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Conserved domains on  [gi|1430550331|ref|WP_113783330|]
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type II toxin-antitoxin system VapC family toxin [Geodermatophilus sp. TF02-6]

Protein Classification

type II toxin-antitoxin system VapC family toxin( domain architecture ID 10008293)

type II toxin-antitoxin (TA) system VapC family toxin functions as a ribonuclease that is neutralized by its cognate antitoxin VapB; similar to Mycobacterium tuberculosis ribonuclease VapC1/VapC3/VapC9/VapC12

Gene Ontology:  GO:0004540
PubMed:  21036780|28279904

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
VapC COG4113
RNA interferase (RNase) VapC, contains PIN domain [Defense mechanisms];
3-124 2.08e-22

RNA interferase (RNase) VapC, contains PIN domain [Defense mechanisms];


:

Pssm-ID: 443289  Cd Length: 125  Bit Score: 85.34  E-value: 2.08e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1430550331   3 VLDASVVTDALAVSGPDGDVARRVLARESSLHAPALLGAEVTSALRAMVARGRLRPEDARGAAARAATLRTRRYPFEPFL 82
Cdd:COG4113     2 VVDASALVKWLLPEEGSEEALRLLERAADELVAPDLALYEVANVLWKAVRRGRLTEEEAEEALELLLELPIEVVPVTELL 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1430550331  83 GRVWDL--HETVTVHDAWYVALAEALDVPLVTADDRLRRAPGPR 124
Cdd:COG4113    82 ERALELarRHGLTAYDAAYLALAERLGAPLVTADRRLARAARAL 125
 
Name Accession Description Interval E-value
VapC COG4113
RNA interferase (RNase) VapC, contains PIN domain [Defense mechanisms];
3-124 2.08e-22

RNA interferase (RNase) VapC, contains PIN domain [Defense mechanisms];


Pssm-ID: 443289  Cd Length: 125  Bit Score: 85.34  E-value: 2.08e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1430550331   3 VLDASVVTDALAVSGPDGDVARRVLARESSLHAPALLGAEVTSALRAMVARGRLRPEDARGAAARAATLRTRRYPFEPFL 82
Cdd:COG4113     2 VVDASALVKWLLPEEGSEEALRLLERAADELVAPDLALYEVANVLWKAVRRGRLTEEEAEEALELLLELPIEVVPVTELL 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1430550331  83 GRVWDL--HETVTVHDAWYVALAEALDVPLVTADDRLRRAPGPR 124
Cdd:COG4113    82 ERALELarRHGLTAYDAAYLALAERLGAPLVTADRRLARAARAL 125
PIN_Pae0151-like cd09873
VapC-like PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; ...
 3-122 1.23e-21

VapC-like PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of the Pyrobaculum aerophilum proteins, Pae0151 and Pae2754, and homologs are included in this subfamily. They are similar to the PIN domains of the Mycobacterium tuberculosis VapC and Neisseria gonorrhoeae FitB toxins of the prokaryotic toxin/antitoxin operons, VapBC and FitAB, respectively, which are believed to be involved in growth inhibition by regulating translation. These toxins are nearly always co-expressed with an antitoxin, a cognate protein inhibitor, forming an inert protein complex. Disassociation of the protein complex activates the ribonuclease activity of the toxin by an, as yet undefined mechanism. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350221  Cd Length: 128  Bit Score: 83.36  E-value: 1.23e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1430550331   3 VLDASVVTdALAVSGPDGDVARRVLAR-ESSLHAPALLGAEVTSALRAMVARGRLRPEDARGAAARAATLRTRRYPFEPF 81
Cdd:cd09873     1 VVDASVAV-KWLLPEEESEAADRLLERlEEELVAPDLWLYEVANVLRKAVRRGRLTEEEAEEALEDLLDLPIEIDPDPEL 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1430550331  82 LGRVWDL--HETVTVHDAWYVALAEALDVPLVTADDRLRRAPG 122
Cdd:cd09873    80 LEEALELarRHGLTAYDAAYLALAERLGAPLVTADRKLARAAK 122
PIN pfam01850
PIN domain;
3-123 4.49e-06

PIN domain;


Pssm-ID: 426475  Cd Length: 121  Bit Score: 42.78  E-value: 4.49e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1430550331   3 VLDASVVTDALAvSGPDGDVARRVLARESSLHAPALLGAEVTSALRAMVARGRLRPEDARGAAARAATLRTRRYPFEPFL 82
Cdd:pfam01850   2 VLDTSVLIALLR-GEPLHEAARELLEAAGELVTSAIVLAELLYGLNRRLGLGKAAELVELLLLLSALEVLPIDAELAEEA 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1430550331  83 GRVWDLHETVTVHDAWYVALAEALDVPLVTADDRLRRAPGP 123
Cdd:pfam01850  81 AELRLKYGKLGPNDALIAATAKEHGAKLITFDEDFARVAKL 121
 
Name Accession Description Interval E-value
VapC COG4113
RNA interferase (RNase) VapC, contains PIN domain [Defense mechanisms];
3-124 2.08e-22

RNA interferase (RNase) VapC, contains PIN domain [Defense mechanisms];


Pssm-ID: 443289  Cd Length: 125  Bit Score: 85.34  E-value: 2.08e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1430550331   3 VLDASVVTDALAVSGPDGDVARRVLARESSLHAPALLGAEVTSALRAMVARGRLRPEDARGAAARAATLRTRRYPFEPFL 82
Cdd:COG4113     2 VVDASALVKWLLPEEGSEEALRLLERAADELVAPDLALYEVANVLWKAVRRGRLTEEEAEEALELLLELPIEVVPVTELL 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1430550331  83 GRVWDL--HETVTVHDAWYVALAEALDVPLVTADDRLRRAPGPR 124
Cdd:COG4113    82 ERALELarRHGLTAYDAAYLALAERLGAPLVTADRRLARAARAL 125
PIN_Pae0151-like cd09873
VapC-like PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; ...
 3-122 1.23e-21

VapC-like PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of the Pyrobaculum aerophilum proteins, Pae0151 and Pae2754, and homologs are included in this subfamily. They are similar to the PIN domains of the Mycobacterium tuberculosis VapC and Neisseria gonorrhoeae FitB toxins of the prokaryotic toxin/antitoxin operons, VapBC and FitAB, respectively, which are believed to be involved in growth inhibition by regulating translation. These toxins are nearly always co-expressed with an antitoxin, a cognate protein inhibitor, forming an inert protein complex. Disassociation of the protein complex activates the ribonuclease activity of the toxin by an, as yet undefined mechanism. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350221  Cd Length: 128  Bit Score: 83.36  E-value: 1.23e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1430550331   3 VLDASVVTdALAVSGPDGDVARRVLAR-ESSLHAPALLGAEVTSALRAMVARGRLRPEDARGAAARAATLRTRRYPFEPF 81
Cdd:cd09873     1 VVDASVAV-KWLLPEEESEAADRLLERlEEELVAPDLWLYEVANVLRKAVRRGRLTEEEAEEALEDLLDLPIEIDPDPEL 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1430550331  82 LGRVWDL--HETVTVHDAWYVALAEALDVPLVTADDRLRRAPG 122
Cdd:cd09873    80 LEEALELarRHGLTAYDAAYLALAERLGAPLVTADRKLARAAK 122
PIN pfam01850
PIN domain;
3-123 4.49e-06

PIN domain;


Pssm-ID: 426475  Cd Length: 121  Bit Score: 42.78  E-value: 4.49e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1430550331   3 VLDASVVTDALAvSGPDGDVARRVLARESSLHAPALLGAEVTSALRAMVARGRLRPEDARGAAARAATLRTRRYPFEPFL 82
Cdd:pfam01850   2 VLDTSVLIALLR-GEPLHEAARELLEAAGELVTSAIVLAELLYGLNRRLGLGKAAELVELLLLLSALEVLPIDAELAEEA 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1430550331  83 GRVWDLHETVTVHDAWYVALAEALDVPLVTADDRLRRAPGP 123
Cdd:pfam01850  81 AELRLKYGKLGPNDALIAATAKEHGAKLITFDEDFARVAKL 121
VapC COG1848
VapC family ribonuclease, toxin component of the VapBC toxin-antitoxin module, contains PIN ...
 1-122 6.49e-04

VapC family ribonuclease, toxin component of the VapBC toxin-antitoxin module, contains PIN domain [Defense mechanisms];


Pssm-ID: 441453  Cd Length: 134  Bit Score: 37.27  E-value: 6.49e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1430550331   1 MNVLDASVVTDALAVSGPDGDVARRVLARESSLHAPALLGAEVTSALRAMVARGRLRPEDARGAAARAATLRTRRYPFEP 80
Cdd:COG1848     1 MILLDTNVLIYALEGDSPFHERARELLERAEEGEEELYTSPLVLAEVLYVLTRPGGLSLEEARELLEALLSNIEVVPVDE 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1430550331  81 FLGRVW-DLHET--VTVHDAWYVALAEALDVP-LVTADDRLRRAPG 122
Cdd:COG1848    81 EILEEAaELLAKygLRLNDALHLATALEHGADaLVTFDRDFARVPG 126
 
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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