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Conserved domains on  [gi|94681038|ref|NP_620145|]
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5'-3' exonuclease PLD4 isoform 2 [Homo sapiens]

Protein Classification

phosphatidylserine synthase; phospholipase D family protein( domain architecture ID 10332449)

phosphatidylserine synthase catalyzes de novo synthesis of phosphatidylserine from CDP-diacylglycerol and L-serine| phospholipase D family protein similar to Escherichia coli cardiolipin synthase C and Neisseria gonorrhoeae phospholipase D; hydrolyzes phospholipid phosphodiester bonds

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PLDc_vPLD4_2 cd09148
Putative catalytic domain, repeat 2, of vertebrate phospholipase PLD4; Putative catalytic ...
 304-490 8.96e-125

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: 361.86  E-value: 8.96e-125
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038 304 YFSASPPALCPQGRTRDLEALLAVMGSAQEFIYASVMEYFPTTRFSHPPRYWPVLDNALRAAAFGKGVRVRLLVGCGLNT 383
Cdd:cd09148   1 YLSASPPALCPTGRTSDLQAILSVISQAQEFIYISVMEYFPTCRFCHPKRYWSVLDNALRAAAFDRRVLIRLLISCGRHS 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038 384 DPTMFPYLRSLQALSNPAANVSVDVKVFIVPVGNHSNIPFSRVNHSKFMVTEKAAYIGTSNWSEDYFSSTAGVGLVVTQS 463
Cdd:cd09148  81 DPDMFPFLRSLNALSNPPLSISVHVKLFIVPVGNQTNIPYSRVNHNKFMVTDKAAYIGTSNWSEDYFLNTAGVGLVILQS 160

                       170       180
                ....*....|....*....|....*..
gi 94681038 464 PGAQPAGATVQEQLRQLFERDWSSRYA 490
Cdd:cd09148 161 PGANEEMLPVQEQLRSLFERDWSSPYA 187
PLDc_SF super family cl15239
Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D ...
 98-267 9.59e-108

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.


The actual alignment was detected with superfamily member cd09145:

Pssm-ID: 472788 [Multi-domain]  Cd Length: 170  Bit Score: 318.00  E-value: 9.59e-108
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038  98 LVESIPQDLPSAAGSPSAQPLGQAWLQLLDTAQESVHVASYYWSLTGPDIGVNDSSSQLGEALLQKLQQLLGRNISLAVA 177
Cdd:cd09145   1 LVESIPEDLTYEGNSTFALPLQKAWTKLLDMAQEQVHVASYYWSLTGEDIGVNDSSSLPGEDILKELAELLSRNVSVRAA 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038 178 TSSPTLARTSTDLQVLAARGAHVRQVPMGRLTRGVLHSKFWVVDGRHIYMGSANMDWRSLTQVKELGAVIYNCSHLAQDL 257
Cdd:cd09145  81 ASIPTLAANSTDLKILRQKGAHVRKVNFGRLTGGVLHSKFWIIDKKHIYVGSANMDWRSLTQVKELGAVIYNCSSLAKDL 160

                       170
                ....*....|
gi 94681038 258 EKTFQTYWVL 267
Cdd:cd09145 161 HKTFQTYWVL 170
 
Name Accession Description Interval E-value
PLDc_vPLD4_2 cd09148
Putative catalytic domain, repeat 2, of vertebrate phospholipase PLD4; Putative catalytic ...
 304-490 8.96e-125

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: 361.86  E-value: 8.96e-125
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038 304 YFSASPPALCPQGRTRDLEALLAVMGSAQEFIYASVMEYFPTTRFSHPPRYWPVLDNALRAAAFGKGVRVRLLVGCGLNT 383
Cdd:cd09148   1 YLSASPPALCPTGRTSDLQAILSVISQAQEFIYISVMEYFPTCRFCHPKRYWSVLDNALRAAAFDRRVLIRLLISCGRHS 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038 384 DPTMFPYLRSLQALSNPAANVSVDVKVFIVPVGNHSNIPFSRVNHSKFMVTEKAAYIGTSNWSEDYFSSTAGVGLVVTQS 463
Cdd:cd09148  81 DPDMFPFLRSLNALSNPPLSISVHVKLFIVPVGNQTNIPYSRVNHNKFMVTDKAAYIGTSNWSEDYFLNTAGVGLVILQS 160

                       170       180
                ....*....|....*....|....*..
gi 94681038 464 PGAQPAGATVQEQLRQLFERDWSSRYA 490
Cdd:cd09148 161 PGANEEMLPVQEQLRSLFERDWSSPYA 187
PLDc_vPLD4_1 cd09145
Putative catalytic domain, repeat 1, of vertebrate phospholipase PLD4; Putative catalytic ...
 98-267 9.59e-108

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: 318.00  E-value: 9.59e-108
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038  98 LVESIPQDLPSAAGSPSAQPLGQAWLQLLDTAQESVHVASYYWSLTGPDIGVNDSSSQLGEALLQKLQQLLGRNISLAVA 177
Cdd:cd09145   1 LVESIPEDLTYEGNSTFALPLQKAWTKLLDMAQEQVHVASYYWSLTGEDIGVNDSSSLPGEDILKELAELLSRNVSVRAA 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038 178 TSSPTLARTSTDLQVLAARGAHVRQVPMGRLTRGVLHSKFWVVDGRHIYMGSANMDWRSLTQVKELGAVIYNCSHLAQDL 257
Cdd:cd09145  81 ASIPTLAANSTDLKILRQKGAHVRKVNFGRLTGGVLHSKFWIIDKKHIYVGSANMDWRSLTQVKELGAVIYNCSSLAKDL 160

                       170
                ....*....|
gi 94681038 258 EKTFQTYWVL 267
Cdd:cd09145 161 HKTFQTYWVL 170
PHA02820 PHA02820
phospholipase-D-like protein; Provisional
 92-502 6.51e-97

phospholipase-D-like protein; Provisional


Pssm-ID: 222934 [Multi-domain]  Cd Length: 424  Bit Score: 299.60  E-value: 6.51e-97
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038   92 DSCQLVLVESIPQDLPSAAGSPSAQPLgqaWLQLLDTAQESVHVASYYWSLTGPDiGVNDSSSQLGEallQKLQQLLGRN 171
Cdd:PHA02820   4 DNTIAVITETIPIGMQFDKVYLSTFNF---WREILSNTTKTLDISSFYWSLSDEV-GTNFGTMILNE---IIQLPKRGVR 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038  172 ISLAVATSSptlaRTSTDLQVLAARGAHVRQVPMGRLTRGVLHSKFWVVDGRHIYMGSANMDWRSLTQVKELGAVIYNCS 251
Cdd:PHA02820  77 VRIAVNKSN----KPLKDVELLQMAGVEVRYIDITNILGGVLHTKFWISDNTHIYLGSANMDWRSLTQVKELGIAIFNNS 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038  252 HLAQDLEKTFQTYWVLGVPKavLPKTWPQNFSSHFNRFQPFHGLFDGVPTTAYFSASPPALCPQGRTRDLEALLAVMGSA 331
Cdd:PHA02820 153 NLAADLTQIFEVYWYLGVNN--LPYNWKNFYPLYYNTDHPLSLNVSGVPHSVFIASAPQQLCTMERTNDLTALLSCIRNA 230

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038  332 QEFIYASVMEYFPTTrFSHPPR--YWPVLDNALRAAAFGKGVRVRLLVGCGLNTDPTMFPYLRSLQALSnpAANVSVDVK 409
Cdd:PHA02820 231 SKFVYVSVMNFIPII-YSKAGKilFWPYIEDELRRAAIDRKVSVKLLISCWQRSSFIMRNFLRSIAMLK--SKNINIEVK 307

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038  410 VFIVPvGNHSNIPFSRVNHSKFMVTEKAAYIGTSNWSEDYFSSTAGVGLVVTQSpgaqpAGATVQEQLRQLFERDWSSRY 489
Cdd:PHA02820 308 LFIVP-DADPPIPYSRVNHAKYMVTDKTAYIGTSNWTGNYFTDTCGVSINITPD-----DGLGLRQQLEDIFIRDWNSKY 381

                        410
                 ....*....|...
gi 94681038  490 AVGLDGQAPGQDC 502
Cdd:PHA02820 382 SYELYDTSPTKRC 394
PLDc_3 pfam13918
PLD-like domain;
236-414 6.00e-36

PLD-like domain;


Pssm-ID: 464040  Cd Length: 180  Bit Score: 131.67  E-value: 6.00e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038   236 SLTQVKELGAVIYNCSHLAQDLEKTFQTYWVLGVPKAVlPKTWPQNFSSHFNRFQPFHGLFDGVPTTAYFSASPPALCPQ 315
Cdd:pfam13918   1 SLGQIKELGLVFTNCKCLALDLMNIFALFSSLIFENKV-PFTWSKRLCCAVDNEKALNFHLNESGGGAFFSDSPELFCGF 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038   316 GRTRDLEALLAVMGSAQEFIYASVMEYFPTTRFSHPPRYWPVLDNALRAAAFGKGVRVRLLVGCGLNTDPTMFPYLRSLQ 395
Cdd:pfam13918  80 NRSFDEDAILHRIDDAKLSIDIALLDMLPIIKHAGAREYWPDIDDAILEAAILRGVKVRLIISEWKEADPLSFNAARSLD 159

                         170
                  ....*....|....*....
gi 94681038   396 ALSNPAANVSVDVKVFIVP 414
Cdd:pfam13918 160 AFCTEIANCDLKVKFFDLE 178
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 120-494 2.30e-19

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


Pssm-ID: 441111 [Multi-domain]  Cd Length: 367  Bit Score: 89.62  E-value: 2.30e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038 120 QAWLQLLDTAQESVHVASYYWSLtgPDIGvndssSQLGEAllqklqqllgrnisLAVAT-----------SSPTLARTST 188
Cdd:COG1502  28 AALLEAIEAARRSIDLEYYIFDD--DEVG-----RRLADA--------------LIAAArrgvkvrvlldGIGSRALNRD 86

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038 189 DLQVLAARGAHVRQ-VPMGRLTR---GVLHSKFWVVDGRHIYMGSANMDWRSLTQVKELGAvIYNCSHL-----AQDLEK 259
Cdd:COG1502  87 FLRRLRAAGVEVRLfNPVRLLFRrlnGRNHRKIVVIDGRVAFVGGANITDEYLGRDPGFGP-WRDTHVRiegpaVADLQA 165

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038 260 TFQTYWvlgvpkavlpktwpqNFSSHFNRFQPFHglfdGVPTTAYFSASPPAlcpqGRTRDLE-ALLAVMGSAQEFIYAs 338
Cdd:COG1502 166 VFAEDW---------------NFATGEALPFPEP----AGDVRVQVVPSGPD----SPRETIErALLAAIASARRRIYI- 221

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038 339 VMEYFPTTRfshpprywpVLDNALRAAAfGKGVRVRLLVGcGLNTDPTMFPYLRS-LQALsnpaanVSVDVKVFIVPVGn 417
Cdd:COG1502 222 ETPYFVPDR---------SLLRALIAAA-RRGVDVRILLP-AKSDHPLVHWASRSyYEEL------LEAGVRIYEYEPG- 283

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038 418 hsnipfsrVNHSKFMVT-EKAAYIGTSNWseDYFSSTAG--VGLVVTqspgaqpaGATVQEQLRQLFERDWSSRYAVGLD 494
Cdd:COG1502 284 --------FLHAKVMVVdDEWALVGSANL--DPRSLRLNfeVNLVIY--------DPEFAAQLRARFEEDLAHSREVTLE 345
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 193-280 2.01e-11

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: 65.35  E-value: 2.01e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038 193 LAARGAHVRqvpmgRLTRGVLHSKFWVVDGRHIYMGSANMDWRSLTQVKELGAVIYNcSHLAQDLEKTFQTYWvlGVPKA 272
Cdd:COG1502 270 LLEAGVRIY-----EYEPGFLHAKVMVVDDEWALVGSANLDPRSLRLNFEVNLVIYD-PEFAAQLRARFEEDL--AHSRE 341


                ....*...
gi 94681038 273 VLPKTWPQ 280
Cdd:COG1502 342 VTLEEWRK 349
PLDc_2 pfam13091
PLD-like domain;
123-265 2.39e-11

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 61.15  E-value: 2.39e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038   123 LQLLDTAQESVHVASYYWsLTGPDIGvndssSQLGEALLQklqqllGRNISL---AVATSSPTLA-RTSTDLQVLAARGA 198
Cdd:pfam13091   2 IDLINSAKKSIDIATYYF-VPDREII-----DALIAAAKR------GVDVRIildSNKDDAGGPKkASLKELRSLLRAGV 69

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 94681038   199 HVRqVPMGRLTRgvLHSKFWVVDGRHIYMGSANMDWRSLTQVKELGAVIYNcSHLAQDLEKTFQTYW 265
Cdd:pfam13091  70 EIR-EYQSFLRS--MHAKFYIIDGKTVIVGSANLTRRALRLNLENNVVIKD-PELAQELEKEFDRLW 132
PLDc smart00155
Phospholipase D. Active site motifs; Phosphatidylcholine-hydrolyzing phospholipase D (PLD) ...
 211-236 7.81e-09

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: 50.85  E-value: 7.81e-09
                           10        20
                   ....*....|....*....|....*.
gi 94681038    211 GVLHSKFWVVDGRHIYMGSANMDWRS 236
Cdd:smart00155   3 GVLHTKLMIVDDEIAYIGSANLDGRS 28
cls PRK01642
cardiolipin synthetase; Reviewed
 207-264 6.36e-05

cardiolipin synthetase; Reviewed


Pssm-ID: 234967 [Multi-domain]  Cd Length: 483  Bit Score: 45.54  E-value: 6.36e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 94681038  207 RLTRGVLHSKFWVVDGRHIYMGSANMDWRSLTQVKELGAVIYNcSHLAQDLEKTFQTY 264
Cdd:PRK01642 394 RYEGGLLHTKSVLVDDELALVGTVNLDMRSFWLNFEITLVIDD-TGFAADLAAMQEDY 450
bac_cardiolipin TIGR04265
cardiolipin synthase; This model is based on experimentally characterized bacterial ...
 210-264 3.27e-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: 43.24  E-value: 3.27e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 94681038   210 RGVLHSKFWVVDGRHIYMGSANMDWRSLTQVKELGAVIYNCShLAQDLEKTFQTY 264
Cdd:TIGR04265 397 NGFLHSKSVLVDDEIASVGTANMDMRSFWLNFEVNAFIYDKG-FAKDLAAAYDDD 450
PLDc smart00155
Phospholipase D. Active site motifs; Phosphatidylcholine-hydrolyzing phospholipase D (PLD) ...
 423-449 1.32e-03

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


Pssm-ID: 197546 [Multi-domain]  Cd Length: 28  Bit Score: 36.21  E-value: 1.32e-03
                           10        20
                   ....*....|....*....|....*...
gi 94681038    423 FSRVNHSKFMVTE-KAAYIGTSNWSEDY 449
Cdd:smart00155   1 YDGVLHTKLMIVDdEIAYIGSANLDGRS 28
 
Name Accession Description Interval E-value
PLDc_vPLD4_2 cd09148
Putative catalytic domain, repeat 2, of vertebrate phospholipase PLD4; Putative catalytic ...
 304-490 8.96e-125

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: 361.86  E-value: 8.96e-125
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038 304 YFSASPPALCPQGRTRDLEALLAVMGSAQEFIYASVMEYFPTTRFSHPPRYWPVLDNALRAAAFGKGVRVRLLVGCGLNT 383
Cdd:cd09148   1 YLSASPPALCPTGRTSDLQAILSVISQAQEFIYISVMEYFPTCRFCHPKRYWSVLDNALRAAAFDRRVLIRLLISCGRHS 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038 384 DPTMFPYLRSLQALSNPAANVSVDVKVFIVPVGNHSNIPFSRVNHSKFMVTEKAAYIGTSNWSEDYFSSTAGVGLVVTQS 463
Cdd:cd09148  81 DPDMFPFLRSLNALSNPPLSISVHVKLFIVPVGNQTNIPYSRVNHNKFMVTDKAAYIGTSNWSEDYFLNTAGVGLVILQS 160

                       170       180
                ....*....|....*....|....*..
gi 94681038 464 PGAQPAGATVQEQLRQLFERDWSSRYA 490
Cdd:cd09148 161 PGANEEMLPVQEQLRSLFERDWSSPYA 187
PLDc_vPLD4_1 cd09145
Putative catalytic domain, repeat 1, of vertebrate phospholipase PLD4; Putative catalytic ...
 98-267 9.59e-108

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: 318.00  E-value: 9.59e-108
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038  98 LVESIPQDLPSAAGSPSAQPLGQAWLQLLDTAQESVHVASYYWSLTGPDIGVNDSSSQLGEALLQKLQQLLGRNISLAVA 177
Cdd:cd09145   1 LVESIPEDLTYEGNSTFALPLQKAWTKLLDMAQEQVHVASYYWSLTGEDIGVNDSSSLPGEDILKELAELLSRNVSVRAA 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038 178 TSSPTLARTSTDLQVLAARGAHVRQVPMGRLTRGVLHSKFWVVDGRHIYMGSANMDWRSLTQVKELGAVIYNCSHLAQDL 257
Cdd:cd09145  81 ASIPTLAANSTDLKILRQKGAHVRKVNFGRLTGGVLHSKFWIIDKKHIYVGSANMDWRSLTQVKELGAVIYNCSSLAKDL 160

                       170
                ....*....|
gi 94681038 258 EKTFQTYWVL 267
Cdd:cd09145 161 HKTFQTYWVL 170
PHA02820 PHA02820
phospholipase-D-like protein; Provisional
 92-502 6.51e-97

phospholipase-D-like protein; Provisional


Pssm-ID: 222934 [Multi-domain]  Cd Length: 424  Bit Score: 299.60  E-value: 6.51e-97
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038   92 DSCQLVLVESIPQDLPSAAGSPSAQPLgqaWLQLLDTAQESVHVASYYWSLTGPDiGVNDSSSQLGEallQKLQQLLGRN 171
Cdd:PHA02820   4 DNTIAVITETIPIGMQFDKVYLSTFNF---WREILSNTTKTLDISSFYWSLSDEV-GTNFGTMILNE---IIQLPKRGVR 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038  172 ISLAVATSSptlaRTSTDLQVLAARGAHVRQVPMGRLTRGVLHSKFWVVDGRHIYMGSANMDWRSLTQVKELGAVIYNCS 251
Cdd:PHA02820  77 VRIAVNKSN----KPLKDVELLQMAGVEVRYIDITNILGGVLHTKFWISDNTHIYLGSANMDWRSLTQVKELGIAIFNNS 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038  252 HLAQDLEKTFQTYWVLGVPKavLPKTWPQNFSSHFNRFQPFHGLFDGVPTTAYFSASPPALCPQGRTRDLEALLAVMGSA 331
Cdd:PHA02820 153 NLAADLTQIFEVYWYLGVNN--LPYNWKNFYPLYYNTDHPLSLNVSGVPHSVFIASAPQQLCTMERTNDLTALLSCIRNA 230

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038  332 QEFIYASVMEYFPTTrFSHPPR--YWPVLDNALRAAAFGKGVRVRLLVGCGLNTDPTMFPYLRSLQALSnpAANVSVDVK 409
Cdd:PHA02820 231 SKFVYVSVMNFIPII-YSKAGKilFWPYIEDELRRAAIDRKVSVKLLISCWQRSSFIMRNFLRSIAMLK--SKNINIEVK 307

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038  410 VFIVPvGNHSNIPFSRVNHSKFMVTEKAAYIGTSNWSEDYFSSTAGVGLVVTQSpgaqpAGATVQEQLRQLFERDWSSRY 489
Cdd:PHA02820 308 LFIVP-DADPPIPYSRVNHAKYMVTDKTAYIGTSNWTGNYFTDTCGVSINITPD-----DGLGLRQQLEDIFIRDWNSKY 381

                        410
                 ....*....|...
gi 94681038  490 AVGLDGQAPGQDC 502
Cdd:PHA02820 382 SYELYDTSPTKRC 394
PLDc_vPLD3_4_5_like_2 cd09107
Putative catalytic domain, repeat 2, of vertebrate phospholipases, PLD3, PLD4 and PLD5, viral ...
 304-486 5.00e-93

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: 280.29  E-value: 5.00e-93
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038 304 YFSASPPALCPQGRTRDLEALLAVMGSAQEFIYASVMEYFPTTRFSHPPRYWPVLDNALRAAAFGKGVRVRLLVGCGLNT 383
Cdd:cd09107   1 FLSSSPPELCPPGRTDDLDALLSTIDSAKKFIDISVMDYVPLSRYADPRKYWPVIDNALRRAAVDRGVKVRLLVSNWKHT 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038 384 DPTMFPYLRSLQALSNPAANVSVDVKVFIVPVGNHSNIPFSRVNHSKFMVTEKAAYIGTSNWSEDYFSSTAGVGLVVTQS 463
Cdd:cd09107  81 DPSMDAFLKSLQLLKSGVGNGDIEVKIFTVPGDQSTKIPFARVNHAKYMVTDERAYIGTSNWSGDYFYNTAGVSLVINDP 160

                       170       180
                ....*....|....*....|...
gi 94681038 464 pgaqpagaTVQEQLRQLFERDWS 486
Cdd:cd09107 161 --------AIVQQLKDVFERDWN 175
PLDc_vPLD3_2 cd09147
Putative catalytic domain, repeat 2, of vertebrate phospholipase PLD3; Putative catalytic ...
 304-490 3.37e-79

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: 245.26  E-value: 3.37e-79
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038 304 YFSASPPALCPQGRTRDLEALLAVMGSAQEFIYASVMEYFPTTRFSHPPRYWPVLDNALRAAAFGKGVRVRLLVGCGLNT 383
Cdd:cd09147   1 YLSSSPPPLCASGRTPDLQSILNVIDNARSFVYIAVMNYLPTLEFSHPHRYWPAIDDGLRRATYERGVKVRLLISCWGHS 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038 384 DPTMFPYLRSLQALSNPAANVSVDVKVFIVPVGN-HSNIPFSRVNHSKFMVTEKAAYIGTSNWSEDYFSSTAGVGLVVTQ 462
Cdd:cd09147  81 EPSMFAFLRSLAALRDNTTHSDIQVKIFVVPADEaQKKIPYARVNHNKYMVTDRVAYIGTSNWSGDYFTNTAGSALVVNQ 160

                       170       180
                ....*....|....*....|....*...
gi 94681038 463 SPGAqpAGATVQEQLRQLFERDWSSRYA 490
Cdd:cd09147 161 TGRS--ASGTLQSQLQAVFERDWDSPYS 186
PLDc_vPLD3_1 cd09144
Putative catalytic domain, repeat 1, of vertebrate phospholipase PLD3; Putative catalytic ...
 97-268 1.28e-61

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: 199.41  E-value: 1.28e-61
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038  97 VLVESIPQDLPSAAGSPSAQPLGQAWLQLLDTAQESVHVASYYWSLTGPDIGVNDSSSQLGEALLQKLQQLLGRNISLAV 176
Cdd:cd09144   1 VLVESIPEGLVFNSSSTINPSIYQAWLNLISAAQSSLDIASFYWTLTNSDTHTQEPSANQGEQILKKLGQLSQSGVYVRI 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038 177 ATSSPTLARTSTDLQVLAARGAHVRQVPMGRLTRGVLHSKFWVVDGRHIYMGSANMDWRSLTQVKELGAVIYNCSHLAQD 256
Cdd:cd09144  81 AVDKPADPKPMEDINALSSYGADVRMVDMRKLTTGVLHTKFWVVDKKHFYIGSANMDWRSLTQVKELGAVVYNCSCLAED 160

                       170
                ....*....|..
gi 94681038 257 LEKTFQTYWVLG 268
Cdd:cd09144 161 LGKIFEAYWYLG 172
PLDc_vPLD3_4_5_like_1 cd09106
Putative catalytic domain, repeat 1, of vertebrate phospholipases, PLD3, PLD4 and PLD5, viral ...
 98-250 9.71e-58

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: 188.61  E-value: 9.71e-58
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038  98 LVESIPQDLPSAAGSpSAQPLGQAWLQLLDTAQESVHVASYYWSLTGPDIGvNDSSSQLGEALLQKLQQLLGRNISLAVA 177
Cdd:cd09106   1 LVESIPEGLTFLSSS-SHLSTFEAWMELISSAKKSIDIASFYWNLRGTDTN-PDSSAQEGEDIFNALLEAAKRGVKIRIL 78

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 94681038 178 TSSPTLARTSTDLQVLAARG-AHVRQVPMGRL-TRGVLHSKFWVVDGRHIYMGSANMDWRSLTQVKELGAVIYNC 250
Cdd:cd09106  79 QDKPSKDKPDEDDLELAALGgAEVRSLDFTKLiGGGVLHTKFWIVDGKHFYLGSANLDWRSLTQVKELGVYIYNC 153
PLDc_vPLD5_2 cd09149
Putative catalytic domain, repeat 2, of inactive veterbrate phospholipase PLD5; Putative ...
 304-493 1.79e-55

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: 183.90  E-value: 1.79e-55
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038 304 YFSASPPALCPQGRTRDLEALLAVMGSAQEFIYASVMEYFPTTRFSHPPRYWPVLDNALRAAAFGKGVRVRLLVGCGLNT 383
Cdd:cd09149   1 YVSTSPKLFCPKHRSNDLEAIYRVIQDAKQFIYISVMDYLPLLSRSYARRYWSRIDSKIREALVLRSVRVRLLISFWRKT 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038 384 DPTMFPYLRSLQALSNPAANVSVDVKVFIVPVgnHSNIPFSRVNHSKFMVTEKAAYIGTSNWSEDYFSSTAGVGLVVTQS 463
Cdd:cd09149  81 DPLTFNFVSSLKSLCTEQANCSLEVKFFDLEE--ESDCTSPRLNRNKYMVTDGAAYIGNFDWVGNDFTQNAGVGLVINQA 158

                       170       180       190
                ....*....|....*....|....*....|
gi 94681038 464 PGAQPAGATVQEQLRQLFERDWSSRYAVGL 493
Cdd:cd09149 159 DGVEENNATIIEQLRAAFERDWYSNYAKSL 188
PHA03003 PHA03003
palmytilated EEV membrane glycoprotein; Provisional
 98-494 5.33e-43

palmytilated EEV membrane glycoprotein; Provisional


Pssm-ID: 177506 [Multi-domain]  Cd Length: 369  Bit Score: 156.36  E-value: 5.33e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038   98 LVESIPQDLPSAAGSPSAQplgQAWLQLLDTAQESVHVASYYWSLTGPDIGVnDSSSQLGEALLQklqqllGRNISLAVA 177
Cdd:PHA03003  15 IVETLPKSLGIATQHMSTY---ECFDEIISQAKKYIYIASFCCNLRSTPEGR-LILDKLKEAAES------GVKVTILVD 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038  178 TSSPTlaRTSTDLqvlaaRGAHVR--QVPMGRLTR-GVLHSKFWVVDGRHIYMGSANMDWRSLTQVKELGavIYN-CSHL 253
Cdd:PHA03003  85 EQSGD--KDEEEL-----QSSNINyiKVDIGKLNNvGVLLGSFWVSDDRRCYIGNASLTGGSISTIKTLG--VYStYPPL 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038  254 AQDLEKTFQTYWVLGVPKAVLPKTWPQ---NFSSHFNRFQPFHGLFdgvpttayFSASPPALCPQGRTRDLEALLAVMGS 330
Cdd:PHA03003 156 ATDLRRRFDTFKAFNKNKSVFNRLCCAcclPVSTKYHINNPIGGVF--------FSDSPEHLLGYSRTLDADVVLHKIKS 227

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038  331 AQEFIYASVMEYFPTTRFSHPPRYWPVLDNALRAAAFGKGVRVRLLVGCGLNTDPTMFPYLRSLQAL-SNPAanvsVDVK 409
Cdd:PHA03003 228 AKKSIDLELLSLVPVIREDDKTTYWPDIYNALIRAAINRGVKVRLLVGSWKKNDVYSMASVKSLQALcVGND----LSVK 303

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038  410 VFIVPvgnhsnipfsrvNHSKFM-VTEKAAYIGTSNWSEDYFSSTAGVGLvvtqspgaqpagATVQEQL----RQLFERD 484
Cdd:PHA03003 304 VFRIP------------NNTKLLiVDDEFAHITSANFDGTHYLHHAFVSF------------NTIDKELvkelSAIFERD 359

                        410
                 ....*....|
gi 94681038  485 WSSRYAVGLD 494
Cdd:PHA03003 360 WTSSYSKPLK 369
PLDc_vPLD5_1 cd09146
Putative catalytic domain, repeat 1, of inactive veterbrate phospholipase PLD5; Putative ...
 97-267 3.90e-38

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: 136.92  E-value: 3.90e-38
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038  97 VLVESIPQDLPSAAGSPSAQPLGQAWLQLLDTAQESVHVASYYWsltgpDIGVNDSSSQLGEALLQKLQQLLGRNISLAV 176
Cdd:cd09146   1 ALVENIPDGINFSEHAPPHLPLSQGWMNLLDMAVKSVEIVSPLW-----DLNASHPSACQGQRLFERLLGLASRGVELKI 75

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038 177 ATSsptLARTSTDLQVLAARGAHVRQVPMGRLTRGVLHSKFWVVDGRHIYMGSANMDWRSLTQVKELGAVIYNCSHLAQD 256
Cdd:cd09146  76 VSG---ITDSTEVLVLLKKKGAEVHYVNMTALTKGRLQSSFWIVDKRHVYIGSASMDWRSLGQRKELGVIVYNCSCLALD 152

                       170
                ....*....|.
gi 94681038 257 LEKTFQTYWVL 267
Cdd:cd09146 153 LHRVFALYWSL 163
PLDc_3 pfam13918
PLD-like domain;
236-414 6.00e-36

PLD-like domain;


Pssm-ID: 464040  Cd Length: 180  Bit Score: 131.67  E-value: 6.00e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038   236 SLTQVKELGAVIYNCSHLAQDLEKTFQTYWVLGVPKAVlPKTWPQNFSSHFNRFQPFHGLFDGVPTTAYFSASPPALCPQ 315
Cdd:pfam13918   1 SLGQIKELGLVFTNCKCLALDLMNIFALFSSLIFENKV-PFTWSKRLCCAVDNEKALNFHLNESGGGAFFSDSPELFCGF 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038   316 GRTRDLEALLAVMGSAQEFIYASVMEYFPTTRFSHPPRYWPVLDNALRAAAFGKGVRVRLLVGCGLNTDPTMFPYLRSLQ 395
Cdd:pfam13918  80 NRSFDEDAILHRIDDAKLSIDIALLDMLPIIKHAGAREYWPDIDDAILEAAILRGVKVRLIISEWKEADPLSFNAARSLD 159

                         170
                  ....*....|....*....
gi 94681038   396 ALSNPAANVSVDVKVFIVP 414
Cdd:pfam13918 160 AFCTEIANCDLKVKFFDLE 178
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 120-494 2.30e-19

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


Pssm-ID: 441111 [Multi-domain]  Cd Length: 367  Bit Score: 89.62  E-value: 2.30e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038 120 QAWLQLLDTAQESVHVASYYWSLtgPDIGvndssSQLGEAllqklqqllgrnisLAVAT-----------SSPTLARTST 188
Cdd:COG1502  28 AALLEAIEAARRSIDLEYYIFDD--DEVG-----RRLADA--------------LIAAArrgvkvrvlldGIGSRALNRD 86

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038 189 DLQVLAARGAHVRQ-VPMGRLTR---GVLHSKFWVVDGRHIYMGSANMDWRSLTQVKELGAvIYNCSHL-----AQDLEK 259
Cdd:COG1502  87 FLRRLRAAGVEVRLfNPVRLLFRrlnGRNHRKIVVIDGRVAFVGGANITDEYLGRDPGFGP-WRDTHVRiegpaVADLQA 165

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038 260 TFQTYWvlgvpkavlpktwpqNFSSHFNRFQPFHglfdGVPTTAYFSASPPAlcpqGRTRDLE-ALLAVMGSAQEFIYAs 338
Cdd:COG1502 166 VFAEDW---------------NFATGEALPFPEP----AGDVRVQVVPSGPD----SPRETIErALLAAIASARRRIYI- 221

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038 339 VMEYFPTTRfshpprywpVLDNALRAAAfGKGVRVRLLVGcGLNTDPTMFPYLRS-LQALsnpaanVSVDVKVFIVPVGn 417
Cdd:COG1502 222 ETPYFVPDR---------SLLRALIAAA-RRGVDVRILLP-AKSDHPLVHWASRSyYEEL------LEAGVRIYEYEPG- 283

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038 418 hsnipfsrVNHSKFMVT-EKAAYIGTSNWseDYFSSTAG--VGLVVTqspgaqpaGATVQEQLRQLFERDWSSRYAVGLD 494
Cdd:COG1502 284 --------FLHAKVMVVdDEWALVGSANL--DPRSLRLNfeVNLVIY--------DPEFAAQLRARFEEDLAHSREVTLE 345
PLDc_2 pfam13091
PLD-like domain;
324-485 1.24e-12

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 65.01  E-value: 1.24e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038   324 LLAVMGSAQEFIYASVMeYFPTTRFshpprywpvLDNALRAAAfGKGVRVRLLVGcGLNTDPTMFPYLRSLQALSNPAAN 403
Cdd:pfam13091   1 LIDLINSAKKSIDIATY-YFVPDRE---------IIDALIAAA-KRGVDVRIILD-SNKDDAGGPKKASLKELRSLLRAG 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038   404 vsVDVKVFivpvgnhsnIPFSRVNHSKFMVT-EKAAYIGTSNWSEDYFSSTAGVGLVVTqspgaqpaGATVQEQLRQLFE 482
Cdd:pfam13091  69 --VEIREY---------QSFLRSMHAKFYIIdGKTVIVGSANLTRRALRLNLENNVVIK--------DPELAQELEKEFD 129


                  ...
gi 94681038   483 RDW 485
Cdd:pfam13091 130 RLW 132
PLDc_SF cd00138
Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D ...
 120-247 6.31e-12

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


Pssm-ID: 197200 [Multi-domain]  Cd Length: 119  Bit Score: 62.53  E-value: 6.31e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038 120 QAWLQLLDTAQESVHVASYYWSLTGPDIGVNDsssqLGEALlqklqqllGRNISLAVATSSPTLARTSTDLQVLAA---R 196
Cdd:cd00138   1 EALLELLKNAKESIFIATPNFSFNSADRLLKA----LLAAA--------ERGVDVRLIIDKPPNAAGSLSAALLEAllrA 68

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|.
gi 94681038 197 GAHVRQVPMGRLTRGVLHSKFWVVDGRHIYMGSANMDWRSLTQVKELGAVI 247
Cdd:cd00138  69 GVNVRSYVTPPHFFERLHAKVVVIDGEVAYVGSANLSTASAAQNREAGVLV 119
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 193-280 2.01e-11

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: 65.35  E-value: 2.01e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038 193 LAARGAHVRqvpmgRLTRGVLHSKFWVVDGRHIYMGSANMDWRSLTQVKELGAVIYNcSHLAQDLEKTFQTYWvlGVPKA 272
Cdd:COG1502 270 LLEAGVRIY-----EYEPGFLHAKVMVVDDEWALVGSANLDPRSLRLNFEVNLVIYD-PEFAAQLRARFEEDL--AHSRE 341


                ....*...
gi 94681038 273 VLPKTWPQ 280
Cdd:COG1502 342 VTLEEWRK 349
PLDc_2 pfam13091
PLD-like domain;
123-265 2.39e-11

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 61.15  E-value: 2.39e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038   123 LQLLDTAQESVHVASYYWsLTGPDIGvndssSQLGEALLQklqqllGRNISL---AVATSSPTLA-RTSTDLQVLAARGA 198
Cdd:pfam13091   2 IDLINSAKKSIDIATYYF-VPDREII-----DALIAAAKR------GVDVRIildSNKDDAGGPKkASLKELRSLLRAGV 69

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 94681038   199 HVRqVPMGRLTRgvLHSKFWVVDGRHIYMGSANMDWRSLTQVKELGAVIYNcSHLAQDLEKTFQTYW 265
Cdd:pfam13091  70 EIR-EYQSFLRS--MHAKFYIIDGKTVIVGSANLTRRALRLNLENNVVIKD-PELAQELEKEFDRLW 132
PLDc_unchar1_2 cd09128
Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins; ...
 322-485 4.90e-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: 54.97  E-value: 4.90e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038 322 EALLAVMGSAQE--FIYASVMEYFPttrfshpprywPVLDnALRAAAfGKGVRVRLLVgcglntdPTMFPYLRSLQALSN 399
Cdd:cd09128  13 EALLALIDSAEEslLIQNEEMGDDA-----------PILD-ALVDAA-KRGVDVRVLL-------PSAWSAEDERQARLR 72

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038 400 PAANVSVDVKVFIVPVGNHsnipfsrvnHSKFMV-TEKAAYIGTSNWSEDYFSSTAGVGLVVTQSPGAQpagatvqeQLR 478
Cdd:cd09128  73 ALEGAGVPVRLLKDKFLKI---------HAKGIVvDGKTALVGSENWSANSLDRNREVGLIFDDPEVAA--------YLQ 135


                ....*..
gi 94681038 479 QLFERDW 485
Cdd:cd09128 136 AVFESDW 142
PLDc smart00155
Phospholipase D. Active site motifs; Phosphatidylcholine-hydrolyzing phospholipase D (PLD) ...
 211-236 7.81e-09

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: 50.85  E-value: 7.81e-09
                           10        20
                   ....*....|....*....|....*.
gi 94681038    211 GVLHSKFWVVDGRHIYMGSANMDWRS 236
Cdd:smart00155   3 GVLHTKLMIVDDEIAYIGSANLDGRS 28
PLDc_SF cd00138
Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D ...
 322-446 9.48e-09

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


Pssm-ID: 197200 [Multi-domain]  Cd Length: 119  Bit Score: 53.29  E-value: 9.48e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038 322 EALLAVMGSAQEFIYAsvmeyfptTRFSHPPRYWPVLDNALRAAAfGKGVRVRLLVGCGlntdPTMFPYLRSLQALSNPA 401
Cdd:cd00138   1 EALLELLKNAKESIFI--------ATPNFSFNSADRLLKALLAAA-ERGVDVRLIIDKP----PNAAGSLSAALLEALLR 67

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*.
gi 94681038 402 ANVSVdvkVFIVPVGNhsnipFSRVNHSKFMVTEKA-AYIGTSNWS 446
Cdd:cd00138  68 AGVNV---RSYVTPPH-----FFERLHAKVVVIDGEvAYVGSANLS 105
PLDc_CLS_2 cd09112
catalytic domain repeat 2 of bacterial cardiolipin synthase and similar proteins; This CD ...
 193-261 2.72e-08

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: 53.64  E-value: 2.72e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 94681038 193 LAARGAHVRQvpmgrLTRGVLHSKFWVVDGRHIYMGSANMDWRSLTQVKELGAVIYNcSHLAQDLEKTF 261
Cdd:cd09112  78 LLKAGVKIYE-----YNKGFLHSKTLIVDDEIASVGTANLDIRSFELNFEVNAVIYD-KEVAKKLEEIF 140
PLDc pfam00614
Phospholipase D Active site motif; Phosphatidylcholine-hydrolysing phospholipase D (PLD) ...
 211-236 9.55e-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: 47.80  E-value: 9.55e-08
                          10        20
                  ....*....|....*....|....*.
gi 94681038   211 GVLHSKFWVVDGRHIYMGSANMDWRS 236
Cdd:pfam00614   3 GRLHRKIVVVDDELAYIGGANLDGRS 28
PLDc_ybhO_like_2 cd09159
Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; ...
 210-262 2.35e-07

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: 50.61  E-value: 2.35e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 94681038 210 RGVLHSKFWVVDGRHIYMGSANMDWRSLTQVKELGAVIYnCSHLAQDLEKTFQ 262
Cdd:cd09159  90 PSMLHAKTAVIDGDWATVGSSNLDPRSLRLNLEANLVVE-DPAFAAQLEELFE 141
PLDc_ymdC_like_2 cd09113
Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and ...
 194-281 6.42e-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: 50.30  E-value: 6.42e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038 194 AARGAHVRQVPMGRLTRGVLHSKFWVVDGRHIYMGSANMDWRSLTQVKELGAVIYN---CSHLAQDLEKTFQT--YWVLG 268
Cdd:cd09113  98 PDAAKRKRLRGLFGSSRASLHAKSFVIDDRLVFVGSFNLDPRSAYLNTEMGLVIDSpelAAQLRAAMEEDLAPsaYWVLL 177

                        90
                ....*....|...
gi 94681038 269 VPKAVLPKTWPQN 281
Cdd:cd09113 178 LDDGGLVWETEED 190
PLDc_unchar1_1 cd09127
Putative catalytic domain, repeat 1, of uncharacterized phospholipase D-like proteins; ...
 322-484 2.20e-06

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


Pssm-ID: 197225 [Multi-domain]  Cd Length: 141  Bit Score: 47.26  E-value: 2.20e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038 322 EALLAVMGSAQEFIYASVMEyfpttrFSHPPrywpvLDNALRAAAfGKGVRVRLLVgcglntDPTMFPYLRSLQALSNPA 401
Cdd:cd09127  11 APVVDAIASAKRSILLKMYE------FTDPA-----LEKALAAAA-KRGVRVRVLL------EGGPVGGISRAEKLLDYL 72

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038 402 ANVSVDVKVfivpvgNHSNIPFsRVNHSKFMVT-EKAAYIGTSNWSEDYFSSTAGVGLVVTQspgaqpagATVQEQLRQL 480
Cdd:cd09127  73 NEAGVEVRW------TNGTARY-RYTHAKYIVVdDERALVLTENFKPSGFTGTRGFGVVTDD--------PAVVAEIADV 137


                ....
gi 94681038 481 FERD 484
Cdd:cd09127 138 FDAD 141
PLDc_CLS_unchar1_2 cd09162
Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial ...
 183-249 1.02e-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: 197259 [Multi-domain]  Cd Length: 172  Bit Score: 46.10  E-value: 1.02e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 94681038 183 LARTSTdLQVLAARGAHVRqvpmgRLTRGVLHSKFWVVDGRHIYMGSANMDWRSLTQVKELGAVIYN 249
Cdd:cd09162  69 LARGSY-LRDLQEAGAEIY-----LYQPGMLHAKAVVVDDKLALVGSANLDMRSLFLNYEVAVFFYS 129
PLDc_SMU_988_like_2 cd09160
Putative catalytic domain, repeat 2, of Streptococcus mutans uncharacterized protein SMU_988 ...
 209-261 1.39e-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: 45.57  E-value: 1.39e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 94681038 209 TRGVLHSKFWVVDGRHIYMGSANMDWRSLTQVKELGAVIYNCSHLA---QDLEKTF 261
Cdd:cd09160  89 TPGFIHAKTFVSDDKAAVVGTINLDYRSLYLHFECGVYMYDTPVISdikEDFEETL 144
PLDc_vPLD1_2_like_2 cd09105
Catalytic domain, repeat 2, of vertebrate phospholipases, PLD1 and PLD2, and similar proteins; ...
 214-248 5.70e-05

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: 43.06  E-value: 5.70e-05
                        10        20        30
                ....*....|....*....|....*....|....*
gi 94681038 214 HSKFWVVDGRHIYMGSANMDWRSLTQVKELGAVIY 248
Cdd:cd09105 111 HSKVVIVDDEWATVGSANLNRRSMTWDTELNLAVV 145
PLDc_CLS_unchar2_2 cd09163
Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial ...
 214-263 6.26e-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: 43.70  E-value: 6.26e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 94681038 214 HSKFWVVDGRHIYMGSANMDWRSLTQVKELGAVIYnCSHLAQDLEKTFQT 263
Cdd:cd09163  94 HSKLMVVDGAWALIGSANWDPRSLRLNFELNLEVY-DTALAGQLDALFDS 142
cls PRK01642
cardiolipin synthetase; Reviewed
 207-264 6.36e-05

cardiolipin synthetase; Reviewed


Pssm-ID: 234967 [Multi-domain]  Cd Length: 483  Bit Score: 45.54  E-value: 6.36e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 94681038  207 RLTRGVLHSKFWVVDGRHIYMGSANMDWRSLTQVKELGAVIYNcSHLAQDLEKTFQTY 264
Cdd:PRK01642 394 RYEGGLLHTKSVLVDDELALVGTVNLDMRSFWLNFEITLVIDD-TGFAADLAAMQEDY 450
COG3886 COG3886
HKD family nuclease [Replication, recombination and repair];
357-447 1.80e-04

HKD family nuclease [Replication, recombination and repair];


Pssm-ID: 443094 [Multi-domain]  Cd Length: 941  Bit Score: 44.20  E-value: 1.80e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038 357 VLDNALRAAAfGKGVRVRLLVGCGLN-TDPTMfpyLRSLQALSNpaanvsVDVKVFivpvgNHSNIPFsrvnHSK---FM 432
Cdd:COG3886  59 LLLDALKELL-ERGVKGRILTSTYLGfTEPKA---LRELLDLPN------IEVRVS-----YDRKTRF----HAKayiFE 119

                        90
                ....*....|....*.
gi 94681038 433 VTEKA-AYIGTSNWSE 447
Cdd:COG3886 120 RTGYGtAIIGSSNLTR 135
PRK12452 PRK12452
cardiolipin synthase;
210-262 2.55e-04

cardiolipin synthase;


Pssm-ID: 171510 [Multi-domain]  Cd Length: 509  Bit Score: 43.37  E-value: 2.55e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 94681038  210 RGVLHSKFWVVDGRHIYMGSANMDWRSLTQVKELGAVIYNcSHLAQDLEKTFQ 262
Cdd:PRK12452 423 DGFMHAKIVLVDDKIATIGTANMDVRSFELNYEIISVLYE-SETVHDIKRDFE 474
PLDc_CLS_1 cd09110
Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Catalytic ...
 322-485 2.81e-04

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: 41.31  E-value: 2.81e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038 322 EALLAVMGSAQEFIYasvMEYF------PTTRFShpprywpvldNALRAAAfGKGVRVRLLV---GCgLNTDPTMFPYLR 392
Cdd:cd09110   8 PALLEAIRAARHSIH---LEYYifrddeIGRRFR----------DALIEKA-RRGVEVRLLYdgfGS-LGLSRRFLRELR 72

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038 393 slqalsnpAANvsVDVKVFIVPVGNHSNIPFSRVNHSKFMVT-EKAAYIGTSNWSEDYFSSTAG------VGLVVTqspg 465
Cdd:cd09110  73 --------EAG--VEVRAFNPLSFPLFLLRLNYRNHRKILVIdGKIAFVGGFNIGDEYLGKDPGfgpwrdTHVRIE---- 138

                       170       180
                ....*....|....*....|
gi 94681038 466 aqpaGATVqEQLRQLFERDW 485
Cdd:cd09110 139 ----GPAV-ADLQAAFLEDW 153
PLDc_Nuc_like cd09116
Catalytic domain of EDTA-resistant nuclease Nuc, vertebrate phospholipase D6, and similar ...
 123-263 3.07e-04

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


Pssm-ID: 197215 [Multi-domain]  Cd Length: 138  Bit Score: 40.74  E-value: 3.07e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038 123 LQLLDTAQESVHVASYywSLTGPDIG--VNDSSSQlgeallqklqqllGRNISLAVATSSPTLARTSTDLQVLAARGAHV 200
Cdd:cd09116  15 VALIANAKSSIDVAMY--ALTDPEIAeaLKRAAKR-------------GVRVRIILDKDSLADNLSITLLALLSNLGIPV 79

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 94681038 201 RQVPmgrlTRGVLHSKFWVVDGRHIYMGSANMDWRSLTQVKELGAVIYNcSHLAQDLEKTFQT 263
Cdd:cd09116  80 RTDS----GSKLMHHKFIIIDGKIVITGSANWTKSGFHRNDENLLIIDD-PKLAASFEEEFNR 137
PLDc_unchar1_2 cd09128
Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins; ...
 188-265 3.24e-04

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


Pssm-ID: 197226 [Multi-domain]  Cd Length: 142  Bit Score: 41.11  E-value: 3.24e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 94681038 188 TDLQVLAARGAHVRQVPMGRLTrgvLHSKFWVVDGRHIYMGSANMDWRSLTQVKELGAVIYNcSHLAQDLEKTFQTYW 265
Cdd:cd09128  69 ARLRALEGAGVPVRLLKDKFLK---IHAKGIVVDGKTALVGSENWSANSLDRNREVGLIFDD-PEVAAYLQAVFESDW 142
bac_cardiolipin TIGR04265
cardiolipin synthase; This model is based on experimentally characterized bacterial ...
 210-264 3.27e-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: 43.24  E-value: 3.27e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 94681038   210 RGVLHSKFWVVDGRHIYMGSANMDWRSLTQVKELGAVIYNCShLAQDLEKTFQTY 264
Cdd:TIGR04265 397 NGFLHSKSVLVDDEIASVGTANMDMRSFWLNFEVNAFIYDKG-FAKDLAAAYDDD 450
PLDc smart00155
Phospholipase D. Active site motifs; Phosphatidylcholine-hydrolyzing phospholipase D (PLD) ...
 423-449 1.32e-03

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


Pssm-ID: 197546 [Multi-domain]  Cd Length: 28  Bit Score: 36.21  E-value: 1.32e-03
                           10        20
                   ....*....|....*....|....*...
gi 94681038    423 FSRVNHSKFMVTE-KAAYIGTSNWSEDY 449
Cdd:smart00155   1 YDGVLHTKLMIVDdEIAYIGSANLDGRS 28
PLDc_ymdC_like_1 cd09111
Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and ...
 360-450 1.60e-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: 39.44  E-value: 1.60e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038 360 NALRAAAfGKGVRVRLLVGcGLNTDPtMFPYLRSLQALSNpaanvsVDVKVFiVPVGNHSNIP------FSRVN---HSK 430
Cdd:cd09111  40 GELLEAA-DRGVRVRLLLD-DLGTSG-RDRLLAALDAHPN------IEVRLF-NPFRNRGGRLlefltdFSRLNrrmHNK 109

                        90       100
                ....*....|....*....|.
gi 94681038 431 -FMVTEKAAYIGTSNWSEDYF 450
Cdd:cd09111 110 lFIVDGAVAIVGGRNIGDEYF 130
PLDc_Nuc_like_unchar1_1 cd09172
Putative catalytic domain, repeat 1, of uncharacterized hypothetical proteins similar to Nuc, ...
 120-238 1.66e-03

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


Pssm-ID: 197269 [Multi-domain]  Cd Length: 144  Bit Score: 38.88  E-value: 1.66e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038 120 QAWLQLLDTAQESVHVASYywSLTGPDIgvndsssqlgeALLQKLQQLLGRNISLAVATSSPTLARTSTDlQVLAARGAH 199
Cdd:cd09172  12 LAFLDEARSAGSSIRLAIY--ELDDPEI-----------IDALKAAKDRGVRVRIILDDSSVTGDPTEES-AAATLSKGP 77

                        90       100       110       120
                ....*....|....*....|....*....|....*....|...
gi 94681038 200 VRQVpMGRLTRGVLHSKFWVVDG----RHIYMGSANMDWRSLT 238
Cdd:cd09172  78 GALV-KRRHSSGLMHNKFLVVDRkdgpNRVLTGSTNFTTSGLY 119
PLDc_unchar3 cd09131
Putative catalytic domain of uncharacterized phospholipase D-like proteins; Putative catalytic ...
 213-261 2.33e-03

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


Pssm-ID: 197229 [Multi-domain]  Cd Length: 143  Bit Score: 38.48  E-value: 2.33e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 94681038 213 LHSKFWVVDGRHIYMGSANMDWRSLTQVKELGAVIyNCSHLAQDLEKTF 261
Cdd:cd09131  93 THTKLVVIDGRTVYVGSHNWTYSALDYNHEASVLI-ESPEVADFAINYF 140
PLDc_EcCLS_like_2 cd09158
Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase and similar proteins; ...
 211-264 6.89e-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: 37.55  E-value: 6.89e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 94681038 211 GVLHSKFWVVDGRHIYMGSANMDWRSLTQVKELGAVIYNcSHLAQDLEKTFQTY 264
Cdd:cd09158  91 GLLHAKTVTVDDEVALVGSSNFDIRSFALNFEISLILYD-KEFTAQLRAIQERY 143
PLDc_unchar1_1 cd09127
Putative catalytic domain, repeat 1, of uncharacterized phospholipase D-like proteins; ...
 123-262 7.76e-03

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: 36.86  E-value: 7.76e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94681038 123 LQLLDTAQESVHVASYywSLTGPDIgvndsSSQLGEALlqklqqllGRNISLAV-ATSSPT--LARTSTDLQVLAARGAH 199
Cdd:cd09127  14 VDAIASAKRSILLKMY--EFTDPAL-----EKALAAAA--------KRGVRVRVlLEGGPVggISRAEKLLDYLNEAGVE 78

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 94681038 200 VRQVPmGRLTRGVLHSKFWVVDGRHIYMGSANMDWRSLTQVKELGAVIYNcSHLAQDLEKTFQ 262
Cdd:cd09127  79 VRWTN-GTARYRYTHAKYIVVDDERALVLTENFKPSGFTGTRGFGVVTDD-PAVVAEIADVFD 139
 
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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