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Conserved domains on  [gi|446523904|ref|WP_000601250|]
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phospholipase D-like domain-containing protein [Leptospira interrogans]

Protein Classification

PLDc_Nuc_like_unchar1_1 and PLDc_Nuc_like_unchar1_2 domain-containing protein( domain architecture ID 10173737)

PLDc_Nuc_like_unchar1_1 and PLDc_Nuc_like_unchar1_2 domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PLDc_Nuc_like_unchar1_2 cd09173
Putative catalytic domain, repeat 2, of uncharacterized hypothetical proteins similar to Nuc, ...
 189-339 5.61e-42

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


:

Pssm-ID: 197270 [Multi-domain]  Cd Length: 159  Bit Score: 148.66  E-value: 5.61e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904 189 YISPAKGRLIQNLILREVDHSQSEIKYLIFDHF-DSVLTSRLALADlKGIKVKGIYDSPVDTEGKFLANVFR----NPSS 263
Cdd:cd09173    1 FSPPPKGNADLALIAELVAKAKSSVLFALFDFSdGALLDALLAAAD-AGLFVRGLVDKRFGGRYYSAAADMGgidpVYPA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904 264 EIAGDGNEETISLDSFGKGGLLHHKTMILDD----QVLISGSYNFSISARDNNREILFKTKDPYLIDSYSKEWERIRWNA 339
Cdd:cd09173   80 ALAPDEPEKFVGEPLLGVGDKLHHKFMVIDPfgddPVVITGSHNFSGAANDNNDENLLVIRDPAIADAYAIEFLRLYDHY 159
PLDc_Nuc_like_unchar1_1 cd09172
Putative catalytic domain, repeat 1, of uncharacterized hypothetical proteins similar to Nuc, ...
 50-174 9.38e-35

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: 128.24  E-value: 9.38e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904  50 AFKKRNVRDKILKLIESSQFSIDLWIYSFDDLEILDALKNANARGVTIQILADPEKEY----------PLELKSLGWFRK 119
Cdd:cd09172    4 SRELREALLAFLDEARSAGSSIRLAIYELDDPEIIDALKAAKDRGVRVRIILDDSSVTgdpteesaaaTLSKGPGALVKR 83

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446523904 120 WEKSGLQHSKILIVDRK----KVFLGSGNFTWYGLENDLNGYVSFDL--FDSEIENFYSFL 174
Cdd:cd09172   84 RHSSGLMHNKFLVVDRKdgpnRVLTGSTNFTTSGLYGQSNNVLIFRNpaFAAAYLAYWNTL 144
 
Name Accession Description Interval E-value
PLDc_Nuc_like_unchar1_2 cd09173
Putative catalytic domain, repeat 2, of uncharacterized hypothetical proteins similar to Nuc, ...
 189-339 5.61e-42

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


Pssm-ID: 197270 [Multi-domain]  Cd Length: 159  Bit Score: 148.66  E-value: 5.61e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904 189 YISPAKGRLIQNLILREVDHSQSEIKYLIFDHF-DSVLTSRLALADlKGIKVKGIYDSPVDTEGKFLANVFR----NPSS 263
Cdd:cd09173    1 FSPPPKGNADLALIAELVAKAKSSVLFALFDFSdGALLDALLAAAD-AGLFVRGLVDKRFGGRYYSAAADMGgidpVYPA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904 264 EIAGDGNEETISLDSFGKGGLLHHKTMILDD----QVLISGSYNFSISARDNNREILFKTKDPYLIDSYSKEWERIRWNA 339
Cdd:cd09173   80 ALAPDEPEKFVGEPLLGVGDKLHHKFMVIDPfgddPVVITGSHNFSGAANDNNDENLLVIRDPAIADAYAIEFLRLYDHY 159
PLDc_Nuc_like_unchar1_1 cd09172
Putative catalytic domain, repeat 1, of uncharacterized hypothetical proteins similar to Nuc, ...
 50-174 9.38e-35

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: 128.24  E-value: 9.38e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904  50 AFKKRNVRDKILKLIESSQFSIDLWIYSFDDLEILDALKNANARGVTIQILADPEKEY----------PLELKSLGWFRK 119
Cdd:cd09172    4 SRELREALLAFLDEARSAGSSIRLAIYELDDPEIIDALKAAKDRGVRVRIILDDSSVTgdpteesaaaTLSKGPGALVKR 83

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446523904 120 WEKSGLQHSKILIVDRK----KVFLGSGNFTWYGLENDLNGYVSFDL--FDSEIENFYSFL 174
Cdd:cd09172   84 RHSSGLMHNKFLVVDRKdgpnRVLTGSTNFTTSGLYGQSNNVLIFRNpaFAAAYLAYWNTL 144
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 57-344 8.44e-21

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: 94.24  E-value: 8.44e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904  57 RDKILKLIESSQFSIDLWIYSFDD----LEILDALKNANARGVTIQILADP------EKEYPLELKSLG---------WF 117
Cdd:COG1502   27 FAALLEAIEAARRSIDLEYYIFDDdevgRRLADALIAAARRGVKVRVLLDGigsralNRDFLRRLRAAGvevrlfnpvRL 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904 118 RKWEKSGLQHSKILIVDRKKVFLGSGNFTWYGLENDLNGYVSFDL-----------FDSEIENFYSFLEEKfvSLNIPPF 186
Cdd:COG1502  107 LFRRLNGRNHRKIVVIDGRVAFVGGANITDEYLGRDPGFGPWRDThvriegpavadLQAVFAEDWNFATGE--ALPFPEP 184

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904 187 E-------FYISPAKGR-LIQNLILREVDHSQSEIK----YLIFDHfdsVLTSRLALADLKGIKVKGIYDSpvDTEGKFL 254
Cdd:COG1502  185 AgdvrvqvVPSGPDSPReTIERALLAAIASARRRIYietpYFVPDR---SLLRALIAAARRGVDVRILLPA--KSDHPLV 259

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904 255 ANVFRNPSSEIAGDGNEetISLDsfgKGGLLHHKTMILDDQVLISGSYNFSISARDNNREILFKTKDPYLIDSYSKEWER 334
Cdd:COG1502  260 HWASRSYYEELLEAGVR--IYEY---EPGFLHAKVMVVDDEWALVGSANLDPRSLRLNFEVNLVIYDPEFAAQLRARFEE 334

                        330
                 ....*....|
gi 446523904 335 IRWNAIPYKP 344
Cdd:COG1502  335 DLAHSREVTL 344
PLDc_2 pfam13091
PLD-like domain;
60-154 6.72e-12

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 63.08  E-value: 6.72e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904   60 ILKLIESSQFSIDLWIYSFD-DLEILDALKNANARGVTIQILADPEKEYP--LELKSLGWFRKWEKSGLQ---------- 126
Cdd:pfam13091   1 LIDLINSAKKSIDIATYYFVpDREIIDALIAAAKRGVDVRIILDSNKDDAggPKKASLKELRSLLRAGVEireyqsflrs 80

                          90       100
                  ....*....|....*....|....*....
gi 446523904  127 -HSKILIVDRKKVFLGSGNFTWYGLENDL 154
Cdd:pfam13091  81 mHAKFYIIDGKTVIVGSANLTRRALRLNL 109
PRK13912 PRK13912
nuclease NucT; Provisional
 47-154 2.02e-11

nuclease NucT; Provisional


Pssm-ID: 184389 [Multi-domain]  Cd Length: 177  Bit Score: 62.87  E-value: 2.02e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904  47 FVPaFKKRNVRDKILKLIESSQFSIDLWIYSFDDLEILDALKNANARGVTIQILADPEKEYPLELKSLGWFRKWE----- 121
Cdd:PRK13912  26 FLP-YEQKDALNKLVSLISNARSSIKIAIYSFTHKDIAKALKSAAKRGVKISIIYDYESNHNNDQSTIGYLDKYPnikvc 104

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 446523904 122 -----------KSGLQHSKILIVDRKKVFLGSGNFTWYGLENDL 154
Cdd:PRK13912 105 llkglkakngkYYGIMHQKVAIIDDKIVVLGSANWSKNAFENNY 148
PRK13912 PRK13912
nuclease NucT; Provisional
 187-342 7.75e-11

nuclease NucT; Provisional


Pssm-ID: 184389 [Multi-domain]  Cd Length: 177  Bit Score: 61.33  E-value: 7.75e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904 187 EFYISPAKGRLIQNLILREVDHSQSEIKYLIFDHFDSVLTSRLALADLKGIKVKGIYDSPVDTegkflanvfRNPSSEIA 266
Cdd:PRK13912  23 SLYFLPYEQKDALNKLVSLISNARSSIKIAIYSFTHKDIAKALKSAAKRGVKISIIYDYESNH---------NNDQSTIG 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904 267 GDGNEETISLDSFgKG---------GLLHHKTMILDDQVLISGSYNFSISARDNNREILFKTKDPYLIDSYSKEWERIRW 337
Cdd:PRK13912  94 YLDKYPNIKVCLL-KGlkakngkyyGIMHQKVAIIDDKIVVLGSANWSKNAFENNYEVLLITDDTETILKAKEYFQKMLG 172


                 ....*
gi 446523904 338 NAIPY 342
Cdd:PRK13912 173 SCVGF 177
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 49-154 6.30e-10

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: 61.11  E-value: 6.30e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904  49 PAFKKRNVRDKILKLIESSQFSIdlWIYSFD---DLEILDALKNANARGVTIQILADPEKEYPL-ELKSLGWFRKWEKSG 124
Cdd:COG1502  197 PDSPRETIERALLAAIASARRRI--YIETPYfvpDRSLLRALIAAARRGVDVRILLPAKSDHPLvHWASRSYYEELLEAG 274

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 446523904 125 LQ---------HSKILIVDRKKVFLGSGNFTWYGLENDL 154
Cdd:COG1502  275 VRiyeyepgflHAKVMVVDDEWALVGSANLDPRSLRLNF 313
PLDc_2 pfam13091
PLD-like domain;
202-336 7.11e-09

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 54.22  E-value: 7.11e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904  202 ILREVDHSQSEIKYLIFdHFDSV--LTSRLALADLKGIKVKGIYDSPVDTEGKFLANVFRNPSSEIAGdGNEETISLDSF 279
Cdd:pfam13091   1 LIDLINSAKKSIDIATY-YFVPDreIIDALIAAAKRGVDVRIILDSNKDDAGGPKKASLKELRSLLRA-GVEIREYQSFL 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 446523904  280 GkggLLHHKTMILDDQVLISGSYNFSISARDNNREILFKTKDPYLIDSYSKEWERIR 336
Cdd:pfam13091  79 R---SMHAKFYIIDGKTVIVGSANLTRRALRLNLENNVVIKDPELAQELEKEFDRLW 132
PLDc smart00155
Phospholipase D. Active site motifs; Phosphatidylcholine-hydrolyzing phospholipase D (PLD) ...
 124-147 2.99e-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: 35.44  E-value: 2.99e-03
                           10        20
                   ....*....|....*....|....
gi 446523904   124 GLQHSKILIVDRKKVFLGSGNFTW 147
Cdd:smart00155   3 GVLHTKLMIVDDEIAYIGSANLDG 26
 
Name Accession Description Interval E-value
PLDc_Nuc_like_unchar1_2 cd09173
Putative catalytic domain, repeat 2, of uncharacterized hypothetical proteins similar to Nuc, ...
 189-339 5.61e-42

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


Pssm-ID: 197270 [Multi-domain]  Cd Length: 159  Bit Score: 148.66  E-value: 5.61e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904 189 YISPAKGRLIQNLILREVDHSQSEIKYLIFDHF-DSVLTSRLALADlKGIKVKGIYDSPVDTEGKFLANVFR----NPSS 263
Cdd:cd09173    1 FSPPPKGNADLALIAELVAKAKSSVLFALFDFSdGALLDALLAAAD-AGLFVRGLVDKRFGGRYYSAAADMGgidpVYPA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904 264 EIAGDGNEETISLDSFGKGGLLHHKTMILDD----QVLISGSYNFSISARDNNREILFKTKDPYLIDSYSKEWERIRWNA 339
Cdd:cd09173   80 ALAPDEPEKFVGEPLLGVGDKLHHKFMVIDPfgddPVVITGSHNFSGAANDNNDENLLVIRDPAIADAYAIEFLRLYDHY 159
PLDc_Nuc_like_unchar1_1 cd09172
Putative catalytic domain, repeat 1, of uncharacterized hypothetical proteins similar to Nuc, ...
 50-174 9.38e-35

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: 128.24  E-value: 9.38e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904  50 AFKKRNVRDKILKLIESSQFSIDLWIYSFDDLEILDALKNANARGVTIQILADPEKEY----------PLELKSLGWFRK 119
Cdd:cd09172    4 SRELREALLAFLDEARSAGSSIRLAIYELDDPEIIDALKAAKDRGVRVRIILDDSSVTgdpteesaaaTLSKGPGALVKR 83

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446523904 120 WEKSGLQHSKILIVDRK----KVFLGSGNFTWYGLENDLNGYVSFDL--FDSEIENFYSFL 174
Cdd:cd09172   84 RHSSGLMHNKFLVVDRKdgpnRVLTGSTNFTTSGLYGQSNNVLIFRNpaFAAAYLAYWNTL 144
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 57-344 8.44e-21

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: 94.24  E-value: 8.44e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904  57 RDKILKLIESSQFSIDLWIYSFDD----LEILDALKNANARGVTIQILADP------EKEYPLELKSLG---------WF 117
Cdd:COG1502   27 FAALLEAIEAARRSIDLEYYIFDDdevgRRLADALIAAARRGVKVRVLLDGigsralNRDFLRRLRAAGvevrlfnpvRL 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904 118 RKWEKSGLQHSKILIVDRKKVFLGSGNFTWYGLENDLNGYVSFDL-----------FDSEIENFYSFLEEKfvSLNIPPF 186
Cdd:COG1502  107 LFRRLNGRNHRKIVVIDGRVAFVGGANITDEYLGRDPGFGPWRDThvriegpavadLQAVFAEDWNFATGE--ALPFPEP 184

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904 187 E-------FYISPAKGR-LIQNLILREVDHSQSEIK----YLIFDHfdsVLTSRLALADLKGIKVKGIYDSpvDTEGKFL 254
Cdd:COG1502  185 AgdvrvqvVPSGPDSPReTIERALLAAIASARRRIYietpYFVPDR---SLLRALIAAARRGVDVRILLPA--KSDHPLV 259

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904 255 ANVFRNPSSEIAGDGNEetISLDsfgKGGLLHHKTMILDDQVLISGSYNFSISARDNNREILFKTKDPYLIDSYSKEWER 334
Cdd:COG1502  260 HWASRSYYEELLEAGVR--IYEY---EPGFLHAKVMVVDDEWALVGSANLDPRSLRLNFEVNLVIYDPEFAAQLRARFEE 334

                        330
                 ....*....|
gi 446523904 335 IRWNAIPYKP 344
Cdd:COG1502  335 DLAHSREVTL 344
PLDc_Nuc_like cd09116
Catalytic domain of EDTA-resistant nuclease Nuc, vertebrate phospholipase D6, and similar ...
 55-178 6.95e-20

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: 86.20  E-value: 6.95e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904  55 NVRDKILKLIESSQFSIDLWIYSFDDLEILDALKNANARGVTIQILADPE--------KEYPLELKSLGWFRKWEKSGLQ 126
Cdd:cd09116    9 NLERLIVALIANAKSSIDVAMYALTDPEIAEALKRAAKRGVRVRIILDKDsladnlsiTLLALLSNLGIPVRTDSGSKLM 88

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 446523904 127 HSKILIVDRKKVFLGSGNFTWYGLENDLNgyvsfDLFDSEIENFYSFLEEKF 178
Cdd:cd09116   89 HHKFIIIDGKIVITGSANWTKSGFHRNDE-----NLLIIDDPKLAASFEEEF 135
PLDc_Nuc_like cd09116
Catalytic domain of EDTA-resistant nuclease Nuc, vertebrate phospholipase D6, and similar ...
 200-335 4.86e-17

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: 78.11  E-value: 4.86e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904 200 NLILREVDHSQSEIKYLIFDHFDSVLTSRLALADLKGIKVKGIYD--SPVDTEGKFLANVFRNPSSEIAGDGNEetisld 277
Cdd:cd09116   12 RLIVALIANAKSSIDVAMYALTDPEIAEALKRAAKRGVRVRIILDkdSLADNLSITLLALLSNLGIPVRTDSGS------ 85

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 446523904 278 sfgkgGLLHHKTMILDDQVLISGSYNFSISARDNNREILFKTKDPYLIDSYSKEWERI 335
Cdd:cd09116   86 -----KLMHHKFIIIDGKIVITGSANWTKSGFHRNDENLLIIDDPKLAASFEEEFNRL 138
PLDc_Nuc cd09170
Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar ...
 187-338 1.54e-16

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


Pssm-ID: 197267 [Multi-domain]  Cd Length: 142  Bit Score: 76.79  E-value: 1.54e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904 187 EFYISPAKGrlIQNLILREVDHSQSEIKYLIFdhfdsVLTSR---LALADLK--GIKVKGIYDSPVDTEGKFLANVFRNP 261
Cdd:cd09170    3 EVYFSPEGG--ARELILDVIDSARRSIDVAAY-----SFTSPpiaRALIAAKkrGVDVRVVLDKSQAGGKYSALNYLANA 75

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446523904 262 SSEIAGDGNeetisldsfgkGGLLHHKTMILDDQVLISGSYNFSISARDNNRE-ILFKTKDPYLIDSYSKEWERiRWN 338
Cdd:cd09170   76 GIPVRIDDN-----------YAIMHNKVMVIDGKTVITGSFNFTASAEKRNAEnLLVIRNPPELAQQYLQEWQR-RWA 141
PLDc_Nuc cd09170
Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar ...
 36-147 3.60e-13

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


Pssm-ID: 197267 [Multi-domain]  Cd Length: 142  Bit Score: 66.77  E-value: 3.60e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904  36 KVETHFSFSGrfvpafkkrNVRDKILKLIESSQFSIDLWIYSFDDLEILDALKNANARGVTIQILADpEKEYPLELKSLG 115
Cdd:cd09170    1 TVEVYFSPEG---------GARELILDVIDSARRSIDVAAYSFTSPPIARALIAAKKRGVDVRVVLD-KSQAGGKYSALN 70

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 446523904 116 WF-------RKWEKSGLQHSKILIVDRKKVFLGSGNFTW 147
Cdd:cd09170   71 YLanagipvRIDDNYAIMHNKVMVIDGKTVITGSFNFTA 109
PLDc_2 pfam13091
PLD-like domain;
60-154 6.72e-12

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 63.08  E-value: 6.72e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904   60 ILKLIESSQFSIDLWIYSFD-DLEILDALKNANARGVTIQILADPEKEYP--LELKSLGWFRKWEKSGLQ---------- 126
Cdd:pfam13091   1 LIDLINSAKKSIDIATYYFVpDREIIDALIAAAKRGVDVRIILDSNKDDAggPKKASLKELRSLLRAGVEireyqsflrs 80

                          90       100
                  ....*....|....*....|....*....
gi 446523904  127 -HSKILIVDRKKVFLGSGNFTWYGLENDL 154
Cdd:pfam13091  81 mHAKFYIIDGKTVIVGSANLTRRALRLNL 109
PRK13912 PRK13912
nuclease NucT; Provisional
 47-154 2.02e-11

nuclease NucT; Provisional


Pssm-ID: 184389 [Multi-domain]  Cd Length: 177  Bit Score: 62.87  E-value: 2.02e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904  47 FVPaFKKRNVRDKILKLIESSQFSIDLWIYSFDDLEILDALKNANARGVTIQILADPEKEYPLELKSLGWFRKWE----- 121
Cdd:PRK13912  26 FLP-YEQKDALNKLVSLISNARSSIKIAIYSFTHKDIAKALKSAAKRGVKISIIYDYESNHNNDQSTIGYLDKYPnikvc 104

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 446523904 122 -----------KSGLQHSKILIVDRKKVFLGSGNFTWYGLENDL 154
Cdd:PRK13912 105 llkglkakngkYYGIMHQKVAIIDDKIVVLGSANWSKNAFENNY 148
PLDc_unchar1_1 cd09127
Putative catalytic domain, repeat 1, of uncharacterized phospholipase D-like proteins; ...
 57-146 4.55e-11

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


Pssm-ID: 197225 [Multi-domain]  Cd Length: 141  Bit Score: 60.74  E-value: 4.55e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904  57 RDKILKLIESSQFSIDLWIYSFDDLEILDALKNANARGVTIQILADPEKEyplelkslGWFRKWEK--SGLQ-------- 126
Cdd:cd09127   10 VAPVVDAIASAKRSILLKMYEFTDPALEKALAAAAKRGVRVRVLLEGGPV--------GGISRAEKllDYLNeagvevrw 81

                         90       100       110
                 ....*....|....*....|....*....|
gi 446523904 127 ----------HSKILIVDRKKVFLGSGNFT 146
Cdd:cd09127   82 tngtaryrytHAKYIVVDDERALVLTENFK 111
PLDc_vPLD3_4_5_like_1 cd09106
Putative catalytic domain, repeat 1, of vertebrate phospholipases, PLD3, PLD4 and PLD5, viral ...
 61-147 5.91e-11

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: 60.72  E-value: 5.91e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904  61 LKLIESSQFSIDL----WIYSFDDL----------EILDALKNANARGVTIQILAD-PEKEYP------------LELKS 113
Cdd:cd09106   25 MELISSAKKSIDIasfyWNLRGTDTnpdssaqegeDIFNALLEAAKRGVKIRILQDkPSKDKPdeddlelaalggAEVRS 104

                         90       100       110
                 ....*....|....*....|....*....|....
gi 446523904 114 LGwFRKWEKSGLQHSKILIVDRKKVFLGSGNFTW 147
Cdd:cd09106  105 LD-FTKLIGGGVLHTKFWIVDGKHFYLGSANLDW 137
PLDc_unchar2_2 cd09130
Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins; ...
 56-154 5.98e-11

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


Pssm-ID: 197228 [Multi-domain]  Cd Length: 157  Bit Score: 61.10  E-value: 5.98e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904  56 VRDKILKLIESSQFSIDLWI--YSFDDLEILDALKNANARGVTIQILADPEKE--------YP-----LELKSLGWFR-- 118
Cdd:cd09130    6 IGEALLKEINSARAGDKIWIgmFYLADRDVIKALIDAANRGVDVRLILDPNKDafgrekngIPnrpvaAELMKKTKGKiq 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 446523904 119 -KWEKSGLQ--HSKILIVDRKK---VFLGSGNFTW-----YGLENDL 154
Cdd:cd09130   86 iRWYNTGGEqfHTKLLLIKKKGqaiIIGGSANFTRrnlrdYNLETDL 132
PRK13912 PRK13912
nuclease NucT; Provisional
 187-342 7.75e-11

nuclease NucT; Provisional


Pssm-ID: 184389 [Multi-domain]  Cd Length: 177  Bit Score: 61.33  E-value: 7.75e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904 187 EFYISPAKGRLIQNLILREVDHSQSEIKYLIFDHFDSVLTSRLALADLKGIKVKGIYDSPVDTegkflanvfRNPSSEIA 266
Cdd:PRK13912  23 SLYFLPYEQKDALNKLVSLISNARSSIKIAIYSFTHKDIAKALKSAAKRGVKISIIYDYESNH---------NNDQSTIG 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904 267 GDGNEETISLDSFgKG---------GLLHHKTMILDDQVLISGSYNFSISARDNNREILFKTKDPYLIDSYSKEWERIRW 337
Cdd:PRK13912  94 YLDKYPNIKVCLL-KGlkakngkyyGIMHQKVAIIDDKIVVLGSANWSKNAFENNYEVLLITDDTETILKAKEYFQKMLG 172


                 ....*
gi 446523904 338 NAIPY 342
Cdd:PRK13912 173 SCVGF 177
PLDc_unchar1_2 cd09128
Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins; ...
 55-146 1.64e-10

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


Pssm-ID: 197226 [Multi-domain]  Cd Length: 142  Bit Score: 59.21  E-value: 1.64e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904  55 NVRDKILKLIESSQFSIDLWIYSF-DDLEILDALKNANARGVTIQILADPEkeYPLELKSLGWFRKWEKSGLQ------- 126
Cdd:cd09128   10 NAREALLALIDSAEESLLIQNEEMgDDAPILDALVDAAKRGVDVRVLLPSA--WSAEDERQARLRALEGAGVPvrllkdk 87

                         90       100
                 ....*....|....*....|....
gi 446523904 127 ----HSKILIVDRKKVFLGSGNFT 146
Cdd:cd09128   88 flkiHAKGIVVDGKTALVGSENWS 111
PLDc_unchar4 cd09132
Putative catalytic domain of uncharacterized phospholipase D-like proteins; Putative catalytic ...
 60-151 4.84e-10

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


Pssm-ID: 197230 [Multi-domain]  Cd Length: 122  Bit Score: 57.28  E-value: 4.84e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904  60 ILKLIESSQFSIDLWIYSFDDL-EILDALKNANARGVTIQILADPEKEYP----LELKSLGWFR-------------KWE 121
Cdd:cd09132    4 LLELIEGAERSLLIVGYSAYKVsELLQALAAALERGVQVRVVVESSEKAGsvlsLDEDELMWPKlagatlyvwpekkRPG 83

                         90       100       110
                 ....*....|....*....|....*....|
gi 446523904 122 KSGLQHSKILIVDRKKVFLGSGNFTWYGLE 151
Cdd:cd09132   84 KRASLHAKVIVADRRRLLVTSANLTGAGME 113
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 49-154 6.30e-10

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: 61.11  E-value: 6.30e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904  49 PAFKKRNVRDKILKLIESSQFSIdlWIYSFD---DLEILDALKNANARGVTIQILADPEKEYPL-ELKSLGWFRKWEKSG 124
Cdd:COG1502  197 PDSPRETIERALLAAIASARRRI--YIETPYfvpDRSLLRALIAAARRGVDVRILLPAKSDHPLvHWASRSYYEELLEAG 274

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 446523904 125 LQ---------HSKILIVDRKKVFLGSGNFTWYGLENDL 154
Cdd:COG1502  275 VRiyeyepgflHAKVMVVDDEWALVGSANLDPRSLRLNF 313
PLDc_vPLD6_like cd09171
Catalytic domain of vertebrate phospholipase D6 and similar proteins; Catalytic domain of ...
 283-337 6.67e-10

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


Pssm-ID: 197268 [Multi-domain]  Cd Length: 136  Bit Score: 57.23  E-value: 6.67e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 446523904 283 GLLHHKTMILDDQVLISGSYNFSISARDNNREILFKTKDPYLIDSYSKEWERIrW 337
Cdd:cd09171   83 GHMHHKFAVIDGKILITGSFNWTRQAVTGNQENVLITNDPKLVKPFTEEFEKL-W 136
PLDc_vPLD6_like cd09171
Catalytic domain of vertebrate phospholipase D6 and similar proteins; Catalytic domain of ...
 57-146 2.32e-09

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


Pssm-ID: 197268 [Multi-domain]  Cd Length: 136  Bit Score: 55.69  E-value: 2.32e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904  57 RDKILKLIESSQFSIDLWIYSFDDLEILDALKNANARGVTIQILADPEKEYplELKS-LGWFRKW-------EKSGLQHS 128
Cdd:cd09171   10 LSKLLRYLLSARKSLDVCVFTITCDDLADAILDLHRRGVRVRIITDDDQME--DKGSdIGKLRKAgipvrtdLSSGHMHH 87

                         90
                 ....*....|....*...
gi 446523904 129 KILIVDRKKVFLGSGNFT 146
Cdd:cd09171   88 KFAVIDGKILITGSFNWT 105
PLDc_2 pfam13091
PLD-like domain;
202-336 7.11e-09

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 54.22  E-value: 7.11e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904  202 ILREVDHSQSEIKYLIFdHFDSV--LTSRLALADLKGIKVKGIYDSPVDTEGKFLANVFRNPSSEIAGdGNEETISLDSF 279
Cdd:pfam13091   1 LIDLINSAKKSIDIATY-YFVPDreIIDALIAAAKRGVDVRIILDSNKDDAGGPKKASLKELRSLLRA-GVEIREYQSFL 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 446523904  280 GkggLLHHKTMILDDQVLISGSYNFSISARDNNREILFKTKDPYLIDSYSKEWERIR 336
Cdd:pfam13091  79 R---SMHAKFYIIDGKTVIVGSANLTRRALRLNLENNVVIKDPELAQELEKEFDRLW 132
PLDc_CLS_1 cd09110
Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Catalytic ...
 58-157 5.74e-08

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: 52.48  E-value: 5.74e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904  58 DKILKLIESSQFSIDLWIYSFDD----LEILDALKNANARGVTIQILADP------EKEYPLELKSLG----WFR--KWE 121
Cdd:cd09110    8 PALLEAIRAARHSIHLEYYIFRDdeigRRFRDALIEKARRGVEVRLLYDGfgslglSRRFLRELREAGvevrAFNplSFP 87

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 446523904 122 KSGLQ-----HSKILIVDRKKVFLGSGNFT--WYGLENDLNGY 157
Cdd:cd09110   88 LFLLRlnyrnHRKILVIDGKIAFVGGFNIGdeYLGKDPGFGPW 130
PLDc_SF cd00138
Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D ...
 60-158 1.14e-07

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


Pssm-ID: 197200 [Multi-domain]  Cd Length: 119  Bit Score: 50.59  E-value: 1.14e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904  60 ILKLIESSQFSIDLWIYSFD---DLEILDALKNANARGVTIQIL--------ADPEKEYPLELKSLGW-FRKW----EKS 123
Cdd:cd00138    3 LLELLKNAKESIFIATPNFSfnsADRLLKALLAAAERGVDVRLIidkppnaaGSLSAALLEALLRAGVnVRSYvtppHFF 82

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 446523904 124 GLQHSKILIVDRKKVFLGSGNFTWYGLENDLNGYV 158
Cdd:cd00138   83 ERLHAKVVVIDGEVAYVGSANLSTASAAQNREAGV 117
PLDc_Nuc_like_unchar2 cd09174
Putative catalytic domain of uncharacterized hypothetical proteins closely related to Nuc, , ...
 54-146 2.65e-07

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


Pssm-ID: 197271 [Multi-domain]  Cd Length: 136  Bit Score: 50.01  E-value: 2.65e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904  54 RNVRDKILKLIESSQFSIDLWIYSFDDLEILDALKNANARGVTIQILADPE---KEYPLELKSLGW------FRKWEKSG 124
Cdd:cd09174    6 DDIENRIIEEIKKAKFSIWIAVAWFTNKDIFNALKNKKKEGVNIQIIINDDdinKKDVLILDEDSFeiyklpGNGSRYGN 85

                         90       100
                 ....*....|....*....|..
gi 446523904 125 LQHSKILIVDRKKVFLGSGNFT 146
Cdd:cd09174   86 LMHNKFCVIDFKTVITGSYNWT 107
PLDc_like_TrmB_middle cd09124
Middle phospholipase D-like domain of the transcriptional regulator TrmB and similar proteins; ...
 54-150 3.92e-07

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


Pssm-ID: 197223 [Multi-domain]  Cd Length: 126  Bit Score: 49.25  E-value: 3.92e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904  54 RNVRDKILKLIESSQFSIDLWIYSFDDLEILDALKNANARGVTIQILADPEKEYPLELKSLGWFRKWEKSGlqHSKILIV 133
Cdd:cd09124    9 ENILAKIREMINSAKEEIYISLPSEELEELLEELEKAAERGVKVVIIIFGDDDLDDLDSPAIEVRVREGGG--RPFLLIV 86

                         90
                 ....*....|....*....
gi 446523904 134 DRKKVFLGSGNFT--WYGL 150
Cdd:cd09124   87 DSKEALIGPSSEEeeTYAL 105
PLDc_unchar3 cd09131
Putative catalytic domain of uncharacterized phospholipase D-like proteins; Putative catalytic ...
 58-172 5.40e-07

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: 49.26  E-value: 5.40e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904  58 DKILKLIESSQFSIDLWIYSFDDLE--------ILDALKNANARGVTIQILADPEKEY-PLELKSLGWFRKWEKSGLQ-- 126
Cdd:cd09131    6 PALLDLINNAKRSIYIAMYMFKYYEnpgngvntLLEALIDAHKRGVDVKVVLEDSIDDdEVTEENDNTYRYLKDNGVEvr 85

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 446523904 127 --------HSKILIVDRKKVFLGSGNFTWYGLENdlNGYVSFDLFDSEIENFYS 172
Cdd:cd09131   86 fdspsvttHTKLVVIDGRTVYVGSHNWTYSALDY--NHEASVLIESPEVADFAI 137
PLDc_unchar1_2 cd09128
Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins; ...
 207-332 9.59e-06

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


Pssm-ID: 197226 [Multi-domain]  Cd Length: 142  Bit Score: 45.73  E-value: 9.59e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904 207 DHSQSEIKYLI-------------FDHFDSVLTsrlALADL--KGIKVKGIYDSPVDTEGKFLANVFRnpsseIAGDGNE 271
Cdd:cd09128    9 DNAREALLALIdsaeeslliqneeMGDDAPILD---ALVDAakRGVDVRVLLPSAWSAEDERQARLRA-----LEGAGVP 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446523904 272 ETISLDSFGKgglLHHKTMILDDQVLISGSYNFSISARDNNREILFKTKDP----YLIDSYSKEW 332
Cdd:cd09128   81 VRLLKDKFLK---IHAKGIVVDGKTALVGSENWSANSLDRNREVGLIFDDPevaaYLQAVFESDW 142
YrhO COG1378
Sugar-specific transcriptional regulator TrmB [Transcription];
55-169 1.16e-05

Sugar-specific transcriptional regulator TrmB [Transcription];


Pssm-ID: 440988 [Multi-domain]  Cd Length: 238  Bit Score: 46.94  E-value: 1.16e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904  55 NVRDKILKLIESSQFSIDL--WIYSFDDLEILDALKNANARGVTIQILADPE-KEYPLELKSLG-WFRKWEKSglqHSKI 130
Cdd:COG1378  117 AILERLRELIASAEEEILIvlSPPELLLEELEEALEEALERGVKVRVLVSPEvLEVPERLEEEGeEVRVLPGL---PGRL 193

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 446523904 131 LIVDRKKVFLGSGNFT--WYGLENDLNGYVSF--DLFDSEIEN 169
Cdd:COG1378  194 LIVDDKEALISVSEPDgeETAIWIEDPELAALlrELFETLWEK 236
PLDc_CLS_2 cd09112
catalytic domain repeat 2 of bacterial cardiolipin synthase and similar proteins; This CD ...
 49-145 2.79e-05

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


Pssm-ID: 197211 [Multi-domain]  Cd Length: 174  Bit Score: 44.78  E-value: 2.79e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904  49 PAFKKRNVRDKILKLIESSQFSIdlWI---YSFDDLEILDALKNANARGVTIQILAdPEK-EYPLELK-SLGWFRKWEKS 123
Cdd:cd09112    5 PDSDWSSIEQAYLKAINSAKKSI--YIqtpYFIPDESLLEALKTAALSGVDVRIMI-PGKpDHKLVYWaSRSYFEELLKA 81

                         90       100       110
                 ....*....|....*....|....*....|.
gi 446523904 124 GLQ---------HSKILIVDRKKVFLGSGNF 145
Cdd:cd09112   82 GVKiyeynkgflHSKTLIVDDEIASVGTANL 112
PLDc_EcCLS_like_1 cd09152
Catalytic domain, repeat 1, of Escherichia coli cardiolipin synthase and similar proteins; ...
 55-144 3.14e-05

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


Pssm-ID: 197250 [Multi-domain]  Cd Length: 163  Bit Score: 44.51  E-value: 3.14e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904  55 NVRDKILKLIESSQFSIDLWIYSFDD----LEILDALKNANARGVTIQILADP-------EKEYPLELKSLG-------- 115
Cdd:cd09152   12 AVIDRLIADIDAAKHHVHLLFYIWADdgtgDRVAEALERAAKRGVTCRLLLDAvgsraffRSSLWKRLREAGvevvealp 91

                         90       100       110
                 ....*....|....*....|....*....|...
gi 446523904 116 ---WFRKWEKSGL-QHSKILIVDRKKVFLGSGN 144
Cdd:cd09152   92 lrlFRRRLARFDLrNHRKIAVIDGRIAYTGSQN 124
PLDc_Nuc_like_unchar2 cd09174
Putative catalytic domain of uncharacterized hypothetical proteins closely related to Nuc, , ...
 280-335 1.53e-04

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


Pssm-ID: 197271 [Multi-domain]  Cd Length: 136  Bit Score: 41.92  E-value: 1.53e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 446523904 280 GKGGLLHHKTMILDDQVLISGSYNFSISARDNNrEILFKTKDPYLIDSYSKEWERI 335
Cdd:cd09174   82 RYGNLMHNKFCVIDFKTVITGSYNWTKNAEYNF-ENIIITDDRELAEQFAKEFIKL 136
PLDc_Nuc_like_unchar1_1 cd09172
Putative catalytic domain, repeat 1, of uncharacterized hypothetical proteins similar to Nuc, ...
 202-334 2.65e-04

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: 41.57  E-value: 2.65e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904 202 ILREVDHSQSEIKYLIFDHFDSVLTSRLALADLKGIKVKGIYDSPVDTEGKFLANVFRnPSSEIAGDGNEETISldsfgk 281
Cdd:cd09172   14 FLDEARSAGSSIRLAIYELDDPEIIDALKAAKDRGVRVRIILDDSSVTGDPTEESAAA-TLSKGPGALVKRRHS------ 86

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 446523904 282 GGLLHHKTMILDD----QVLISGSYNFSISA--RDNNREILFktKDPYLIDSYSKEWER 334
Cdd:cd09172   87 SGLMHNKFLVVDRkdgpNRVLTGSTNFTTSGlyGQSNNVLIF--RNPAFAAAYLAYWNT 143
PLDc_PaCLS_like_2 cd09161
Putative catalytic domain, repeat 2, of Pseudomonas aeruginosa cardiolipin synthase and ...
 73-145 3.65e-04

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


Pssm-ID: 197258 [Multi-domain]  Cd Length: 176  Bit Score: 41.51  E-value: 3.65e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904  73 LWI---YSFDDLEILDALKNANARGVTIQILAdPEK-----------EYPLELKSLGwFRKWE-KSGLQHSKILIVDRKK 137
Cdd:cd09161   27 LWIaspYFVPDEGVLAALQLAALRGVDVRILI-PERpdhllvylasfSYLPELIRAG-VKVYRyQPGFLHQKVVLVDDEL 104


                 ....*...
gi 446523904 138 VFLGSGNF 145
Cdd:cd09161  105 AAVGTANL 112
PLDc_unchar3 cd09131
Putative catalytic domain of uncharacterized phospholipase D-like proteins; Putative catalytic ...
 223-335 7.03e-04

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


Pssm-ID: 197229 [Multi-domain]  Cd Length: 143  Bit Score: 40.40  E-value: 7.03e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904 223 SVLTSRLALADLKGIKVK-----GIYDSPVDTEGKFLANVFRNPSSEIAGDGNEETisldsfgkgglLHHKTMILDDQVL 297
Cdd:cd09131   37 NTLLEALIDAHKRGVDVKvvledSIDDDEVTEENDNTYRYLKDNGVEVRFDSPSVT-----------THTKLVVIDGRTV 105

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 446523904 298 ISGSYNFSISARDNNREILFKTKDPYLIDSYSKEWERI 335
Cdd:cd09131  106 YVGSHNWTYSALDYNHEASVLIESPEVADFAINYFDSI 143
PLDc_SF cd00138
Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D ...
 201-319 7.83e-04

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: 39.42  E-value: 7.83e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904 201 LILREVDHSQSEIK---YLIFDHFDSVLTSRLALADLKGIKVKGIYDSPVDTEGKFLANVfrnpsseiAGDGNEETISLD 277
Cdd:cd00138    2 ALLELLKNAKESIFiatPNFSFNSADRLLKALLAAAERGVDVRLIIDKPPNAAGSLSAAL--------LEALLRAGVNVR 73

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 446523904 278 SFGKG----GLLHHKTMILDDQVLISGSYNFSISARDNNREILFKT 319
Cdd:cd00138   74 SYVTPphffERLHAKVVVIDGEVAYVGSANLSTASAAQNREAGVLV 119
PLDc_unchar5 cd09133
Putative catalytic domain of uncharacterized hypothetical proteins with one or two copies of ...
 82-153 1.25e-03

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


Pssm-ID: 197231 [Multi-domain]  Cd Length: 127  Bit Score: 39.24  E-value: 1.25e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904  82 EILDALKNANARGVTIQIL------ADPEKEYPLELKSLGWFRKWEKSGLQ--------HSKILIVDRKKVFLGSGNFTW 147
Cdd:cd09133   31 NLLEALEKAAERGVKIDILwgissdEEKEKKALSEIAEKLLADRGLRGGVNvhlrttgsHAKFLVCDDWFALVGSCNWLS 110


                 ....*.
gi 446523904 148 YGLEND 153
Cdd:cd09133  111 SGGDDF 116
PLDc_FAM83D_N cd09184
N-terminal phospholipase D-like domain of the protein, Family with sequence similarity 83D; ...
 34-147 1.41e-03

N-terminal phospholipase D-like domain of the protein, Family with sequence similarity 83D; N-terminal phospholipase D (PLD)-like domain of the protein Family with sequence similarity 83D (FAM83D), also known as spindle protein CHICA. CHICA is a cell-cycle-regulated spindle component, which localizes to the mitotic spindle and is both upregulated and phosphorylated during mitosis. CHICA is required to localize the chromokinesin Kid to the mitotic spindle and serves as a novel interaction partner of Kid, which is required for the generation of polar ejection forces and chromosome congression. Since the N-terminal PLD-like domain of FAM83D shows only trace similarity to the PLD catalytic domain and lacks the functionally important histidine residue, FAM83D may share a similar three-dimensional fold with PLD enzymes, but is unlikely to carry PLD activity.


Pssm-ID: 197281  Cd Length: 271  Bit Score: 41.01  E-value: 1.41e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904  34 LRKVETHFSFSGRFVPAFKKRNVRdkilKLIESSQFSIDLWIYSFDDLEILDALKNA-NARGVTIQILAD---------- 102
Cdd:cd09184  107 VTRVEAHFQPSYGDCIYGCKEAAR----RQIRSAREVIALVMDSFTDLDIFRDLREAcRKRRVPVYILLDqssvshflqm 182

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 446523904 103 -------PEKEYPLELKSLGWFRKWEKSGLQ-----HSKILIVDRKKVFLGSGNFTW 147
Cdd:cd09184  183 cknlgvhLEQEKLMRVRTITGNTYYTRSGAKiigkvHEKFMLIDGIKVATGSYSFTW 239
PLDc_CLS_unchar2_1 cd09157
Putative catalytic domain, repeat 1, of uncharacterized proteins similar to bacterial ...
 61-144 1.50e-03

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


Pssm-ID: 197254 [Multi-domain]  Cd Length: 155  Bit Score: 39.47  E-value: 1.50e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904  61 LKLIESSQFSIDLWIYSFDD----LEILDALKNANARGVTIQILADPEKeyplELKSLG-WFRKWEKSGLQ--------- 126
Cdd:cd09157   11 LEAIDAARHSIALSSYIFDNdgvgREFVDALAEAVARGVDVRVLIDGVG----ARYSRPsIRRRLRRAGVPvarflpprl 86

                         90       100
                 ....*....|....*....|....*....
gi 446523904 127 -----------HSKILIVDRKKVFLGSGN 144
Cdd:cd09157   87 pprlpfinlrnHRKILVVDGRTGFTGGMN 115
PLDc smart00155
Phospholipase D. Active site motifs; Phosphatidylcholine-hydrolyzing phospholipase D (PLD) ...
 124-147 2.99e-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: 35.44  E-value: 2.99e-03
                           10        20
                   ....*....|....*....|....
gi 446523904   124 GLQHSKILIVDRKKVFLGSGNFTW 147
Cdd:smart00155   3 GVLHTKLMIVDDEIAYIGSANLDG 26
PLDc_vPLD3_1 cd09144
Putative catalytic domain, repeat 1, of vertebrate phospholipase PLD3; Putative catalytic ...
 61-150 3.22e-03

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


Pssm-ID: 197242 [Multi-domain]  Cd Length: 172  Bit Score: 38.78  E-value: 3.22e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904  61 LKLIESSQFSIDL----WIYSFDDL-----------EILDALKNANARGVTIQILAD-PEKEYPLE----LKSLGW---- 116
Cdd:cd09144   27 LNLISAAQSSLDIasfyWTLTNSDThtqepsanqgeQILKKLGQLSQSGVYVRIAVDkPADPKPMEdinaLSSYGAdvrm 106

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 446523904 117 --FRKWeKSGLQHSKILIVDRKKVFLGSGNFTWYGL 150
Cdd:cd09144  107 vdMRKL-TTGVLHTKFWVVDKKHFYIGSANMDWRSL 141
PLDc_CLS_unchar2_2 cd09163
Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial ...
 80-144 4.42e-03

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


Pssm-ID: 197260 [Multi-domain]  Cd Length: 176  Bit Score: 38.30  E-value: 4.42e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446523904  80 DLEILDALKNANARGVTIQILAdPEK-EYPL----------ELKSLGwFRKWEKSG-LQHSKILIVDRKKVFLGSGN 144
Cdd:cd09163   37 DRTLITALQAAALRGVEVDIVL-PERnNLPLvdwamranlwELLEHG-VRIYLQPPpFDHSKLMVVDGAWALIGSAN 111
PLDc_yjhR_C_like cd09118
C-terminal domain of Escherichia coli uncharacterized protein yjhR and similar proteins; ...
 60-176 4.89e-03

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


Pssm-ID: 197217 [Multi-domain]  Cd Length: 144  Bit Score: 37.68  E-value: 4.89e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904  60 ILKLIESSQFSIDL---WIySFDDLE---ILDALKNANARGVTIQILADPEKEY----PLELKSLGWFRKWEKSGLQ--- 126
Cdd:cd09118    6 LLKALATVRERIVIvspWI-SLDALEadgLLEAIREAVSRGVDVTIYTDPHLNTgdanDTKANLEDAAEALAEAGIRihe 84

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446523904 127 ----HSKILIVDrkKVFLGSGNFTWYGLENDLNG--------YVSFDLFDsEIENFYSFLEE 176
Cdd:cd09118   85 vngvHSKIVIVD--NHLLAVGSFNWLSAVRDGKYarhetslvYRGEGLEK-EINTILDSLNS 143
cls PRK01642
cardiolipin synthetase; Reviewed
 58-144 6.04e-03

cardiolipin synthetase; Reviewed


Pssm-ID: 234967 [Multi-domain]  Cd Length: 483  Bit Score: 39.38  E-value: 6.04e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446523904  58 DKILKLIESSQFSIDL--WIYSFDDL--EILDALKNANARGVTIQILAD-------PEKEYPLELK------------SL 114
Cdd:PRK01642 129 QAIIRDIELARHYILMefYIWRPDGLgdQVAEALIAAAKRGVRVRLLYDsigsfafFRSPYPEELRnagvevveflkvNL 208

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 446523904 115 GW-------FRkweksglQHSKILIVDRKKVFLGSGN 144
Cdd:PRK01642 209 GRvfrrrldLR-------NHRKIVVIDGYIAYTGSMN 238
 
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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