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Conserved domains on  [gi|2113648141|ref|XP_044125040|]
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5'-3' exonuclease PLD3 [Bufo gargarizans]

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
 79-492 1.70e-125

phospholipase-D-like protein; Provisional


The actual alignment was detected with superfamily member PHA02820:

Pssm-ID: 222934 [Multi-domain]  Cd Length: 424  Bit Score: 372.41  E-value: 1.70e-125
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141  79 CNDSCSIVLVESMPEGLEYapnSTFNPTVFDSWMNLLSQAKSSVDIASFYWTLTNNDThtqhptANEGELILQEMLKLKQ 158
Cdd:PHA02820    2 NPDNTIAVITETIPIGMQF---DKVYLSTFNFWREILSNTTKTLDISSFYWSLSDEVG------TNFGTMILNEIIQLPK 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 159 RGISLRVAVNPSGSPAKDadVNALRGSGAEVRVVNLPSLTNGVLHTKFWVVDGKHLYIGSANMDWRSLTQVKELGTTIYN 238
Cdd:PHA02820   73 RGVRVRIAVNKSNKPLKD--VELLQMAGVEVRYIDITNILGGVLHTKFWISDNTHIYLGSANMDWRSLTQVKELGIAIFN 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 239 CTCLAEDLGKIFEAYWVLGEANttIPSPWPDKFSTVYNKETPMEVSLNNTASLVYLSSSPPPLSAKGRTDDIDSILSIID 318
Cdd:PHA02820  151 NSNLAADLTQIFEVYWYLGVNN--LPYNWKNFYPLYYNTDHPLSLNVSGVPHSVFIASAPQQLCTMERTNDLTALLSCIR 228

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 319 DAKKFVYISVMDYTPTeEFSRPRR--YWPAIDNHLRKAVYERHVTVRLLISCWANSNPNMFAFLNSLAALHSEKTHykIE 396
Cdd:PHA02820  229 NASKFVYVSVMNFIPI-IYSKAGKilFWPYIEDELRRAAIDRKVSVKLLISCWQRSSFIMRNFLRSIAMLKSKNIN--IE 305

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 397 VKIFIVPvsPEQKHIPFARVNHNKYMVTDRVAYIGTSNWAGDYFIRTAGSAIvvnqTIAANATNTMQEQLKDVFLRDWNS 476
Cdd:PHA02820  306 VKLFIVP--DADPPIPYSRVNHAKYMVTDKTAYIGTSNWTGNYFTDTCGVSI----NITPDDGLGLRQQLEDIFIRDWNS 379

                         410
                  ....*....|....*.
gi 2113648141 477 NYTKVLhSLTSYKEKC 492
Cdd:PHA02820  380 KYSYEL-YDTSPTKRC 394
 
Name Accession Description Interval E-value
PHA02820 PHA02820
phospholipase-D-like protein; Provisional
 79-492 1.70e-125

phospholipase-D-like protein; Provisional


Pssm-ID: 222934 [Multi-domain]  Cd Length: 424  Bit Score: 372.41  E-value: 1.70e-125
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141  79 CNDSCSIVLVESMPEGLEYapnSTFNPTVFDSWMNLLSQAKSSVDIASFYWTLTNNDThtqhptANEGELILQEMLKLKQ 158
Cdd:PHA02820    2 NPDNTIAVITETIPIGMQF---DKVYLSTFNFWREILSNTTKTLDISSFYWSLSDEVG------TNFGTMILNEIIQLPK 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 159 RGISLRVAVNPSGSPAKDadVNALRGSGAEVRVVNLPSLTNGVLHTKFWVVDGKHLYIGSANMDWRSLTQVKELGTTIYN 238
Cdd:PHA02820   73 RGVRVRIAVNKSNKPLKD--VELLQMAGVEVRYIDITNILGGVLHTKFWISDNTHIYLGSANMDWRSLTQVKELGIAIFN 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 239 CTCLAEDLGKIFEAYWVLGEANttIPSPWPDKFSTVYNKETPMEVSLNNTASLVYLSSSPPPLSAKGRTDDIDSILSIID 318
Cdd:PHA02820  151 NSNLAADLTQIFEVYWYLGVNN--LPYNWKNFYPLYYNTDHPLSLNVSGVPHSVFIASAPQQLCTMERTNDLTALLSCIR 228

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 319 DAKKFVYISVMDYTPTeEFSRPRR--YWPAIDNHLRKAVYERHVTVRLLISCWANSNPNMFAFLNSLAALHSEKTHykIE 396
Cdd:PHA02820  229 NASKFVYVSVMNFIPI-IYSKAGKilFWPYIEDELRRAAIDRKVSVKLLISCWQRSSFIMRNFLRSIAMLKSKNIN--IE 305

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 397 VKIFIVPvsPEQKHIPFARVNHNKYMVTDRVAYIGTSNWAGDYFIRTAGSAIvvnqTIAANATNTMQEQLKDVFLRDWNS 476
Cdd:PHA02820  306 VKLFIVP--DADPPIPYSRVNHAKYMVTDKTAYIGTSNWTGNYFTDTCGVSI----NITPDDGLGLRQQLEDIFIRDWNS 379

                         410
                  ....*....|....*.
gi 2113648141 477 NYTKVLhSLTSYKEKC 492
Cdd:PHA02820  380 KYSYEL-YDTSPTKRC 394
PLDc_vPLD3_2 cd09147
Putative catalytic domain, repeat 2, of vertebrate phospholipase PLD3; Putative catalytic ...
 293-479 6.50e-114

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: 333.86  E-value: 6.50e-114
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 293 YLSSSPPPLSAKGRTDDIDSILSIIDDAKKFVYISVMDYTPTEEFSRPRRYWPAIDNHLRKAVYERHVTVRLLISCWANS 372
Cdd:cd09147     1 YLSSSPPPLCASGRTPDLQSILNVIDNARSFVYIAVMNYLPTLEFSHPHRYWPAIDDGLRRATYERGVKVRLLISCWGHS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 373 NPNMFAFLNSLAALHSEKTHYKIEVKIFIVPVSPEQKHIPFARVNHNKYMVTDRVAYIGTSNWAGDYFIRTAGSAIVVNQ 452
Cdd:cd09147    81 EPSMFAFLRSLAALRDNTTHSDIQVKIFVVPADEAQKKIPYARVNHNKYMVTDRVAYIGTSNWSGDYFTNTAGSALVVNQ 160

                         170       180
                  ....*....|....*....|....*..
gi 2113648141 453 TiAANATNTMQEQLKDVFLRDWNSNYT 479
Cdd:cd09147   161 T-GRSASGTLQSQLQAVFERDWDSPYS 186
PLDc_3 pfam13918
PLD-like domain;
225-403 2.85e-40

PLD-like domain;


Pssm-ID: 464040  Cd Length: 180  Bit Score: 143.23  E-value: 2.85e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 225 SLTQVKELGTTIYNCTCLAEDLGKIFEAYWVLGEANTtIPSPWPDKFSTVYNKETPMEVSLNNTASLVYLSSSPPPLSAK 304
Cdd:pfam13918   1 SLGQIKELGLVFTNCKCLALDLMNIFALFSSLIFENK-VPFTWSKRLCCAVDNEKALNFHLNESGGGAFFSDSPELFCGF 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 305 GRTDDIDSILSIIDDAKKFVYISVMDYTPTEEFSRPRRYWPAIDNHLRKAVYERHVTVRLLISCWANSNPNMFAFLNSLA 384
Cdd:pfam13918  80 NRSFDEDAILHRIDDAKLSIDIALLDMLPIIKHAGAREYWPDIDDAILEAAILRGVKVRLIISEWKEADPLSFNAARSLD 159

                         170
                  ....*....|....*....
gi 2113648141 385 ALHSEKTHYKIEVKIFIVP 403
Cdd:pfam13918 160 AFCTEIANCDLKVKFFDLE 178
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 108-475 4.79e-29

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: 117.74  E-value: 4.79e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 108 FDSWMNLLSQAKSSVDIASFYWTltnNDthtqhptaNEGELILQEMLKLKQRGISLRVAVNPSGSPAKDAD-VNALRGSG 186
Cdd:COG1502    27 FAALLEAIEAARRSIDLEYYIFD---DD--------EVGRRLADALIAAARRGVKVRVLLDGIGSRALNRDfLRRLRAAG 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 187 AEVRVVN----LPSLTNGVLHTKFWVVDGKHLYIGSANMDWRSLTQVKELGtTIYNCTCLAE-----DLGKIFEAYWvlg 257
Cdd:COG1502    96 VEVRLFNpvrlLFRRLNGRNHRKIVVIDGRVAFVGGANITDEYLGRDPGFG-PWRDTHVRIEgpavaDLQAVFAEDW--- 171

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 258 EANTTIPSPWPDKFSTVynketPMEVslnntaslvyLSSSPpplsaKGRTDDI-DSILSIIDDAKKFVYISVMDYTPTEE 336
Cdd:COG1502   172 NFATGEALPFPEPAGDV-----RVQV----------VPSGP-----DSPRETIeRALLAAIASARRRIYIETPYFVPDRS 231

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 337 fsrprrywpaIDNHLRKAVyERHVTVRLLISCWANSNPNMFA---FLNSLAALHsekthykieVKIFIVPvspeqkhipf 413
Cdd:COG1502   232 ----------LLRALIAAA-RRGVDVRILLPAKSDHPLVHWAsrsYYEELLEAG---------VRIYEYE---------- 281

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2113648141 414 ARVNHNKYMVTD-RVAYIGTSNWagDYfiRTAG-----SAIVVNQTIAAnatntmqeQLKDVFLRDWN 475
Cdd:COG1502   282 PGFLHAKVMVVDdEWALVGSANL--DP--RSLRlnfevNLVIYDPEFAA--------QLRARFEEDLA 337
PLDc smart00155
Phospholipase D. Active site motifs; Phosphatidylcholine-hydrolyzing phospholipase D (PLD) ...
 198-225 4.80e-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: 54.32  E-value: 4.80e-10
                           10        20
                   ....*....|....*....|....*...
gi 2113648141  198 TNGVLHTKFWVVDGKHLYIGSANMDWRS 225
Cdd:smart00155   1 YDGVLHTKLMIVDDEIAYIGSANLDGRS 28
bac_cardiolipin TIGR04265
cardiolipin synthase; This model is based on experimentally characterized bacterial ...
 199-253 2.29e-04

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: 43.63  E-value: 2.29e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2113648141 199 NGVLHTKFWVVDGKHLYIGSANMDWRSLTQVKELGTTIYNcTCLAEDLGKIFEAY 253
Cdd:TIGR04265 397 NGFLHSKSVLVDDEIASVGTANMDMRSFWLNFEVNAFIYD-KGFAKDLAAAYDDD 450
 
Name Accession Description Interval E-value
PHA02820 PHA02820
phospholipase-D-like protein; Provisional
 79-492 1.70e-125

phospholipase-D-like protein; Provisional


Pssm-ID: 222934 [Multi-domain]  Cd Length: 424  Bit Score: 372.41  E-value: 1.70e-125
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141  79 CNDSCSIVLVESMPEGLEYapnSTFNPTVFDSWMNLLSQAKSSVDIASFYWTLTNNDThtqhptANEGELILQEMLKLKQ 158
Cdd:PHA02820    2 NPDNTIAVITETIPIGMQF---DKVYLSTFNFWREILSNTTKTLDISSFYWSLSDEVG------TNFGTMILNEIIQLPK 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 159 RGISLRVAVNPSGSPAKDadVNALRGSGAEVRVVNLPSLTNGVLHTKFWVVDGKHLYIGSANMDWRSLTQVKELGTTIYN 238
Cdd:PHA02820   73 RGVRVRIAVNKSNKPLKD--VELLQMAGVEVRYIDITNILGGVLHTKFWISDNTHIYLGSANMDWRSLTQVKELGIAIFN 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 239 CTCLAEDLGKIFEAYWVLGEANttIPSPWPDKFSTVYNKETPMEVSLNNTASLVYLSSSPPPLSAKGRTDDIDSILSIID 318
Cdd:PHA02820  151 NSNLAADLTQIFEVYWYLGVNN--LPYNWKNFYPLYYNTDHPLSLNVSGVPHSVFIASAPQQLCTMERTNDLTALLSCIR 228

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 319 DAKKFVYISVMDYTPTeEFSRPRR--YWPAIDNHLRKAVYERHVTVRLLISCWANSNPNMFAFLNSLAALHSEKTHykIE 396
Cdd:PHA02820  229 NASKFVYVSVMNFIPI-IYSKAGKilFWPYIEDELRRAAIDRKVSVKLLISCWQRSSFIMRNFLRSIAMLKSKNIN--IE 305

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 397 VKIFIVPvsPEQKHIPFARVNHNKYMVTDRVAYIGTSNWAGDYFIRTAGSAIvvnqTIAANATNTMQEQLKDVFLRDWNS 476
Cdd:PHA02820  306 VKLFIVP--DADPPIPYSRVNHAKYMVTDKTAYIGTSNWTGNYFTDTCGVSI----NITPDDGLGLRQQLEDIFIRDWNS 379

                         410
                  ....*....|....*.
gi 2113648141 477 NYTKVLhSLTSYKEKC 492
Cdd:PHA02820  380 KYSYEL-YDTSPTKRC 394
PLDc_vPLD3_2 cd09147
Putative catalytic domain, repeat 2, of vertebrate phospholipase PLD3; Putative catalytic ...
 293-479 6.50e-114

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: 333.86  E-value: 6.50e-114
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 293 YLSSSPPPLSAKGRTDDIDSILSIIDDAKKFVYISVMDYTPTEEFSRPRRYWPAIDNHLRKAVYERHVTVRLLISCWANS 372
Cdd:cd09147     1 YLSSSPPPLCASGRTPDLQSILNVIDNARSFVYIAVMNYLPTLEFSHPHRYWPAIDDGLRRATYERGVKVRLLISCWGHS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 373 NPNMFAFLNSLAALHSEKTHYKIEVKIFIVPVSPEQKHIPFARVNHNKYMVTDRVAYIGTSNWAGDYFIRTAGSAIVVNQ 452
Cdd:cd09147    81 EPSMFAFLRSLAALRDNTTHSDIQVKIFVVPADEAQKKIPYARVNHNKYMVTDRVAYIGTSNWSGDYFTNTAGSALVVNQ 160

                         170       180
                  ....*....|....*....|....*..
gi 2113648141 453 TiAANATNTMQEQLKDVFLRDWNSNYT 479
Cdd:cd09147   161 T-GRSASGTLQSQLQAVFERDWDSPYS 186
PLDc_vPLD3_1 cd09144
Putative catalytic domain, repeat 1, of vertebrate phospholipase PLD3; Putative catalytic ...
 86-257 8.23e-102

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: 302.64  E-value: 8.23e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141  86 VLVESMPEGLEYAPNSTFNPTVFDSWMNLLSQAKSSVDIASFYWTLTNNDTHTQHPTANEGELILQEMLKLKQRGISLRV 165
Cdd:cd09144     1 VLVESIPEGLVFNSSSTINPSIYQAWLNLISAAQSSLDIASFYWTLTNSDTHTQEPSANQGEQILKKLGQLSQSGVYVRI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 166 AVNPSGSPAKDADVNALRGSGAEVRVVNLPSLTNGVLHTKFWVVDGKHLYIGSANMDWRSLTQVKELGTTIYNCTCLAED 245
Cdd:cd09144    81 AVDKPADPKPMEDINALSSYGADVRMVDMRKLTTGVLHTKFWVVDKKHFYIGSANMDWRSLTQVKELGAVVYNCSCLAED 160

                         170
                  ....*....|..
gi 2113648141 246 LGKIFEAYWVLG 257
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 ...
 293-475 1.85e-90

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: 273.36  E-value: 1.85e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 293 YLSSSPPPLSAKGRTDDIDSILSIIDDAKKFVYISVMDYTPTEEFSRPRRYWPAIDNHLRKAVYERHVTVRLLISCWANS 372
Cdd:cd09107     1 FLSSSPPELCPPGRTDDLDALLSTIDSAKKFIDISVMDYVPLSRYADPRKYWPVIDNALRRAAVDRGVKVRLLVSNWKHT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 373 NPNMFAFLNSLAALHSEKTHYKIEVKIFIVPVSPEQKhIPFARVNHNKYMVTDRVAYIGTSNWAGDYFIRTAGSAIVVNQ 452
Cdd:cd09107    81 DPSMDAFLKSLQLLKSGVGNGDIEVKIFTVPGDQSTK-IPFARVNHAKYMVTDERAYIGTSNWSGDYFYNTAGVSLVIND 159

                         170       180
                  ....*....|....*....|...
gi 2113648141 453 tiaanatNTMQEQLKDVFLRDWN 475
Cdd:cd09107   160 -------PAIVQQLKDVFERDWN 175
PLDc_vPLD4_2 cd09148
Putative catalytic domain, repeat 2, of vertebrate phospholipase PLD4; Putative catalytic ...
 293-478 8.42e-85

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: 259.39  E-value: 8.42e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 293 YLSSSPPPLSAKGRTDDIDSILSIIDDAKKFVYISVMDYTPTEEFSRPRRYWPAIDNHLRKAVYERHVTVRLLISCWANS 372
Cdd:cd09148     1 YLSASPPALCPTGRTSDLQAILSVISQAQEFIYISVMEYFPTCRFCHPKRYWSVLDNALRAAAFDRRVLIRLLISCGRHS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 373 NPNMFAFLNSLAALHSEKTHYKIEVKIFIVPVSpEQKHIPFARVNHNKYMVTDRVAYIGTSNWAGDYFIRTAGSAIVVNQ 452
Cdd:cd09148    81 DPDMFPFLRSLNALSNPPLSISVHVKLFIVPVG-NQTNIPYSRVNHNKFMVTDKAAYIGTSNWSEDYFLNTAGVGLVILQ 159

                         170       180
                  ....*....|....*....|....*..
gi 2113648141 453 TIAAN-ATNTMQEQLKDVFLRDWNSNY 478
Cdd:cd09148   160 SPGANeEMLPVQEQLRSLFERDWSSPY 186
PLDc_vPLD3_4_5_like_1 cd09106
Putative catalytic domain, repeat 1, of vertebrate phospholipases, PLD3, PLD4 and PLD5, viral ...
 87-239 5.14e-65

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: 207.10  E-value: 5.14e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141  87 LVESMPEGLEYAPNSTFNPTvFDSWMNLLSQAKSSVDIASFYWTLTNNDTHTqHPTANEGELILQEMLKLKQRGISLRVA 166
Cdd:cd09106     1 LVESIPEGLTFLSSSSHLST-FEAWMELISSAKKSIDIASFYWNLRGTDTNP-DSSAQEGEDIFNALLEAAKRGVKIRIL 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2113648141 167 VN-PSGSPAKDADVNALRGSGAEVRVVNLPSLTN-GVLHTKFWVVDGKHLYIGSANMDWRSLTQVKELGTTIYNC 239
Cdd:cd09106    79 QDkPSKDKPDEDDLELAALGGAEVRSLDFTKLIGgGVLHTKFWIVDGKHFYLGSANLDWRSLTQVKELGVYIYNC 153
PLDc_vPLD4_1 cd09145
Putative catalytic domain, repeat 1, of vertebrate phospholipase PLD4; Putative catalytic ...
 87-256 6.72e-65

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: 207.45  E-value: 6.72e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141  87 LVESMPEGLEYAPNSTFNPTVFDSWMNLLSQAKSSVDIASFYWTLTNNDTHTQHPTANEGELILQEMLKLKQRGISLRVA 166
Cdd:cd09145     1 LVESIPEDLTYEGNSTFALPLQKAWTKLLDMAQEQVHVASYYWSLTGEDIGVNDSSSLPGEDILKELAELLSRNVSVRAA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 167 VNPSGSPAKDADVNALRGSGAEVRVVNLPSLTNGVLHTKFWVVDGKHLYIGSANMDWRSLTQVKELGTTIYNCTCLAEDL 246
Cdd:cd09145    81 ASIPTLAANSTDLKILRQKGAHVRKVNFGRLTGGVLHSKFWIIDKKHIYVGSANMDWRSLTQVKELGAVIYNCSSLAKDL 160

                         170
                  ....*....|
gi 2113648141 247 GKIFEAYWVL 256
Cdd:cd09145   161 HKTFQTYWVL 170
PLDc_vPLD5_2 cd09149
Putative catalytic domain, repeat 2, of inactive veterbrate phospholipase PLD5; Putative ...
 293-482 1.75e-57

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: 188.91  E-value: 1.75e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 293 YLSSSPPPLSAKGRTDDIDSILSIIDDAKKFVYISVMDYTPTEEFSRPRRYWPAIDNHLRKAVYERHVTVRLLISCWANS 372
Cdd:cd09149     1 YVSTSPKLFCPKHRSNDLEAIYRVIQDAKQFIYISVMDYLPLLSRSYARRYWSRIDSKIREALVLRSVRVRLLISFWRKT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 373 NPNMFAFLNSLAALHSEKTHYKIEVKIFivpVSPEQKHIPFARVNHNKYMVTDRVAYIGTSNWAGDYFIRTAGSAIVVNQ 452
Cdd:cd09149    81 DPLTFNFVSSLKSLCTEQANCSLEVKFF---DLEEESDCTSPRLNRNKYMVTDGAAYIGNFDWVGNDFTQNAGVGLVINQ 157

                         170       180       190
                  ....*....|....*....|....*....|.
gi 2113648141 453 TIAANATN-TMQEQLKDVFLRDWNSNYTKVL 482
Cdd:cd09149   158 ADGVEENNaTIIEQLRAAFERDWYSNYAKSL 188
PLDc_vPLD5_1 cd09146
Putative catalytic domain, repeat 1, of inactive veterbrate phospholipase PLD5; Putative ...
 86-256 1.53e-50

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: 169.66  E-value: 1.53e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141  86 VLVESMPEGLEYAPNSTFNPTVFDSWMNLLSQAKSSVDIASFYWtltnnDTHTQHPTANEGELILQEMLKLKQRGISLRV 165
Cdd:cd09146     1 ALVENIPDGINFSEHAPPHLPLSQGWMNLLDMAVKSVEIVSPLW-----DLNASHPSACQGQRLFERLLGLASRGVELKI 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 166 AvnpSGSPAKDADVNALRGSGAEVRVVNLPSLTNGVLHTKFWVVDGKHLYIGSANMDWRSLTQVKELGTTIYNCTCLAED 245
Cdd:cd09146    76 V---SGITDSTEVLVLLKKKGAEVHYVNMTALTKGRLQSSFWIVDKRHVYIGSASMDWRSLGQRKELGVIVYNCSCLALD 152

                         170
                  ....*....|.
gi 2113648141 246 LGKIFEAYWVL 256
Cdd:cd09146   153 LHRVFALYWSL 163
PHA03003 PHA03003
palmytilated EEV membrane glycoprotein; Provisional
 87-482 4.22e-47

palmytilated EEV membrane glycoprotein; Provisional


Pssm-ID: 177506 [Multi-domain]  Cd Length: 369  Bit Score: 167.15  E-value: 4.22e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141  87 LVESMPEGLEYApnsTFNPTVFDSWMNLLSQAKSSVDIASFYWTLTNNDthtqhptanEGELILQEMLKLKQRGISLRVA 166
Cdd:PHA03003   15 IVETLPKSLGIA---TQHMSTYECFDEIISQAKKYIYIASFCCNLRSTP---------EGRLILDKLKEAAESGVKVTIL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 167 VNPSgSPAKDADvnALRGSGAEVRVVNLPSLTN-GVLHTKFWVVDGKHLYIGSANMDWRSLTQVKELGttIYN-CTCLAE 244
Cdd:PHA03003   83 VDEQ-SGDKDEE--ELQSSNINYIKVDIGKLNNvGVLLGSFWVSDDRRCYIGNASLTGGSISTIKTLG--VYStYPPLAT 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 245 DLGKIFEAYWVLGEAN---TTIPSPWPDKFSTVYNketpmevsLNNTASLVYLSSSPPPLSAKGRTDDIDSILSIIDDAK 321
Cdd:PHA03003  158 DLRRRFDTFKAFNKNKsvfNRLCCACCLPVSTKYH--------INNPIGGVFFSDSPEHLLGYSRTLDADVVLHKIKSAK 229

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 322 KFVYISVMDYTPTEEFSRPRRYWPAIDNHLRKAVYERHVTVRLLISCWANSNPNMFAFLNSLAALHSEKthyKIEVKIFI 401
Cdd:PHA03003  230 KSIDLELLSLVPVIREDDKTTYWPDIYNALIRAAINRGVKVRLLVGSWKKNDVYSMASVKSLQALCVGN---DLSVKVFR 306

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 402 VPvspeqkhipfarvNHNKYMVTD-RVAYIGTSNWAGDYFIRtagSAIVVNQTIAANATNtmqeQLKDVFLRDWNSNYTK 480
Cdd:PHA03003  307 IP-------------NNTKLLIVDdEFAHITSANFDGTHYLH---HAFVSFNTIDKELVK----ELSAIFERDWTSSYSK 366


                  ..
gi 2113648141 481 VL 482
Cdd:PHA03003  367 PL 368
PLDc_3 pfam13918
PLD-like domain;
225-403 2.85e-40

PLD-like domain;


Pssm-ID: 464040  Cd Length: 180  Bit Score: 143.23  E-value: 2.85e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 225 SLTQVKELGTTIYNCTCLAEDLGKIFEAYWVLGEANTtIPSPWPDKFSTVYNKETPMEVSLNNTASLVYLSSSPPPLSAK 304
Cdd:pfam13918   1 SLGQIKELGLVFTNCKCLALDLMNIFALFSSLIFENK-VPFTWSKRLCCAVDNEKALNFHLNESGGGAFFSDSPELFCGF 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 305 GRTDDIDSILSIIDDAKKFVYISVMDYTPTEEFSRPRRYWPAIDNHLRKAVYERHVTVRLLISCWANSNPNMFAFLNSLA 384
Cdd:pfam13918  80 NRSFDEDAILHRIDDAKLSIDIALLDMLPIIKHAGAREYWPDIDDAILEAAILRGVKVRLIISEWKEADPLSFNAARSLD 159

                         170
                  ....*....|....*....
gi 2113648141 385 ALHSEKTHYKIEVKIFIVP 403
Cdd:pfam13918 160 AFCTEIANCDLKVKFFDLE 178
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 108-475 4.79e-29

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: 117.74  E-value: 4.79e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 108 FDSWMNLLSQAKSSVDIASFYWTltnNDthtqhptaNEGELILQEMLKLKQRGISLRVAVNPSGSPAKDAD-VNALRGSG 186
Cdd:COG1502    27 FAALLEAIEAARRSIDLEYYIFD---DD--------EVGRRLADALIAAARRGVKVRVLLDGIGSRALNRDfLRRLRAAG 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 187 AEVRVVN----LPSLTNGVLHTKFWVVDGKHLYIGSANMDWRSLTQVKELGtTIYNCTCLAE-----DLGKIFEAYWvlg 257
Cdd:COG1502    96 VEVRLFNpvrlLFRRLNGRNHRKIVVIDGRVAFVGGANITDEYLGRDPGFG-PWRDTHVRIEgpavaDLQAVFAEDW--- 171

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 258 EANTTIPSPWPDKFSTVynketPMEVslnntaslvyLSSSPpplsaKGRTDDI-DSILSIIDDAKKFVYISVMDYTPTEE 336
Cdd:COG1502   172 NFATGEALPFPEPAGDV-----RVQV----------VPSGP-----DSPRETIeRALLAAIASARRRIYIETPYFVPDRS 231

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 337 fsrprrywpaIDNHLRKAVyERHVTVRLLISCWANSNPNMFA---FLNSLAALHsekthykieVKIFIVPvspeqkhipf 413
Cdd:COG1502   232 ----------LLRALIAAA-RRGVDVRILLPAKSDHPLVHWAsrsYYEELLEAG---------VRIYEYE---------- 281

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2113648141 414 ARVNHNKYMVTD-RVAYIGTSNWagDYfiRTAG-----SAIVVNQTIAAnatntmqeQLKDVFLRDWN 475
Cdd:COG1502   282 PGFLHAKVMVVDdEWALVGSANL--DP--RSLRlnfevNLVIYDPEFAA--------QLRARFEEDLA 337
PLDc_SF cd00138
Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D ...
 111-236 2.80e-17

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: 77.56  E-value: 2.80e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 111 WMNLLSQAKSSVDIASFYWTltnndthtqhptANEGELILQEMLKLKQRGISLRVAVNPSGSPA---KDADVNALRGSGA 187
Cdd:cd00138     3 LLELLKNAKESIFIATPNFS------------FNSADRLLKALLAAAERGVDVRLIIDKPPNAAgslSAALLEALLRAGV 70

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 2113648141 188 EVRVVNLPSLTNGVLHTKFWVVDGKHLYIGSANMDWRSLTQVKELGTTI 236
Cdd:cd00138    71 NVRSYVTPPHFFERLHAKVVVIDGEVAYVGSANLSTASAAQNREAGVLV 119
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 104-270 2.63e-16

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: 80.37  E-value: 2.63e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 104 NPTVFDSWMNLLSQAKSSVDIASFYWTLtnndthtqhptaneGELILQEMLKLKQRGISLRVAVNPSG-SPAKD----AD 178
Cdd:COG1502   201 RETIERALLAAIASARRRIYIETPYFVP--------------DRSLLRALIAAARRGVDVRILLPAKSdHPLVHwasrSY 266

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 179 VNALRGSGAEVRVvnlpsLTNGVLHTKFWVVDGKHLYIGSANMDWRSLTQVKELGTTIYNCTcLAEDLGKIFEAYWvlGE 258
Cdd:COG1502   267 YEELLEAGVRIYE-----YEPGFLHAKVMVVDDEWALVGSANLDPRSLRLNFEVNLVIYDPE-FAAQLRARFEEDL--AH 338

                         170
                  ....*....|..
gi 2113648141 259 ANTTIPSPWPDK 270
Cdd:COG1502   339 SREVTLEEWRKR 350
PLDc_2 pfam13091
PLD-like domain;
113-254 8.49e-15

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 71.17  E-value: 8.49e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 113 NLLSQAKSSVDIASFYWtltnndthtqhptaNEGELILQEMLKLKQRGISLRV------AVNPSGSPAKDADVNALRGSG 186
Cdd:pfam13091   3 DLINSAKKSIDIATYYF--------------VPDREIIDALIAAAKRGVDVRIildsnkDDAGGPKKASLKELRSLLRAG 68

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2113648141 187 AEVRVVNLpslTNGVLHTKFWVVDGKHLYIGSANMDWRSLTQVKELGTTIYNCTcLAEDLGKIFEAYW 254
Cdd:pfam13091  69 VEIREYQS---FLRSMHAKFYIIDGKTVIVGSANLTRRALRLNLENNVVIKDPE-LAQELEKEFDRLW 132
PLDc_unchar1_1 cd09127
Putative catalytic domain, repeat 1, of uncharacterized phospholipase D-like proteins; ...
 112-252 6.82e-11

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


Pssm-ID: 197225 [Multi-domain]  Cd Length: 141  Bit Score: 59.97  E-value: 6.82e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 112 MNLLSQAKSSVDIASFYWTltnndthtqHPTanegelILQEMLKLKQRGISLRVAVNPS---GSPAKDADVNALRGSGAE 188
Cdd:cd09127    14 VDAIASAKRSILLKMYEFT---------DPA------LEKALAAAAKRGVRVRVLLEGGpvgGISRAEKLLDYLNEAGVE 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2113648141 189 VRVVNlPSLTNGVLHTKFWVVDGKHLYIGSANMDWRSLTQVKELGTTIYNCTcLAEDLGKIFEA 252
Cdd:cd09127    79 VRWTN-GTARYRYTHAKYIVVDDERALVLTENFKPSGFTGTRGFGVVTDDPA-VVAEIADVFDA 140
PLDc_vPLD6_like cd09171
Catalytic domain of vertebrate phospholipase D6 and similar proteins; Catalytic domain of ...
 103-220 2.03e-10

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: 58.77  E-value: 2.03e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 103 FNPTV--FDSWMNLLSQAKSSVDIASFywTLTNNDthtqhptanegelILQEMLKLKQRGISLRVAVNPSGSPAKDADVN 180
Cdd:cd09171     3 FFPGEtsLSKLLRYLLSARKSLDVCVF--TITCDD-------------LADAILDLHRRGVRVRIITDDDQMEDKGSDIG 67

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 2113648141 181 ALRGSGAEVRVvnlpSLTNGVLHTKFWVVDGKHLYIGSAN 220
Cdd:cd09171    68 KLRKAGIPVRT----DLSSGHMHHKFAVIDGKILITGSFN 103
PLDc_Nuc_like cd09116
Catalytic domain of EDTA-resistant nuclease Nuc, vertebrate phospholipase D6, and similar ...
 113-227 2.89e-10

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


Pssm-ID: 197215 [Multi-domain]  Cd Length: 138  Bit Score: 58.08  E-value: 2.89e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 113 NLLSQAKSSVDIASFywTLTNNDthtqhptanegelILQEMLKLKQRGISLRVAVNP--SGSPAKDADVNALRGSGAEVR 190
Cdd:cd09116    16 ALIANAKSSIDVAMY--ALTDPE-------------IAEALKRAAKRGVRVRIILDKdsLADNLSITLLALLSNLGIPVR 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2113648141 191 VVNlpslTNGVLHTKFWVVDGKHLYIGSANMDWRSLT 227
Cdd:cd09116    81 TDS----GSKLMHHKFIIIDGKIVITGSANWTKSGFH 113
PLDc smart00155
Phospholipase D. Active site motifs; Phosphatidylcholine-hydrolyzing phospholipase D (PLD) ...
 198-225 4.80e-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: 54.32  E-value: 4.80e-10
                           10        20
                   ....*....|....*....|....*...
gi 2113648141  198 TNGVLHTKFWVVDGKHLYIGSANMDWRS 225
Cdd:smart00155   1 YDGVLHTKLMIVDDEIAYIGSANLDGRS 28
PLDc_unchar1_2 cd09128
Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins; ...
 114-254 1.82e-09

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: 56.13  E-value: 1.82e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 114 LLSQAKSSVDIasfywtltnndthtQHPTANEGELILQEMLKLKQRGISLRV--AVNPSGSPAKDADVNALRGSGAEVRV 191
Cdd:cd09128    18 LIDSAEESLLI--------------QNEEMGDDAPILDALVDAAKRGVDVRVllPSAWSAEDERQARLRALEGAGVPVRL 83

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2113648141 192 VNLPSLTngvLHTKFWVVDGKHLYIGSANMDWRSLTQVKELGTTIYNcTCLAEDLGKIFEAYW 254
Cdd:cd09128    84 LKDKFLK---IHAKGIVVDGKTALVGSENWSANSLDRNREVGLIFDD-PEVAAYLQAVFESDW 142
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 310-476 2.31e-09

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


Pssm-ID: 441111 [Multi-domain]  Cd Length: 367  Bit Score: 59.19  E-value: 2.31e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 310 IDSILSIIDDAKKFVYISVMDYTPteefsrprrywPAIDNHLRKAVYERH---VTVRLL---ISCWAnSNPNMFAFLNSL 383
Cdd:COG1502    27 FAALLEAIEAARRSIDLEYYIFDD-----------DEVGRRLADALIAAArrgVKVRVLldgIGSRA-LNRDFLRRLRAA 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 384 aalhsekthyKIEVKIFiVPVSPEQKHIPfaRVNHNKYMVTD-RVAYIGTSNWAGDYFIRTAGS------AIVVNQTIAA 456
Cdd:COG1502    95 ----------GVEVRLF-NPVRLLFRRLN--GRNHRKIVVIDgRVAFVGGANITDEYLGRDPGFgpwrdtHVRIEGPAVA 161

                         170       180
                  ....*....|....*....|
gi 2113648141 457 natntmqeQLKDVFLRDWNS 476
Cdd:COG1502   162 --------DLQAVFAEDWNF 173
PLDc_SF cd00138
Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D ...
 313-435 1.27e-08

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


Pssm-ID: 197200 [Multi-domain]  Cd Length: 119  Bit Score: 52.90  E-value: 1.27e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 313 ILSIIDDAKKFVYISVMDYTPteefsrprRYWPAIDNHLRKAVyERHVTVRLLIscwansNPNMFAFLNSLAALHSEKTH 392
Cdd:cd00138     3 LLELLKNAKESIFIATPNFSF--------NSADRLLKALLAAA-ERGVDVRLII------DKPPNAAGSLSAALLEALLR 67

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 2113648141 393 YKIEVKIFivpvspeQKHIPFARVNHNKYMVTD-RVAYIGTSNW 435
Cdd:cd00138    68 AGVNVRSY-------VTPPHFFERLHAKVVVIDgEVAYVGSANL 104
PLDc pfam00614
Phospholipase D Active site motif; Phosphatidylcholine-hydrolysing phospholipase D (PLD) ...
 198-225 1.75e-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: 50.11  E-value: 1.75e-08
                          10        20
                  ....*....|....*....|....*...
gi 2113648141 198 TNGVLHTKFWVVDGKHLYIGSANMDWRS 225
Cdd:pfam00614   1 YDGRLHRKIVVVDDELAYIGGANLDGRS 28
PLDc_2 pfam13091
PLD-like domain;
313-474 1.00e-07

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 50.75  E-value: 1.00e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 313 ILSIIDDAKKFVYISVMDYTPTEEfsrprrywpaIDNHLRKAVyERHVTVRLLISCWANSNPnmFAFLNSLAALHsEKTH 392
Cdd:pfam13091   1 LIDLINSAKKSIDIATYYFVPDRE----------IIDALIAAA-KRGVDVRIILDSNKDDAG--GPKKASLKELR-SLLR 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 393 YKIEVKIFIvpvspeqkhiPFARVNHNKYMVTD-RVAYIGTSNWAGDYFIRTAGSAIVVNQTIAAnatntmqEQLKDVFL 471
Cdd:pfam13091  67 AGVEIREYQ----------SFLRSMHAKFYIIDgKTVIVGSANLTRRALRLNLENNVVIKDPELA-------QELEKEFD 129


                  ...
gi 2113648141 472 RDW 474
Cdd:pfam13091 130 RLW 132
PLDc_unchar1_1 cd09127
Putative catalytic domain, repeat 1, of uncharacterized phospholipase D-like proteins; ...
 313-473 1.61e-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: 50.34  E-value: 1.61e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 313 ILSIIDDAKKFVYISVMDYTPteefsrprrywPAIDNHLRKAVyERHVTVRLLI----SCWANSNPNMFAFLNSlaalhs 388
Cdd:cd09127    13 VVDAIASAKRSILLKMYEFTD-----------PALEKALAAAA-KRGVRVRVLLeggpVGGISRAEKLLDYLNE------ 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 389 ekthYKIEVKIfivpVSPEQKHipfaRVNHNKYMVTDR-VAYIGTSNWAGDYFIRTAGSAIVV-NQTIAAnatntmqeQL 466
Cdd:cd09127    75 ----AGVEVRW----TNGTARY----RYTHAKYIVVDDeRALVLTENFKPSGFTGTRGFGVVTdDPAVVA--------EI 134


                  ....*..
gi 2113648141 467 KDVFLRD 473
Cdd:cd09127   135 ADVFDAD 141
PLDc_ymdC_like_2 cd09113
Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and ...
 105-256 1.69e-07

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: 51.84  E-value: 1.69e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 105 PTVFDSWMNLLSQAKSSVDIASFYWTLTNndthtqhptanEGeliLQEMLKLKQRGISLRV-----AVNP-----SG-SP 173
Cdd:cd09113    16 PVLAYQLAELLKNAKREVLIVSPYFVPGD-----------EG---VALLAELARRGVRVRIltnslAATDvpavhSGyAR 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 174 AKDADVNA------LRGSGAEVRVVNLPSLTNGV-LHTKFWVVDGKHLYIGSANMDWRSLTQVKELGTTIYNCTcLAEDL 246
Cdd:cd09113    82 YRKRLLKAgvelyeLKPDAAKRKRLRGLFGSSRAsLHAKSFVIDDRLVFVGSFNLDPRSAYLNTEMGLVIDSPE-LAAQL 160

                         170
                  ....*....|....*.
gi 2113648141 247 GKIFE------AYWVL 256
Cdd:cd09113   161 RAAMEedlapsAYWVL 176
PLDc_Nuc cd09170
Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar ...
 117-220 2.70e-07

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


Pssm-ID: 197267 [Multi-domain]  Cd Length: 142  Bit Score: 49.82  E-value: 2.70e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 117 QAKSSVDIASFYwtLTNNDthtqhptanegelILQEMLKLKQRGISLRVAVNPSGSPAKDADVNALRGSGAEVRVVNLPs 196
Cdd:cd09170    22 SARRSIDVAAYS--FTSPP-------------IARALIAAKKRGVDVRVVLDKSQAGGKYSALNYLANAGIPVRIDDNY- 85

                          90       100
                  ....*....|....*....|....
gi 2113648141 197 ltnGVLHTKFWVVDGKHLYIGSAN 220
Cdd:cd09170    86 ---AIMHNKVMVIDGKTVITGSFN 106
PLDc_CLS_2 cd09112
catalytic domain repeat 2 of bacterial cardiolipin synthase and similar proteins; This CD ...
 99-251 3.61e-07

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: 50.17  E-value: 3.61e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141  99 PNSTFnPTVFDSWMNLLSQAKSSVDIASFYWTLTNNdthtqhptanegeliLQEMLKLK-QRGISLRVAVnpSGSPAKDA 177
Cdd:cd09112     5 PDSDW-SSIEQAYLKAINSAKKSIYIQTPYFIPDES---------------LLEALKTAaLSGVDVRIMI--PGKPDHKL 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 178 DVNA--------LRgSGAEVRvvnlpSLTNGVLHTKFWVVDGKHLYIGSANMDWRSLTQVKELGTTIYNCTcLAEDLGKI 249
Cdd:cd09112    67 VYWAsrsyfeelLK-AGVKIY-----EYNKGFLHSKTLIVDDEIASVGTANLDIRSFELNFEVNAVIYDKE-VAKKLEEI 139


                  ..
gi 2113648141 250 FE 251
Cdd:cd09112   140 FE 141
PLDc_Nuc_like_unchar1_1 cd09172
Putative catalytic domain, repeat 1, of uncharacterized hypothetical proteins similar to Nuc, ...
 114-254 4.84e-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: 49.28  E-value: 4.84e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 114 LLSQA---KSSVDIASFywtltnndtHTQHPTanegelILQEMLKLKQRGISLRVAVNPSGSPAkDADVNALRGSGAEVR 190
Cdd:cd09172    14 FLDEArsaGSSIRLAIY---------ELDDPE------IIDALKAAKDRGVRVRIILDDSSVTG-DPTEESAAATLSKGP 77

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2113648141 191 VVNLPSLTN-GVLHTKFWVVDGK----HLYIGSANMDWRSLTQVKELGTTIYNctclaEDLGKIFEAYW 254
Cdd:cd09172    78 GALVKRRHSsGLMHNKFLVVDRKdgpnRVLTGSTNFTTSGLYGQSNNVLIFRN-----PAFAAAYLAYW 141
PLDc_ybhO_like_2 cd09159
Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; ...
 112-251 1.11e-06

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: 48.69  E-value: 1.11e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 112 MNLLSQAKSSVDIASFYWTltnndthtqhPtaneGELILQEMLKLKQRGISLRVAVnpsgsPAKDADVNALRGS------ 185
Cdd:cd09159    17 LVAIAAARRRIWIANAYFV----------P----DRRLRRALIEAARRGVDVRLLL-----PGKSDDPLTVAASralygk 77

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2113648141 186 --GAEVRVVnlpSLTNGVLHTKFWVVDGKHLYIGSANMDWRSLTQVKELGTTIYNCTcLAEDLGKIFE 251
Cdd:cd09159    78 llRAGVRIF---EYQPSMLHAKTAVIDGDWATVGSSNLDPRSLRLNLEANLVVEDPA-FAAQLEELFE 141
PLDc_CLS_1 cd09110
Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Catalytic ...
 107-221 1.93e-06

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


Pssm-ID: 197209 [Multi-domain]  Cd Length: 154  Bit Score: 47.47  E-value: 1.93e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 107 VFDSWMNLLSQAKSSVDIASFYWTltNNDThtqhptaneGELILQEMLKLKQRGISLRVAVNPSGSPA-KDADVNALRGS 185
Cdd:cd09110     6 FFPALLEAIRAARHSIHLEYYIFR--DDEI---------GRRFRDALIEKARRGVEVRLLYDGFGSLGlSRRFLRELREA 74

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 2113648141 186 GAEVRVVNLPSLTNGVL------HTKFWVVDGKHLYIGSANM 221
Cdd:cd09110    75 GVEVRAFNPLSFPLFLLrlnyrnHRKILVIDGKIAFVGGFNI 116
PLDc_CLS_unchar2_1 cd09157
Putative catalytic domain, repeat 1, of uncharacterized proteins similar to bacterial ...
 314-475 1.69e-05

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: 44.86  E-value: 1.69e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 314 LSIIDDAKKFVYIS--VMDYTPT-EEFSrprrywpaidNHLRKAVyERHVTVRLLI----SCWanSNPNMFAFLNSLAal 386
Cdd:cd09157    11 LEAIDAARHSIALSsyIFDNDGVgREFV----------DALAEAV-ARGVDVRVLIdgvgARY--SRPSIRRRLRRAG-- 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 387 hsekthykIEVKIFIVPVSPEQkhIPFARV-NHNKYMVTD-RVAYIGTSNWAGDYFIRTAGSAIVvnQTIAANATNTMQE 464
Cdd:cd09157    76 --------VPVARFLPPRLPPR--LPFINLrNHRKILVVDgRTGFTGGMNIRDGHLVADDPKNPV--QDLHFRVEGPVVA 143

                         170
                  ....*....|.
gi 2113648141 465 QLKDVFLRDWN 475
Cdd:cd09157   144 QLQEVFAEDWY 154
PLDc_unchar3 cd09131
Putative catalytic domain of uncharacterized phospholipase D-like proteins; Putative catalytic ...
 113-250 4.74e-05

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


Pssm-ID: 197229 [Multi-domain]  Cd Length: 143  Bit Score: 43.48  E-value: 4.74e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 113 NLLSQAKSSVDIASFYWTLTNNDthtqhptANEGELILQEMLKLKQRGISLRVAVNPSGS-----PAKDADVNALRGSGA 187
Cdd:cd09131    10 DLINNAKRSIYIAMYMFKYYENP-------GNGVNTLLEALIDAHKRGVDVKVVLEDSIDddevtEENDNTYRYLKDNGV 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2113648141 188 EVRVVNlPSLTngvLHTKFWVVDGKHLYIGSANMDWRSLTQVKELGTTIyNCTCLAEDLGKIF 250
Cdd:cd09131    83 EVRFDS-PSVT---THTKLVVIDGRTVYVGSHNWTYSALDYNHEASVLI-ESPEVADFAINYF 140
PLDc_CLS_unchar2_2 cd09163
Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial ...
 203-252 4.80e-05

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: 44.08  E-value: 4.80e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2113648141 203 HTKFWVVDGKHLYIGSANMDWRSLTQVKELGTTIYnCTCLAEDLGKIFEA 252
Cdd:cd09163    94 HSKLMVVDGAWALIGSANWDPRSLRLNFELNLEVY-DTALAGQLDALFDS 142
PLDc_SMU_988_like_2 cd09160
Putative catalytic domain, repeat 2, of Streptococcus mutans uncharacterized protein SMU_988 ...
 198-244 5.09e-05

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


Pssm-ID: 197257 [Multi-domain]  Cd Length: 176  Bit Score: 44.02  E-value: 5.09e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2113648141 198 TNGVLHTKFWVVDGKHLYIGSANMDWRSLTQVKELGTTIYNCTCLAE 244
Cdd:cd09160    89 TPGFIHAKTFVSDDKAAVVGTINLDYRSLYLHFECGVYMYDTPVISD 135
PLDc_Nuc_like_unchar1_2 cd09173
Putative catalytic domain, repeat 2, of uncharacterized hypothetical proteins similar to Nuc, ...
 113-221 9.68e-05

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


Pssm-ID: 197270 [Multi-domain]  Cd Length: 159  Bit Score: 42.73  E-value: 9.68e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 113 NLLSQAKSSVDIASFYWTltnndthtqhptanEGElILQEMLKLKQRGISLRVAVNPSGSPAKDADVNALRG-------- 184
Cdd:cd09173    16 ELVAKAKSSVLFALFDFS--------------DGA-LLDALLAAADAGLFVRGLVDKRFGGRYYSAAADMGGidpvypaa 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2113648141 185 -----SGAEVRVVNLPSltNGVLHTKFWVVD--GKH--LYIGSANM 221
Cdd:cd09173    81 lapdePEKFVGEPLLGV--GDKLHHKFMVIDpfGDDpvVITGSHNF 124
PLDc_vPLD3_4_5_like_2 cd09107
Putative catalytic domain, repeat 2, of vertebrate phospholipases, PLD3, PLD4 and PLD5, viral ...
 188-254 1.01e-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: 43.01  E-value: 1.01e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2113648141 188 EVRVVNLPSLTNG------VLHTKFWVVDgKHLYIGSANMDWRSLTQVKELGTTIYNcTCLAEDLGKIFEAYW 254
Cdd:cd09107   104 EVKIFTVPGDQSTkipfarVNHAKYMVTD-ERAYIGTSNWSGDYFYNTAGVSLVIND-PAIVQQLKDVFERDW 174
PLDc_CLS_unchar1_2 cd09162
Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial ...
 147-238 1.24e-04

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


Pssm-ID: 197259 [Multi-domain]  Cd Length: 172  Bit Score: 42.63  E-value: 1.24e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 147 ELILQEMLKLKQRGISLRVAVnPSGSPAKDADVNalRGS--------GAEVRvvnlpSLTNGVLHTKFWVVDGKHLYIGS 218
Cdd:cd09162    38 EVLLRALRLAARRGVDVRLIV-PKRSNHRIADLA--RGSylrdlqeaGAEIY-----LYQPGMLHAKAVVVDDKLALVGS 109

                          90       100
                  ....*....|....*....|
gi 2113648141 219 ANMDWRSLTQVKELGTTIYN 238
Cdd:cd09162   110 ANLDMRSLFLNYEVAVFFYS 129
bac_cardiolipin TIGR04265
cardiolipin synthase; This model is based on experimentally characterized bacterial ...
 199-253 2.29e-04

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: 43.63  E-value: 2.29e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2113648141 199 NGVLHTKFWVVDGKHLYIGSANMDWRSLTQVKELGTTIYNcTCLAEDLGKIFEAY 253
Cdd:TIGR04265 397 NGFLHSKSVLVDDEIASVGTANMDMRSFWLNFEVNAFIYD-KGFAKDLAAAYDDD 450
PLDc smart00155
Phospholipase D. Active site motifs; Phosphatidylcholine-hydrolyzing phospholipase D (PLD) ...
 415-439 2.51e-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: 38.14  E-value: 2.51e-04
                           10        20
                   ....*....|....*....|....*.
gi 2113648141  415 RVNHNKYMVTD-RVAYIGTSNWAGDY 439
Cdd:smart00155   3 GVLHTKLMIVDdEIAYIGSANLDGRS 28
COG3886 COG3886
HKD family nuclease [Replication, recombination and repair];
147-221 3.02e-04

HKD family nuclease [Replication, recombination and repair];


Pssm-ID: 443094 [Multi-domain]  Cd Length: 941  Bit Score: 43.43  E-value: 3.02e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 147 ELILQEMLKLKQRGISLRVAVnpsGSPAKDADVNALRG----SGAEVRVVNLPsltNGVLHTKFWVVDGKH---LYIGSA 219
Cdd:COG3886    58 RLLLDALKELLERGVKGRILT---STYLGFTEPKALRElldlPNIEVRVSYDR---KTRFHAKAYIFERTGygtAIIGSS 131


                  ..
gi 2113648141 220 NM 221
Cdd:COG3886   132 NL 133
cls PRK01642
cardiolipin synthetase; Reviewed
 200-253 3.71e-04

cardiolipin synthetase; Reviewed


Pssm-ID: 234967 [Multi-domain]  Cd Length: 483  Bit Score: 42.85  E-value: 3.71e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2113648141 200 GVLHTKFWVVDGKHLYIGSANMDWRSLTQVKELGTTIYNcTCLAEDLGKIFEAY 253
Cdd:PRK01642  398 GLLHTKSVLVDDELALVGTVNLDMRSFWLNFEITLVIDD-TGFAADLAAMQEDY 450
PLDc_Bfil_DEXD_like cd09117
Catalytic domain of type II restriction endonucleases BfiI and NgoFVII, and uncharacterized ...
 120-236 5.35e-04

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: 39.69  E-value: 5.35e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 120 SSVDIASFYWTLTNndthtqhptanegeliLQEMLKLKQRGISLRVAVNPS---GSPAKDADVNALRGSGAEVRVVNLps 196
Cdd:cd09117    15 DTIRIAVAFASAGG----------------AIKLLDKFREGKKIRLIVGLDfggTSPADFALKLLLALGNLNVRIFDA-- 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2113648141 197 ltNGVLHTK---FWVVDGKHLYIGSANMDWRSLTQVKELGTTI 236
Cdd:cd09117    77 --GPLLHAKlylFENDDPTRAIVGSANLTQGGLSGNIEAAVVI 117
PLDc_vPLD1_2_like_2 cd09105
Catalytic domain, repeat 2, of vertebrate phospholipases, PLD1 and PLD2, and similar proteins; ...
 203-237 9.96e-04

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: 39.59  E-value: 9.96e-04
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 2113648141 203 HTKFWVVDGKHLYIGSANMDWRSLTQVKELGTTIY 237
Cdd:cd09105   111 HSKVVIVDDEWATVGSANLNRRSMTWDTELNLAVV 145
PLDc_unchar1_2 cd09128
Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins; ...
 310-474 1.93e-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: 1.93e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 310 IDSILSIIDDAKKFVYISvmdytpTEEFSrprrYWPAIDNHLRKAVyERHVTVRLLIScwaNSNPNMFAFLNSLAALHse 389
Cdd:cd09128    12 REALLALIDSAEESLLIQ------NEEMG----DDAPILDALVDAA-KRGVDVRVLLP---SAWSAEDERQARLRALE-- 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 390 ktHYKIEVKIFIVPvspeqkhipFARVnHNKYMVTD-RVAYIGTSNWagdyfirTAGSA-------IVVNQTIAAnatnt 461
Cdd:cd09128    76 --GAGVPVRLLKDK---------FLKI-HAKGIVVDgKTALVGSENW-------SANSLdrnrevgLIFDDPEVA----- 131

                         170
                  ....*....|...
gi 2113648141 462 mqEQLKDVFLRDW 474
Cdd:cd09128   132 --AYLQAVFESDW 142
PLDc_unchar4 cd09132
Putative catalytic domain of uncharacterized phospholipase D-like proteins; Putative catalytic ...
 113-220 2.01e-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: 197230 [Multi-domain]  Cd Length: 122  Bit Score: 38.02  E-value: 2.01e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 113 NLLSQAKSSVDIASFYWTLTnndthtqhptanegELILQEMLKLKQRGISLRVAVNPS----GSPAKDADVNA-LRGSGA 187
Cdd:cd09132     6 ELIEGAERSLLIVGYSAYKV--------------SELLQALAAALERGVQVRVVVESSekagSVLSLDEDELMwPKLAGA 71

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 2113648141 188 EVRVVNLPSLTN--GVLHTKFWVVDGKHLYIGSAN 220
Cdd:cd09132    72 TLYVWPEKKRPGkrASLHAKVIVADRRRLLVTSAN 106
PLDc_CLS_unchar1_1 cd09156
Putative catalytic domain, repeat 1, of uncharacterized proteins similar to bacterial ...
 107-222 3.17e-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: 197253 [Multi-domain]  Cd Length: 154  Bit Score: 38.39  E-value: 3.17e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 107 VFDSWMNLLSQAKSSVDIASFywTLTNNDThtqhptaneGELILQEMLKLKQRGISLRVAVNPSGS-PAKDADVNALRGS 185
Cdd:cd09156     6 AYQALIQLIESAKHSIDVCTF--ILGDDAT---------GRRVIDALARKAREGVEVRLLLDALGSfFLSRRALKKLRAA 74

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2113648141 186 GAEVR----VVNLPSLTNGVL--HTKFWVVDGKHLYIGSANMD 222
Cdd:cd09156    75 GGKVAffmpVFRLPFRGRTNLrnHRKIAIADGSTAISGGMNLA 117
PLDc_EcCLS_like_2 cd09158
Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase and similar proteins; ...
 200-226 3.45e-03

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: 38.33  E-value: 3.45e-03
                          10        20
                  ....*....|....*....|....*..
gi 2113648141 200 GVLHTKFWVVDGKHLYIGSANMDWRSL 226
Cdd:cd09158    91 GLLHAKTVTVDDEVALVGSSNFDIRSF 117
PLDc_ymdC_like_1 cd09111
Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and ...
 349-440 4.05e-03

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: 37.90  E-value: 4.05e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 349 NHLRKAVyERHVTVRLLIScwANSNPNMFAFLNSLAAlhsektHYKIEVKIFiVPVSPEQKHIP-----FARVN---HNK 420
Cdd:cd09111    40 GELLEAA-DRGVRVRLLLD--DLGTSGRDRLLAALDA------HPNIEVRLF-NPFRNRGGRLLefltdFSRLNrrmHNK 109

                          90       100
                  ....*....|....*....|.
gi 2113648141 421 YMVTD-RVAYIGTSNWAGDYF 440
Cdd:cd09111   110 LFIVDgAVAIVGGRNIGDEYF 130
PRK12452 PRK12452
cardiolipin synthase;
101-251 7.31e-03

cardiolipin synthase;


Pssm-ID: 171510 [Multi-domain]  Cd Length: 509  Bit Score: 38.75  E-value: 7.31e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2113648141 101 STFNPTVFDSWMNLLSQAKSSVDIASFYWtLTNNDTHTqhptanegelilqeMLKLKQR-GISLRVAvnpsgSPAKDADV 179
Cdd:PRK12452  339 SSDDKSIRNTLLAVMGSAKKSIWIATPYF-IPDQETLT--------------LLRLSAIsGIDVRIL-----YPGKSDSI 398

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2113648141 180 NALRGSGAEVRV-----VNLPSLTNGVLHTKFWVVDGKHLYIGSANMDWRSLTQVKELGTTIYNCTCLAeDLGKIFE 251
Cdd:PRK12452  399 ISDQASQSYFTPllkagASIYSYKDGFMHAKIVLVDDKIATIGTANMDVRSFELNYEIISVLYESETVH-DIKRDFE 474
 
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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