS----PADIKELSD--WIESLISQCTEGAPPP 154
PLDc_Nuc_like_unchar1_1 cd09172
Putative catalytic domain, repeat 1, of uncharacterized hypothetical proteins similar to Nuc, ...
 146-252 3.23e-07

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


Pssm-ID: 197269 [Multi-domain]  Cd Length: 144  Bit Score: 49.66  E-value: 3.23e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 146 EVLRQLQTLAPKGVNVRI--AVSKPSGPQPQADLQALLQSGAQVRMVDMQklTHGVLHTKFWVVDQ----THFYLGSANM 219
Cdd:cd09172   36 EIIDALKAAKDRGVRVRIilDDSSVTGDPTEESAAATLSKGPGALVKRRH--SSGLMHNKFLVVDRkdgpNRVLTGSTNF 113

                         90       100       110
                 ....*....|....*....|....*....|...
gi 166197683 220 DWRSLTQVKELGVVMYNcsclaRDLTKIFEAYW 252
Cdd:cd09172  114 TTSGLYGQSNNVLIFRN-----PAFAAAYLAYW 141
PLDc_vPLD6_like cd09171
Catalytic domain of vertebrate phospholipase D6 and similar proteins; Catalytic domain of ...
 113-252 3.60e-07

Catalytic domain of vertebrate phospholipase D6 and similar proteins; Catalytic domain of vertebrate phospholipase D6 (PLD6, EC 3.1.4.4), a homolog of the EDTA-resistant nuclease Nuc from Salmonella typhimurium, and similar proteins. PLD6 can selectively hydrolyze the terminal phosphodiester bond of phosphatidylcholine (PC) with the formation of phosphatidic acid and alcohols. Phosphatidic acid is an essential compound involved in signal transduction. It also catalyzes the transphosphatidylation of phospholipids to acceptor alcohols, by which various phospholipids can be synthesized. PLD6 belongs to the phospholipase D (PLD) superfamily. Its monomer contains a short conserved sequence motif, H-x-K-x(4)-D (where x represents any amino acid residue), termed the HKD motif, which is essential in catalysis. PLD6 is more closely related to the nuclease Nuc than to other vertebrate phospholipases, which have two copies of the HKD motif in a single polypeptide chain. Like Nuc, PLD6 may utilize a two-step mechanism to cleave phosphodiester bonds: Upon substrate binding, the bond is first attacked by a histidine residue from the HKD motif of one subunit to form a covalent phosphohistidine intermediate, which is then hydrolyzed by water with the aid of a second histidine residue from the other HKD motif in the opposite subunit.


Pssm-ID: 197268 [Multi-domain]  Cd Length: 136  Bit Score: 49.14  E-value: 3.60e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 113 LAGAHSSLDIASFywTLTNNDthtqepsaqqgeeVLRQLQTLAPKGVNVRIAVSKPSGPQPQADLQALLQSGAQVRMvdm 192
Cdd:cd09171   17 LLSARKSLDVCVF--TITCDD-------------LADAILDLHRRGVRVRIITDDDQMEDKGSDIGKLRKAGIPVRT--- 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 166197683 193 qKLTHGVLHTKFWVVDQTHFYLGSANmdW-RSLTQV-KELGVVMYNcSCLARDLTKIFEAYW 252
Cdd:cd09171   79 -DLSSGHMHHKFAVIDGKILITGSFN--WtRQAVTGnQENVLITND-PKLVKPFTEEFEKLW 136
PLDc_unchar1_1 cd09127
Putative catalytic domain, repeat 1, of uncharacterized phospholipase D-like proteins; ...
 110-250 9.73e-07

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: 48.03  E-value: 9.73e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 110 LGLLAGAHSSLDIASFYWTltnndthtqepsaqqGEEVLRQLQTLAPKGVNVRIAV-SKPSGPQPQAD--LQALLQSGAQ 186
Cdd:cd09127   14 VDAIASAKRSILLKMYEFT---------------DPALEKALAAAAKRGVRVRVLLeGGPVGGISRAEklLDYLNEAGVE 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 166197683 187 VR-MVDMQKLTHgvLHTKFWVVDQTHFYLGSANMDWRSLTQVKELGVVMYNcSCLARDLTKIFEA 250
Cdd:cd09127   79 VRwTNGTARYRY--THAKYIVVDDERALVLTENFKPSGFTGTRGFGVVTDD-PAVVAEIADVFDA 140
PLDc_EcCLS_like_2 cd09158
Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase and similar proteins; ...
 89-224 2.95e-06

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: 47.57  E-value: 2.95e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683  89 IPEGLDFPNASTgnpstSQAWLGLLAGAHSSLDIASFYWTltnndthtqePSaqqgEEVLRQLQTLAPKGVNVRIAVSKp 168
Cdd:cd09158    1 VPSGPDYPTENI-----PQLLLSAIHAARRRVVITTPYFV----------PD----ESLLQALCTAALRGVEVTLILPA- 60

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 166197683 169 SGPQPQADL------QALLQSGAQVRMvdmqkLTHGVLHTKFWVVDQTHFYLGSANMDWRSL 224
Cdd:cd09158   61 KNDSFLVGAasrsyyEELLEAGVKIYL-----YRGGLLHAKTVTVDDEVALVGSSNFDIRSF 117
cls PRK01642
cardiolipin synthetase; Reviewed
 60-251 4.07e-06

cardiolipin synthetase; Reviewed


Pssm-ID: 234967 [Multi-domain]  Cd Length: 483  Bit Score: 49.01  E-value: 4.07e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683  60 WEYGDLHLFGPNQRPAPCYDPCEAVLVESIPEGLDFPNastgnPSTSQAWLGLLAGAHSSLDIASFYWTltnndthtqeP 139
Cdd:PRK01642 279 WETGERILPPPPDVLIMPFEEASGHTVQVIASGPGDPE-----ETIHQFLLTAIYSARERLWITTPYFV----------P 343

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 140 SaqqgEEVLRQLQTLAPKGVNVRIAV-SKP--------SgpqpQADLQALLQSGaqVRMVDMQKlthGVLHTKFWVVDQT 210
Cdd:PRK01642 344 D----EDLLAALKTAALRGVDVRIIIpSKNdsllvfwaS----RAFFTELLEAG--VKIYRYEG---GLLHTKSVLVDDE 410

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 166197683 211 HFYLGSANMDWRSLTQVKELGVVMYNcSCLARDLTKIFEAY 251
Cdd:PRK01642 411 LALVGTVNLDMRSFWLNFEITLVIDD-TGFAADLAAMQEDY 450
PLDc_unchar1_1 cd09127
Putative catalytic domain, repeat 1, of uncharacterized phospholipase D-like proteins; ...
 306-443 9.38e-06

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: 45.33  E-value: 9.38e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 306 PD--LKALLNVVDNARSFIYVAVmnYlptlEFSHPhrfwpAIDDGLRRATyERGVKVRLLIscwghsEPSMRAFLLSLAA 383
Cdd:cd09127    6 PDdgVAPVVDAIASAKRSILLKM--Y----EFTDP-----ALEKALAAAA-KRGVRVRVLL------EGGPVGGISRAEK 67

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 166197683 384 LRDNHTHSDIQVKLfvvpaDEAQARIPYarvNHNKYMVT-ERATYIGTSNWSGNYFTETAG 443
Cdd:cd09127   68 LLDYLNEAGVEVRW-----TNGTARYRY---THAKYIVVdDERALVLTENFKPSGFTGTRG 120
bac_cardiolipin TIGR04265
cardiolipin synthase; This model is based on experimentally characterized bacterial ...
 107-251 3.11e-05

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: 46.32  E-value: 3.11e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683  107 QAWLGLLAGAHSSLDIASFYWTltnndthtqePSaqqgEEVLRQLQTLAPKGVNVRIAV-SKPSGP----QPQADLQALL 181
Cdd:TIGR04265 321 YGYLKMIYSAKKSIYIQSPYFI----------PD----DDLLHAIKIAALSGVDVSIMIpNKPDHPlvfwASRSNFTELL 386

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683  182 QSGAQVRMVDmqkltHGVLHTKFWVVDQTHFYLGSANMDWRSLTQVKELGVVMYNCScLARDLTKIFEAY 251
Cdd:TIGR04265 387 AAGVKIYQYE-----NGFLHSKSVLVDDEIASVGTANMDMRSFWLNFEVNAFIYDKG-FAKDLAAAYDDD 450
PLDc_vPLD3_4_5_like_2 cd09107
Putative catalytic domain, repeat 2, of vertebrate phospholipases, PLD3, PLD4 and PLD5, viral ...
 96-252 1.78e-04

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


Pssm-ID: 197206 [Multi-domain]  Cd Length: 175  Bit Score: 42.24  E-value: 1.78e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683  96 PNASTGNPSTS--QAWLGLLAGAHSSLDIA-------SFYwtlTNNDTHTQEPsaqqgEEVLRQlqTLAPKGVNVRIAVS 166
Cdd:cd09107    6 PPELCPPGRTDdlDALLSTIDSAKKFIDISvmdyvplSRY---ADPRKYWPVI-----DNALRR--AAVDRGVKVRLLVS 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 167 KPSGPQPQADlQALLQSGA----------QVRMVDM-----QKLTH-GVLHTKFWVVDqTHFYLGSANMDWRSLTQVKEL 230
Cdd:cd09107   76 NWKHTDPSMD-AFLKSLQLlksgvgngdiEVKIFTVpgdqsTKIPFaRVNHAKYMVTD-ERAYIGTSNWSGDYFYNTAGV 153

                        170       180
                 ....*....|....*....|..
gi 166197683 231 GVVMYNCScLARDLTKIFEAYW 252
Cdd:cd09107  154 SLVINDPA-IVQQLKDVFERDW 174
PLDc_Nuc_like cd09116
Catalytic domain of EDTA-resistant nuclease Nuc, vertebrate phospholipase D6, and similar ...
 308-436 2.24e-04

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


Pssm-ID: 197215 [Multi-domain]  Cd Length: 138  Bit Score: 41.13  E-value: 2.24e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 308 LKALLNVVDNARSFIYVAVmnylptLEFSHPhrfwpAIDDGLRRATyERGVKVRLLISCWGHSEPSMRAFLLSLAALRdn 387
Cdd:cd09116   11 ERLIVALIANAKSSIDVAM------YALTDP-----EIAEALKRAA-KRGVRVRIILDKDSLADNLSITLLALLSNLG-- 76

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 166197683 388 hthsdIQVKLfvvpaDEAQARIpyarvnHNK-YMVTERATYIGTSNWSGN 436
Cdd:cd09116   77 -----IPVRT-----DSGSKLM------HHKfIIIDGKIVITGSANWTKS 110
PLDc_ymdC_like_1 cd09111
Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and ...
 349-438 4.30e-04

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: 40.98  E-value: 4.30e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 349 LRRATyERGVKVRLLISCWGHSepSMRAFLLSLAAlrdnhtHSDIQVKLF------VVPADEAQARIPyaRVN---HNKY 419
Cdd:cd09111   42 LLEAA-DRGVRVRLLLDDLGTS--GRDRLLAALDA------HPNIEVRLFnpfrnrGGRLLEFLTDFS--RLNrrmHNKL 110

                         90       100
                 ....*....|....*....|
gi 166197683 420 M-VTERATYIGTSNWSGNYF 438
Cdd:cd09111  111 FiVDGAVAIVGGRNIGDEYF 130
PLDc smart00155
Phospholipase D. Active site motifs; Phosphatidylcholine-hydrolyzing phospholipase D (PLD) ...
 411-437 5.57e-04

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


Pssm-ID: 197546 [Multi-domain]  Cd Length: 28  Bit Score: 37.37  E-value: 5.57e-04
                           10        20
                   ....*....|....*....|....*...
gi 166197683   411 YARVNHNKYMVTE-RATYIGTSNWSGNY 437
Cdd:smart00155   1 YDGVLHTKLMIVDdEIAYIGSANLDGRS 28
PRK12452 PRK12452
cardiolipin synthase;
99-249 9.59e-04

cardiolipin synthase;


Pssm-ID: 171510 [Multi-domain]  Cd Length: 509  Bit Score: 41.83  E-value: 9.59e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683  99 STGNPSTSQAWLGLLAGAHSSLDIASFYWTLTNndthtqepsaqqgeEVLRQLQTLAPKGVNVRIAV-----SKPSGPQP 173
Cdd:PRK12452 339 SSDDKSIRNTLLAVMGSAKKSIWIATPYFIPDQ--------------ETLTLLRLSAISGIDVRILYpgksdSIISDQAS 404

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 166197683 174 QADLQALLQSGAQVrmvdmQKLTHGVLHTKFWVVDQTHFYLGSANMDWRSLTQVKELGVVMYNcSCLARDLTKIFE 249
Cdd:PRK12452 405 QSYFTPLLKAGASI-----YSYKDGFMHAKIVLVDDKIATIGTANMDVRSFELNYEIISVLYE-SETVHDIKRDFE 474
PLDc_PaCLS_like_2 cd09161
Putative catalytic domain, repeat 2, of Pseudomonas aeruginosa cardiolipin synthase and ...
 144-224 1.10e-03

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: 39.96  E-value: 1.10e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 144 GEEVLRQLQTLAPKGVNVRIAV-SKPSGPQPQ----ADLQALLQSGAQVrmvdmQKLTHGVLHTKFWVVDQTHFYLGSAN 218
Cdd:cd09161   37 DEGVLAALQLAALRGVDVRILIpERPDHLLVYlasfSYLPELIRAGVKV-----YRYQPGFLHQKVVLVDDELAAVGTAN 111


                 ....*.
gi 166197683 219 MDWRSL 224
Cdd:cd09161  112 LDNRSF 117
PLDc_CLS_unchar2_2 cd09163
Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial ...
 145-250 1.34e-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: 197260 [Multi-domain]  Cd Length: 176  Bit Score: 39.85  E-value: 1.34e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 145 EEVLRQLQTLAPKGVNVRIAVskpsgpqPQ------------ADLQALLQSGAQVRmvdmqkLTHGVL-HTKFWVVDQTH 211
Cdd:cd09163   38 RTLITALQAAALRGVEVDIVL-------PErnnlplvdwamrANLWELLEHGVRIY------LQPPPFdHSKLMVVDGAW 104

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 166197683 212 FYLGSANMDWRSLTQVKELGVVMYNCScLARDLTKIFEA 250
Cdd:cd09163  105 ALIGSANWDPRSLRLNFELNLEVYDTA-LAGQLDALFDS 142
PLDc_unchar1_2 cd09128
Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins; ...
 305-468 1.48e-03

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


Pssm-ID: 197226 [Multi-domain]  Cd Length: 142  Bit Score: 38.80  E-value: 1.48e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 305 TPD--LKALLNVVDNARSFIYVAvmnylpTLEFSHphrfWPAIDDGLRRATyERGVKVRLLIScwghSEPSMRAFLLSLA 382
Cdd:cd09128    7 SPDnaREALLALIDSAEESLLIQ------NEEMGD----DAPILDALVDAA-KRGVDVRVLLP----SAWSAEDERQARL 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 383 ALRDNHthsDIQVKLFVVPAdeaqariPYarvNHNKYMV-TERATYIGTSNWSGNYFTETAGTSLLVTQngrGGLRSQLE 461
Cdd:cd09128   72 RALEGA---GVPVRLLKDKF-------LK---IHAKGIVvDGKTALVGSENWSANSLDRNREVGLIFDD---PEVAAYLQ 135


                 ....*..
gi 166197683 462 AIFLRDW 468
Cdd:cd09128  136 AVFESDW 142
PLDc_Nuc cd09170
Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar ...
 305-474 1.51e-03

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


Pssm-ID: 197267 [Multi-domain]  Cd Length: 142  Bit Score: 39.04  E-value: 1.51e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 305 TPD---LKALLNVVDNARSFIYVAVmnYlptlEFSHphrfwPAIDDGLRRAtYERGVKVRLLIscwghSEPSMRAFLLSL 381
Cdd:cd09170    7 SPEggaRELILDVIDSARRSIDVAA--Y----SFTS-----PPIARALIAA-KKRGVDVRVVL-----DKSQAGGKYSAL 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 382 AALRDNHthsdIQVKLFVVPAdeaqaripyarVNHNKYMVTERATYI-GTSNWSGNYFTETAGTSLLVTQNgrgglrSQL 460
Cdd:cd09170   70 NYLANAG----IPVRIDDNYA-----------IMHNKVMVIDGKTVItGSFNFTASAEKRNAENLLVIRNP------PEL 128

                        170
                 ....*....|....
gi 166197683 461 EAIFLRDWDSPYSH 474
Cdd:cd09170  129 AQQYLQEWQRRWAQ 142
PLDc_Bfil_DEXD_like cd09117
Catalytic domain of type II restriction endonucleases BfiI and NgoFVII, and uncharacterized ...
 110-234 2.44e-03

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


Pssm-ID: 197216 [Multi-domain]  Cd Length: 117  Bit Score: 37.76  E-value: 2.44e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 110 LGLLAGAHSSLDIASFYWTLTNndthtqepsaqqGEEVLRQlqtlAPKGVNVRIAVSKPSGPQPQADLQALL---QSGAQ 186
Cdd:cd09117    7 LTRLIERADTIRIAVAFASAGG------------AIKLLDK----FREGKKIRLIVGLDFGGTSPADFALKLllaLGNLN 70

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 166197683 187 VRMVDmqklTHGVLHTK---FWVVDQTHFYLGSANMDWRSLTQVKELGVVM 234
Cdd:cd09117   71 VRIFD----AGPLLHAKlylFENDDPTRAIVGSANLTQGGLSGNIEAAVVI 117
PLDc_CLS_unchar2_1 cd09157
Putative catalytic domain, repeat 1, of uncharacterized proteins similar to bacterial ...
 347-468 3.33e-03

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: 38.32  E-value: 3.33e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 347 DGLRRAtYERGVKVRLLI----SCWghSEPSMRAFLlslaalrdnhTHSDIQVKLFVVPAdeAQARIPYARV-NHNKYMV 421
Cdd:cd09157   39 DALAEA-VARGVDVRVLIdgvgARY--SRPSIRRRL----------RRAGVPVARFLPPR--LPPRLPFINLrNHRKILV 103

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 166197683 422 TERAT-YIGTSNWSGNYFTETAGTsllvtqNG--------RGGLRSQLEAIFLRDW 468
Cdd:cd09157  104 VDGRTgFTGGMNIRDGHLVADDPK------NPvqdlhfrvEGPVVAQLQEVFAEDW 153
PLDc_vPLD1_2_like_2 cd09105
Catalytic domain, repeat 2, of vertebrate phospholipases, PLD1 and PLD2, and similar proteins; ...
 201-235 5.10e-03

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: 37.67  E-value: 5.10e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 166197683 201 HTKFWVVDQTHFYLGSANMDWRSLTQVKELGVVMY 235
Cdd:cd09105  111 HSKVVIVDDEWATVGSANLNRRSMTWDTELNLAVV 145
PLDc_unchar3 cd09131
Putative catalytic domain of uncharacterized phospholipase D-like proteins; Putative catalytic ...
 309-448 5.59e-03

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


Pssm-ID: 197229 [Multi-domain]  Cd Length: 143  Bit Score: 37.32  E-value: 5.59e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 166197683 309 KALLNVVDNARSFIYVA--VMNYLPtlefshPHRFWPA-IDDGLRRAtYERGVKVRLL----ISCWGHSEPSMRAFllsl 381
Cdd:cd09131    6 PALLDLINNAKRSIYIAmyMFKYYE------NPGNGVNtLLEALIDA-HKRGVDVKVVledsIDDDEVTEENDNTY---- 74

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 166197683 382 AALRDNHthsdIQVKLfvvpaDEAQARIpyarvnHNKYMVT-ERATYIGTSNWSGNYFTETAGTSLLV 448
Cdd:cd09131   75 RYLKDNG----VEVRF-----DSPSVTT------HTKLVVIdGRTVYVGSHNWTYSALDYNHEASVLI 127
 
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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