NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|119576122|gb|EAW55718|]
View 

similar to CG12314 gene product, partial [Homo sapiens]

Protein Classification

phospholipase D-like domain-containing protein( domain architecture ID 10173734)

phospholipase D-like domain-containing protein such as mitochondrial cardiolipin hydrolase, which acts as endonuclease that plays a critical role in PIWI-interacting RNA (piRNA) biogenesis during spermatogenesis

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

Name Accession Description Interval E-value
PLDc_vPLD6_like cd09171
Catalytic domain of vertebrate phospholipase D6 and similar proteins; Catalytic domain of ...
105-216 4.18e-66

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: 201.68  E-value: 4.18e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119576122 105 DLCLFAFSSPQLGRAVQLLHQRGVRVRVVTDCDYMALNGSQIGLLRKAGIQVRHDQDPGYMHHKFAIVDKRVLITGSLNW 184
Cdd:cd09171   25 DVCVFTITCDDLADAILDLHRRGVRVRIITDDDQMEDKGSDIGKLRKAGIPVRTDLSSGHMHHKFAVIDGKILITGSFNW 104
                         90       100       110
                 ....*....|....*....|....*....|..
gi 119576122 185 TTQAIQNNRENVLITEDDEYVRLFLEEFERIW 216
Cdd:cd09171  105 TRQAVTGNQENVLITNDPKLVKPFTEEFEKLW 136
 
Name Accession Description Interval E-value
PLDc_vPLD6_like cd09171
Catalytic domain of vertebrate phospholipase D6 and similar proteins; Catalytic domain of ...
105-216 4.18e-66

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: 201.68  E-value: 4.18e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119576122 105 DLCLFAFSSPQLGRAVQLLHQRGVRVRVVTDCDYMALNGSQIGLLRKAGIQVRHDQDPGYMHHKFAIVDKRVLITGSLNW 184
Cdd:cd09171   25 DVCVFTITCDDLADAILDLHRRGVRVRIITDDDQMEDKGSDIGKLRKAGIPVRTDLSSGHMHHKFAVIDGKILITGSFNW 104
                         90       100       110
                 ....*....|....*....|....*....|..
gi 119576122 185 TTQAIQNNRENVLITEDDEYVRLFLEEFERIW 216
Cdd:cd09171  105 TRQAVTGNQENVLITNDPKLVKPFTEEFEKLW 136
PLDc_2 pfam13091
PLD-like domain;
105-216 1.39e-29

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 108.15  E-value: 1.39e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119576122  105 DLCLFAF-SSPQLGRAVQLLHQRGVRVRVVTD--CDYMALN----GSQIGLLRKAGIQVR-HDQDPGYMHHKFAIVDKRV 176
Cdd:pfam13091  13 DIATYYFvPDREIIDALIAAAKRGVDVRIILDsnKDDAGGPkkasLKELRSLLRAGVEIReYQSFLRSMHAKFYIIDGKT 92
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 119576122  177 LITGSLNWTTQAIQNNRENVLITEDDEYVRLFLEEFERIW 216
Cdd:pfam13091  93 VIVGSANLTRRALRLNLENNVVIKDPELAQELEKEFDRLW 132
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
113-218 5.72e-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: 90.39  E-value: 5.72e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119576122 113 SPQLGRAVQLLHQRGVRVRVVTDC--DYMALNG---SQIGLLRKAGIQVRHDQdPGYMHHKFAIVDKRVLITGSLNWTTQ 187
Cdd:COG1502  229 DRSLLRALIAAARRGVDVRILLPAksDHPLVHWasrSYYEELLEAGVRIYEYE-PGFLHAKVMVVDDEWALVGSANLDPR 307
                         90       100       110
                 ....*....|....*....|....*....|.
gi 119576122 188 AIQNNRENVLITEDDEYVRLFLEEFERIWEQ 218
Cdd:COG1502  308 SLRLNFEVNLVIYDPEFAAQLRARFEEDLAH 338
PRK13912 PRK13912
nuclease NucT; Provisional
105-221 7.68e-17

nuclease NucT; Provisional


Pssm-ID: 184389 [Multi-domain]  Cd Length: 177  Bit Score: 75.97  E-value: 7.68e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119576122 105 DLCLFAFSSPQLGRAVQLLHQRGVRVRVVTDCDYMALNG-SQIGLLRKA---------GIQVRHDQDPGYMHHKFAIVDK 174
Cdd:PRK13912  50 KIAIYSFTHKDIAKALKSAAKRGVKISIIYDYESNHNNDqSTIGYLDKYpnikvcllkGLKAKNGKYYGIMHQKVAIIDD 129
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 119576122 175 RVLITGSLNWTTQAIQNNRENVLITEDDEYVRLFLEEFERIWEQFNP 221
Cdd:PRK13912 130 KIVVLGSANWSKNAFENNYEVLLITDDTETILKAKEYFQKMLGSCVG 176
PLDc smart00155
Phospholipase D. Active site motifs; Phosphatidylcholine-hydrolyzing phospholipase D (PLD) ...
162-185 6.06e-05

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: 39.30  E-value: 6.06e-05
                           10        20
                   ....*....|....*....|....
gi 119576122   162 PGYMHHKFAIVDKRVLITGSLNWT 185
Cdd:smart00155   2 DGVLHTKLMIVDDEIAYIGSANLD 25
 
Name Accession Description Interval E-value
PLDc_vPLD6_like cd09171
Catalytic domain of vertebrate phospholipase D6 and similar proteins; Catalytic domain of ...
105-216 4.18e-66

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: 201.68  E-value: 4.18e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119576122 105 DLCLFAFSSPQLGRAVQLLHQRGVRVRVVTDCDYMALNGSQIGLLRKAGIQVRHDQDPGYMHHKFAIVDKRVLITGSLNW 184
Cdd:cd09171   25 DVCVFTITCDDLADAILDLHRRGVRVRIITDDDQMEDKGSDIGKLRKAGIPVRTDLSSGHMHHKFAVIDGKILITGSFNW 104
                         90       100       110
                 ....*....|....*....|....*....|..
gi 119576122 185 TTQAIQNNRENVLITEDDEYVRLFLEEFERIW 216
Cdd:cd09171  105 TRQAVTGNQENVLITNDPKLVKPFTEEFEKLW 136
PLDc_Nuc_like cd09116
Catalytic domain of EDTA-resistant nuclease Nuc, vertebrate phospholipase D6, and similar ...
105-215 2.66e-44

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: 146.29  E-value: 2.66e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119576122 105 DLCLFAFSSPQLGRAVQLLHQRGVRVRVVTDCDYMALNGS--QIGLLRKAGIQVRHDQDPGYMHHKFAIVDKRVLITGSL 182
Cdd:cd09116   26 DVAMYALTDPEIAEALKRAAKRGVRVRIILDKDSLADNLSitLLALLSNLGIPVRTDSGSKLMHHKFIIIDGKIVITGSA 105
                         90       100       110
                 ....*....|....*....|....*....|...
gi 119576122 183 NWTTQAIQNNRENVLITEDDEYVRLFLEEFERI 215
Cdd:cd09116  106 NWTKSGFHRNDENLLIIDDPKLAASFEEEFNRL 138
PLDc_Nuc cd09170
Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar ...
109-218 1.79e-33

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: 118.39  E-value: 1.79e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119576122 109 FAFSSPQLGRAVQLLHQRGVRVRVVTDCDYMALNGSQIGLLRKAGIQVRHDQDPGYMHHKFAIVDKRVLITGSLNWTTQA 188
Cdd:cd09170   32 YSFTSPPIARALIAAKKRGVDVRVVLDKSQAGGKYSALNYLANAGIPVRIDDNYAIMHNKVMVIDGKTVITGSFNFTASA 111
                         90       100       110
                 ....*....|....*....|....*....|.
gi 119576122 189 IQNNRENVLITEDD-EYVRLFLEEFERIWEQ 218
Cdd:cd09170  112 EKRNAENLLVIRNPpELAQQYLQEWQRRWAQ 142
PLDc_2 pfam13091
PLD-like domain;
105-216 1.39e-29

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 108.15  E-value: 1.39e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119576122  105 DLCLFAF-SSPQLGRAVQLLHQRGVRVRVVTD--CDYMALN----GSQIGLLRKAGIQVR-HDQDPGYMHHKFAIVDKRV 176
Cdd:pfam13091  13 DIATYYFvPDREIIDALIAAAKRGVDVRIILDsnKDDAGGPkkasLKELRSLLRAGVEIReYQSFLRSMHAKFYIIDGKT 92
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 119576122  177 LITGSLNWTTQAIQNNRENVLITEDDEYVRLFLEEFERIW 216
Cdd:pfam13091  93 VIVGSANLTRRALRLNLENNVVIKDPELAQELEKEFDRLW 132
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
113-218 5.72e-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: 90.39  E-value: 5.72e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119576122 113 SPQLGRAVQLLHQRGVRVRVVTDC--DYMALNG---SQIGLLRKAGIQVRHDQdPGYMHHKFAIVDKRVLITGSLNWTTQ 187
Cdd:COG1502  229 DRSLLRALIAAARRGVDVRILLPAksDHPLVHWasrSYYEELLEAGVRIYEYE-PGFLHAKVMVVDDEWALVGSANLDPR 307
                         90       100       110
                 ....*....|....*....|....*....|.
gi 119576122 188 AIQNNRENVLITEDDEYVRLFLEEFERIWEQ 218
Cdd:COG1502  308 SLRLNFEVNLVIYDPEFAAQLRARFEEDLAH 338
PLDc_unchar1_2 cd09128
Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins; ...
125-216 1.77e-17

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: 76.54  E-value: 1.77e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119576122 125 QRGVRVRVVTDCDYMALNGSQIGL--LRKAGIQVR-HDQDPGYMHHKFAIVDKRVLITGSLNWTTQAIQNNRENVLITED 201
Cdd:cd09128   48 KRGVDVRVLLPSAWSAEDERQARLraLEGAGVPVRlLKDKFLKIHAKGIVVDGKTALVGSENWSANSLDRNREVGLIFDD 127
                         90
                 ....*....|....*
gi 119576122 202 DEYVRLFLEEFERIW 216
Cdd:cd09128  128 PEVAAYLQAVFESDW 142
PRK13912 PRK13912
nuclease NucT; Provisional
105-221 7.68e-17

nuclease NucT; Provisional


Pssm-ID: 184389 [Multi-domain]  Cd Length: 177  Bit Score: 75.97  E-value: 7.68e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119576122 105 DLCLFAFSSPQLGRAVQLLHQRGVRVRVVTDCDYMALNG-SQIGLLRKA---------GIQVRHDQDPGYMHHKFAIVDK 174
Cdd:PRK13912  50 KIAIYSFTHKDIAKALKSAAKRGVKISIIYDYESNHNNDqSTIGYLDKYpnikvcllkGLKAKNGKYYGIMHQKVAIIDD 129
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 119576122 175 RVLITGSLNWTTQAIQNNRENVLITEDDEYVRLFLEEFERIWEQFNP 221
Cdd:PRK13912 130 KIVVLGSANWSKNAFENNYEVLLITDDTETILKAKEYFQKMLGSCVG 176
PLDc_Nuc_like_unchar2 cd09174
Putative catalytic domain of uncharacterized hypothetical proteins closely related to Nuc, , ...
111-215 7.73e-16

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: 71.96  E-value: 7.73e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119576122 111 FSSPQLGRAVQLLHQRGVRVRVVTDCD------YMALNGSQIgllRKAGIQVRHDQDPGYMHHKFAIVDKRVLITGSLNW 184
Cdd:cd09174   30 FTNKDIFNALKNKKKEGVNIQIIINDDdinkkdVLILDEDSF---EIYKLPGNGSRYGNLMHNKFCVIDFKTVITGSYNW 106
                         90       100       110
                 ....*....|....*....|....*....|.
gi 119576122 185 TTQAiQNNRENVLITEDDEYVRLFLEEFERI 215
Cdd:cd09174  107 TKNA-EYNFENIIITDDRELAEQFAKEFIKL 136
PLDc_Nuc_like_unchar1_2 cd09173
Putative catalytic domain, repeat 2, of uncharacterized hypothetical proteins similar to Nuc, ...
105-219 8.14e-16

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: 72.77  E-value: 8.14e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119576122 105 DLCLFAFSSPQLGRAVQLLHQRGVRVRVVTDCDYMALNGSQI---GLLRKAGIQ----------VRHDQDP--GYMHHKF 169
Cdd:cd09173   26 LFALFDFSDGALLDALLAAADAGLFVRGLVDKRFGGRYYSAAadmGGIDPVYPAalapdepekfVGEPLLGvgDKLHHKF 105
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 119576122 170 AIVD----KRVLITGSLNWTTQAIQNNRENVLITEDDEYVRLFLEEFERIWEQF 219
Cdd:cd09173  106 MVIDpfgdDPVVITGSHNFSGAANDNNDENLLVIRDPAIADAYAIEFLRLYDHY 159
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
105-217 2.59e-15

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: 74.59  E-value: 2.59e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119576122 105 DLCLFAFSSPQLGRAV-QLL---HQRGVRVRVVTDcDY--MALNGSQIGLLRKAGIQVR--HDQDP------GYMHHKFA 170
Cdd:COG1502   42 DLEYYIFDDDEVGRRLaDALiaaARRGVKVRVLLD-GIgsRALNRDFLRRLRAAGVEVRlfNPVRLlfrrlnGRNHRKIV 120
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 119576122 171 IVDKRVLITGSLNWT------TQAIQNNRENVLITEDDEyVRLFLEEFERIWE 217
Cdd:COG1502  121 VIDGRVAFVGGANITdeylgrDPGFGPWRDTHVRIEGPA-VADLQAVFAEDWN 172
PLDc_Nuc_like_unchar1_1 cd09172
Putative catalytic domain, repeat 1, of uncharacterized hypothetical proteins similar to Nuc, ...
105-219 8.27e-15

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: 69.69  E-value: 8.27e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119576122 105 DLCLFAFSSPQLGRAVQLLHQRGVRVRVVTDC----DYMALNGSQIGLLRKAGIQVRHDQDPGYMHHKFAIVDK----RV 176
Cdd:cd09172   26 RLAIYELDDPEIIDALKAAKDRGVRVRIILDDssvtGDPTEESAAATLSKGPGALVKRRHSSGLMHNKFLVVDRkdgpNR 105
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 119576122 177 LITGSLNWTTQAI--QNNreNVLITEDDEyvrlFLEEFERIWEQF 219
Cdd:cd09172  106 VLTGSTNFTTSGLygQSN--NVLIFRNPA----FAAAYLAYWNTL 144
PLDc_SF cd00138
Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D ...
107-199 2.60e-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: 62.15  E-value: 2.60e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119576122 107 CLFAFSSPQLGRAVQLLHQRGVRVRVVTD---CDYMALNGSQIGLLRKAGIQVRHDQDP----GYMHHKFAIVDKRVLIT 179
Cdd:cd00138   20 NFSFNSADRLLKALLAAAERGVDVRLIIDkppNAAGSLSAALLEALLRAGVNVRSYVTPphffERLHAKVVVIDGEVAYV 99
                         90       100
                 ....*....|....*....|
gi 119576122 180 GSLNWTTQAIQNNRENVLIT 199
Cdd:cd00138  100 GSANLSTASAAQNREAGVLV 119
PLDc_unchar1_1 cd09127
Putative catalytic domain, repeat 1, of uncharacterized phospholipase D-like proteins; ...
105-213 2.76e-12

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: 62.67  E-value: 2.76e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119576122 105 DLCLFAFSSPQLGRAVQLLHQRGVRVRVVtdcdymaLNGS----------QIGLLRKAGIQVRHDQDPG---YMHHKFAI 171
Cdd:cd09127   25 LLKMYEFTDPALEKALAAAAKRGVRVRVL-------LEGGpvggisraekLLDYLNEAGVEVRWTNGTAryrYTHAKYIV 97
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 119576122 172 VD-KRVLITgSLNWTTQAIQNNRENVLITEDDEYVRLFLEEFE 213
Cdd:cd09127   98 VDdERALVL-TENFKPSGFTGTRGFGVVTDDPAVVAEIADVFD 139
PLDc_unchar3 cd09131
Putative catalytic domain of uncharacterized phospholipase D-like proteins; Putative catalytic ...
115-215 6.58e-11

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


Pssm-ID: 197229 [Multi-domain]  Cd Length: 143  Bit Score: 58.89  E-value: 6.58e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119576122 115 QLGRAVQLLHQRGVRVRVVTD-----CDYMALNGSQIGLLRKAGIQVRHDQDPGYMHHKFAIVDKRVLITGSLNWTTQAI 189
Cdd:cd09131   38 TLLEALIDAHKRGVDVKVVLEdsiddDEVTEENDNTYRYLKDNGVEVRFDSPSVTTHTKLVVIDGRTVYVGSHNWTYSAL 117
                         90       100
                 ....*....|....*....|....*.
gi 119576122 190 QNNRENVLITEDDEYVRLFLEEFERI 215
Cdd:cd09131  118 DYNHEASVLIESPEVADFAINYFDSI 143
PLDc_N_DEXD_b2 cd09204
N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family ...
123-216 7.65e-10

N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain; N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain. All members of this subfamily are uncharacterized. Other characterized members of the superfamily that have a related domain architecture ( containing a DEAD/DEAH box helicase domain), include the DNA/RNA helicase superfamily II (SF2) and Res-subunit of type III restriction endonucleases. In addition to the helicase-like region, members of this subfamily also contain one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) in the N-terminal putative catalytic domain. The HKD motif characterizes the phospholipase D (PLD, EC 3.1.4.4) superfamily.


Pssm-ID: 197298 [Multi-domain]  Cd Length: 139  Bit Score: 55.63  E-value: 7.65e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119576122 123 LHQRGVRVRVVTDcDYmaLNGSQIGLLRK----AGIQVR-HDQDPGYmHHKFAIVDKR---VLITGSLNWTTQAIQNNRE 194
Cdd:cd09204   39 LEERGIKGRILTS-TY--LNFNEPKAFREllklPNIEVRiYDEDEGF-HAKGYIFEHEdyyTIIVGSSNLTQSALKSNYE 114
                         90       100
                 ....*....|....*....|....*
gi 119576122 195 -NVLIT--EDDEYVRLFLEEFERIW 216
Cdd:cd09204  115 wNLKVSstENGDLVEQVLEEFERLW 139
COG3886 COG3886
HKD family nuclease [Replication, recombination and repair];
123-227 5.27e-09

HKD family nuclease [Replication, recombination and repair];


Pssm-ID: 443094 [Multi-domain]  Cd Length: 941  Bit Score: 56.53  E-value: 5.27e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119576122 123 LHQRGVRVRVVTDcDYMalNGSQIGLLRK----AGIQVR-HDQDPGYMHHKFAIVDKR---VLITGSLNWTTQAIQNNRE 194
Cdd:COG3886   67 LLERGVKGRILTS-TYL--GFTEPKALRElldlPNIEVRvSYDRKTRFHAKAYIFERTgygTAIIGSSNLTRSALTDNLE 143
                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 119576122 195 -NVLIT--EDDEYVRLFLEEFERIWEQFNPTKYTFF 227
Cdd:COG3886  144 wNVKLSsaEDPDLIEKFRAEFESLWEDSEFVTLDPW 179
YrhO COG1378
Sugar-specific transcriptional regulator TrmB [Transcription];
114-218 7.20e-08

Sugar-specific transcriptional regulator TrmB [Transcription];


Pssm-ID: 440988 [Multi-domain]  Cd Length: 238  Bit Score: 51.94  E-value: 7.20e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119576122 114 PQLGRAVQLLHQRGVRVRVVTDCDYMALngsqIGLLRKAGIQVRHDQDPgymHHKFAIVDKRVLITGSLNwttqaiQNNR 193
Cdd:COG1378  145 EELEEALEEALERGVKVRVLVSPEVLEV----PERLEEEGEEVRVLPGL---PGRLLIVDDKEALISVSE------PDGE 211
                         90       100
                 ....*....|....*....|....*
gi 119576122 194 ENVLITEDDEYVRLFLEEFERIWEQ 218
Cdd:COG1378  212 ETAIWIEDPELAALLRELFETLWEK 236
PLDc_ybhO_like_2 cd09159
Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; ...
125-214 4.50e-06

Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; Catalytic domain, repeat 2, of Escherichia coli cardiolipin (CL) synthase ybhO and similar proteins. In Escherichia coli, there are two genes, f413 (ybhO) and o493 (ymdC), which are homologous to gene cls that encodes the Escherichia coli CL synthase. The prototype of this subfamily is Escherichia coli CL synthase ybhO specified by the f413 (ybhO) gene. ybhO is a membrane-bound protein that catalyzes the formation of cardiolipin (CL) by transferring phosphatidyl group between two phosphatidylglycerol molecules. It can also catalyze phosphatidyl group transfer to water to form phosphatidate. In contrast to the Escherichia coli CL synthase encoded by the cls gene (EcCLS), ybhO does not hydrolyze CL. Moreover, ybhO lacks an N-terminal segment encoded by Escherichia coli cls, which makes ybhO easy to denature. The monomer of ybhO consists of two catalytic domains. Each catalytic domain contains one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. Two HKD motifs from two domains form a single active site involved in phosphatidyl group transfer. ybhO can be stimulated by phosphate and inhibited by CL, the product of the reaction, and by phosphatidate. Phosphate stimulation may be unique to enzymes with CL synthase activity belonging to the PLD superfamily.


Pssm-ID: 197256 [Multi-domain]  Cd Length: 170  Bit Score: 45.61  E-value: 4.50e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119576122 125 QRGVRVRVVT--DCDY-MALNGSQIG---LLRkAGIQVrHDQDPGYMHHKFAIVDKRVLITGSLNWTTQAIQNNRENVLI 198
Cdd:cd09159   49 RRGVDVRLLLpgKSDDpLTVAASRALygkLLR-AGVRI-FEYQPSMLHAKTAVIDGDWATVGSSNLDPRSLRLNLEANLV 126
                         90
                 ....*....|....*.
gi 119576122 199 TEDDEYVRLFLEEFER 214
Cdd:cd09159  127 VEDPAFAAQLEELFEE 142
PLDc_CLS_1 cd09110
Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Catalytic ...
105-183 6.48e-06

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


Pssm-ID: 197209 [Multi-domain]  Cd Length: 154  Bit Score: 45.16  E-value: 6.48e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119576122 105 DLCLFAFSSPQLGRAV-QLL---HQRGVRVRVVTDcDY--MALNGSQIGLLRKAGIQVR------HDQDPGYM----HHK 168
Cdd:cd09110   22 HLEYYIFRDDEIGRRFrDALiekARRGVEVRLLYD-GFgsLGLSRRFLRELREAGVEVRafnplsFPLFLLRLnyrnHRK 100
                         90
                 ....*....|....*
gi 119576122 169 FAIVDKRVLITGSLN 183
Cdd:cd09110  101 ILVIDGKIAFVGGFN 115
PLDc_unchar4 cd09132
Putative catalytic domain of uncharacterized phospholipase D-like proteins; Putative catalytic ...
125-198 7.75e-06

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


Pssm-ID: 197230 [Multi-domain]  Cd Length: 122  Bit Score: 44.19  E-value: 7.75e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119576122 125 QRGVRVRVVTDCDYMALNGSQIGLLRK-----AGIQVRHDQDP------GYMHHKFAIVDKRVLITGSLNWTTQAIQNNR 193
Cdd:cd09132   37 ERGVQVRVVVESSEKAGSVLSLDEDELmwpklAGATLYVWPEKkrpgkrASLHAKVIVADRRRLLVTSANLTGAGMERNI 116

                 ....*.
gi 119576122 194 E-NVLI 198
Cdd:cd09132  117 EaGVLV 122
PLDc_unchar2_2 cd09130
Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins; ...
124-217 2.65e-05

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: 43.39  E-value: 2.65e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119576122 124 HQRGVRVRVVTDCDYMALNGSQIGL-----------LRKAGIQVRHDQDPGYMHH-KFAIVDKR---VLITGSLNWTTQA 188
Cdd:cd09130   43 ANRGVDVRLILDPNKDAFGREKNGIpnrpvaaelmkKTKGKIQIRWYNTGGEQFHtKLLLIKKKgqaIIIGGSANFTRRN 122
                         90       100       110
                 ....*....|....*....|....*....|...
gi 119576122 189 IQN-NRE-NVLIT--EDDEYVRLFLEEFERIWE 217
Cdd:cd09130  123 LRDyNLEtDLKILapNDSPVSKDVDAYFDRLWN 155
PLDc_vPLD4_1 cd09145
Putative catalytic domain, repeat 1, of vertebrate phospholipase PLD4; Putative catalytic ...
112-194 2.81e-05

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: 43.36  E-value: 2.81e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119576122 112 SSPQLGRAV----QLLHQRGVRVRVVTDCDYMALNGSQIGLLRKAGIQVRhdQDP------GYMHHKFAIVDKRVLITGS 181
Cdd:cd09145   55 SSSLPGEDIlkelAELLSRNVSVRAAASIPTLAANSTDLKILRQKGAHVR--KVNfgrltgGVLHSKFWIIDKKHIYVGS 132
                         90
                 ....*....|...
gi 119576122 182 LNWTTQAIQNNRE 194
Cdd:cd09145  133 ANMDWRSLTQVKE 145
PLDc smart00155
Phospholipase D. Active site motifs; Phosphatidylcholine-hydrolyzing phospholipase D (PLD) ...
162-185 6.06e-05

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: 39.30  E-value: 6.06e-05
                           10        20
                   ....*....|....*....|....
gi 119576122   162 PGYMHHKFAIVDKRVLITGSLNWT 185
Cdd:smart00155   2 DGVLHTKLMIVDDEIAYIGSANLD 25
PLDc_yjhR_C_like cd09118
C-terminal domain of Escherichia coli uncharacterized protein yjhR and similar proteins; ...
125-184 7.33e-05

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: 41.91  E-value: 7.33e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 119576122 125 QRGVRVRVVTD--CDYMALNGSQIGL------LRKAGIQVrHDQDpgYMHHKFAIVDKRVLITGSLNW 184
Cdd:cd09118   43 SRGVDVTIYTDphLNTGDANDTKANLedaaeaLAEAGIRI-HEVN--GVHSKIVIVDNHLLAVGSFNW 107
PLDc_vPLD3_4_5_like_2 cd09107
Putative catalytic domain, repeat 2, of vertebrate phospholipases, PLD3, PLD4 and PLD5, viral ...
126-216 2.38e-04

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


Pssm-ID: 197206 [Multi-domain]  Cd Length: 175  Bit Score: 40.70  E-value: 2.38e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119576122 126 RGVRVRVV------TDCDYMALNGS---QIGLLRKAGIQVRHDQDPGY----------MHHKFAIVDKRVLITGSlNWTT 186
Cdd:cd09107   66 RGVKVRLLvsnwkhTDPSMDAFLKSlqlLKSGVGNGDIEVKIFTVPGDqstkipfarvNHAKYMVTDERAYIGTS-NWSG 144
                         90       100       110
                 ....*....|....*....|....*....|.
gi 119576122 187 QAIQNNReNV-LITEDDEYVRLFLEEFERIW 216
Cdd:cd09107  145 DYFYNTA-GVsLVINDPAIVQQLKDVFERDW 174
PLDc_vPLD3_4_5_like_1 cd09106
Putative catalytic domain, repeat 1, of vertebrate phospholipases, PLD3, PLD4 and PLD5, viral ...
111-185 3.65e-04

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: 39.92  E-value: 3.65e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119576122 111 FSSPQLGRAV--QLLH--QRGVRVRVVTDcdYMALNGSQIG---LLRKAGIQVR-----HDQDPGYMHHKFAIVDKRVLI 178
Cdd:cd09106   52 DSSAQEGEDIfnALLEaaKRGVKIRILQD--KPSKDKPDEDdleLAALGGAEVRsldftKLIGGGVLHTKFWIVDGKHFY 129

                 ....*..
gi 119576122 179 TGSLNWT 185
Cdd:cd09106  130 LGSANLD 136
PLDc_FAM83_N cd09119
N-terminal phospholipase D-like domain of proteins from the Family with sequence similarity 83; ...
120-212 3.88e-04

N-terminal phospholipase D-like domain of proteins from the Family with sequence similarity 83; N-terminal phospholipase D (PLD)-like domain of vetebrate proteins from the Family with sequence similarity 83 (FAM83), which is comprised of 8 members, designated FAM83A through FAM83H. Since the N-terminal PLD-like domain of FAM83 proteins shows only trace similarity to the PLD catalytic domain and lacks the functionally important histidine residue, the FAM83 proteins may share a similar three-dimensional fold with PLD enzymes, but are unlikely to carry PLD activity. Members of the FAM83 are mostly uncharacterized proteins. FAM83A, also known as tumor antigen BJ-TSA-9, is a novel tumor-specific gene highly expressed in human lung adenocarcinoma. FAM83D, also known as spindle protein CHICA, is a cell-cycle-regulated spindle component which localizes to the mitotic spindle and is both upregulated and phosphorylated during mitosis. The gene encoding protein FAM83H is the first gene involved in the etiology of amelogenesis imperfecta (AI), that encodes a non-secreted protein due to the absence of a signal peptide. Defects in gene FAM83H cause autosomal dominant hypocalcified amelogenesis imperfecta (ADHCAI). FAM83B, FAM83C, FAM83F, and FAM83G are uncharacterized proteins present across vertebrates while FAM83E is an uncharacterized protein found only in mammals.


Pssm-ID: 197218  Cd Length: 269  Bit Score: 40.82  E-value: 3.88e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119576122 120 VQLLHQRGVRVRVVTDCDYMALNGSQIgllrkagiqvrhdqdPGYMHHKFAIVDKRVLITGSLNWTTQAIQNNRENVLIT 199
Cdd:cd09119  186 LSDEHLKNMRVRSVGGKTYCSRSGKKF---------------KGQMKEKFLLVDGDRVVSGSYSFTWSDAKLHRSMLSVL 250
                         90
                 ....*....|...
gi 119576122 200 EdDEYVRLFLEEF 212
Cdd:cd09119  251 T-GQVVESFDEEF 262
PLDc_N_Snf2_like cd09178
N-terminal putative catalytic domain of uncharacterized HKD family nucleases fused to putative ...
146-217 4.27e-04

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


Pssm-ID: 197275 [Multi-domain]  Cd Length: 134  Bit Score: 39.46  E-value: 4.27e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 119576122 146 IGLLRKAGIQVR-HDQDP----GY-MHHKFAIVDKRVLITGSLNWTTQAIQNNRE-NVLITEDDEYvRLFLEEFERIWE 217
Cdd:cd09178   55 IELIKEGKVEIRvYTKGFlhakAYlFDGPDNDNGPGTAIVGSSNFTKAGLTGNLElNVEVKDRDDV-EELKEWFEELWE 132
PLDc_CLS_unchar1_1 cd09156
Putative catalytic domain, repeat 1, of uncharacterized proteins similar to bacterial ...
105-183 7.76e-04

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


Pssm-ID: 197253 [Multi-domain]  Cd Length: 154  Bit Score: 39.17  E-value: 7.76e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119576122 105 DLCLFAFSSPQLGRAV-QLLHQR---GVRVRVVTDcDYMALNGSQIGL--LRKAGIQVR------HDQDPGYM----HHK 168
Cdd:cd09156   22 DVCTFILGDDATGRRViDALARKareGVEVRLLLD-ALGSFFLSRRALkkLRAAGGKVAffmpvfRLPFRGRTnlrnHRK 100
                         90
                 ....*....|....*
gi 119576122 169 FAIVDKRVLITGSLN 183
Cdd:cd09156  101 IAIADGSTAISGGMN 115
PLDc_CLS_2 cd09112
catalytic domain repeat 2 of bacterial cardiolipin synthase and similar proteins; This CD ...
126-218 1.27e-03

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: 38.61  E-value: 1.27e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119576122 126 RGVRVRVV----TDCD--YMAlNGSQIGLLRKAGIQVRHDQDpGYMHHKFAIVDKRVLITGSLNWTTQAIQNNRE-NVLI 198
Cdd:cd09112   50 SGVDVRIMipgkPDHKlvYWA-SRSYFEELLKAGVKIYEYNK-GFLHSKTLIVDDEIASVGTANLDIRSFELNFEvNAVI 127
                         90       100
                 ....*....|....*....|
gi 119576122 199 teddeYVRLFLEEFERIWEQ 218
Cdd:cd09112  128 -----YDKEVAKKLEEIFEE 142
PLDc_C_DEXD_like cd09126
C-terminal putative phospholipase D-like domain of uncharacterized prokaryotic HKD family ...
112-183 1.42e-03

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


Pssm-ID: 197224 [Multi-domain]  Cd Length: 126  Bit Score: 37.62  E-value: 1.42e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119576122 112 SSPQLGRA-----VQLLH---QRGVRVRVVTD--CDYMALngsqIGLLRKAGIQVRHDQDpgyMHHKFAIVDKRVLITGS 181
Cdd:cd09126   27 SSPYVSQKritklINLLKeaqERGVEVTVVTRepKEYKEL----IEELRSAGVKVKLKEE---IHEKFAIIDKKIVWYGS 99

                 ..
gi 119576122 182 LN 183
Cdd:cd09126  100 IN 101
PLDc_N_DEXD_a cd09179
N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family ...
154-217 2.45e-03

N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain; N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain. All members of this subfamily are uncharacterized. Other characterized members of the superfamily that have a related domain architecture ( containing a DEAD/DEAH box helicase domain), include the DNA/RNA helicase superfamily II (SF2) and Res-subunit of type III restriction endonucleases. In addition to the helicase-like region, members of this subfamily also contain one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) in the N-terminal putative catalytic domain. The HKD motif characterizes the phospholipase D (PLD, EC 3.1.4.4) superfamily.


Pssm-ID: 197276 [Multi-domain]  Cd Length: 190  Bit Score: 37.99  E-value: 2.45e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 119576122 154 IQVRHDQDPGYMHHKFAIV----DKRVLITGSLNWTTQAIQNNRENVLI-----TEDDEYVRLFLEEFERIWE 217
Cdd:cd09179  117 VAFPKNEGAGIFHEKAGIFtdadGNKVAFSGSANETASAWKRNYESIDVfrswdDGDAERVQWKEEEFEALWN 189
PLDc_N_DEXD_b3 cd09205
N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family ...
125-216 2.54e-03

N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain; N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain. All members of this subfamily are uncharacterized. Other characterized members of the superfamily that have a related domain architecture ( containing a DEAD/DEAH box helicase domain), include the DNA/RNA helicase superfamily II (SF2) and Res-subunit of type III restriction endonucleases. In addition to the helicase-like region, members of this subfamily also contain one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) in the N-terminal putative catalytic domain. The HKD motif characterizes the phospholipase D (PLD, EC 3.1.4.4) superfamily. A few family members contain additional domains, like a C-terminal peptidase S24-like domain.


Pssm-ID: 197299 [Multi-domain]  Cd Length: 143  Bit Score: 37.22  E-value: 2.54e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119576122 125 QRGVRVRVVTDcDYM------ALngSQIGLLRKAGIQVR-HDQDPGYMHHK---FAIVDKR-VLITGSLNWTTQAIQNNR 193
Cdd:cd09205   41 SRGARIRILTG-DYLditqpeAL--RRLLDLLGDGIEIRvFESGGRSFHPKaylFEREDGGgAAFVGSSNLSKSALTDGI 117
                         90       100
                 ....*....|....*....|....*.
gi 119576122 194 E-NVLI--TEDDEYVRLFLEEFERIW 216
Cdd:cd09205  118 EwNLRIdrSADPDAFDEAKEAFEKLF 143
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH