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Conserved domains on  [gi|517056506|ref|WP_018245324|]
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MULTISPECIES: type II toxin-antitoxin system VapC family toxin [Rhizobium]

Protein Classification

type II toxin-antitoxin system VapC family toxin( domain architecture ID 10003923)

type II toxin-antitoxin (TA) system VapC family toxin functions as a ribonuclease that is neutralized by its cognate VapB family antitoxin; contains a PIN domain

EC:  3.1.-.-
Gene Ontology:  GO:0004540
PubMed:  21036780

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
VapC COG1487
Ribonuclease/mRNA interferase VapC, contains PIN domain [Defense mechanisms];
2-107 5.26e-07

Ribonuclease/mRNA interferase VapC, contains PIN domain [Defense mechanisms];


:

Pssm-ID: 441096  Cd Length: 128  Bit Score: 45.24  E-value: 5.26e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517056506   2 ILADTSIWIDHFRHVDAELRTI---IEDDRLLCHPAVVGELALGSLRD-----RGRVIAFLAAQRQAFV--ATHDEVMTM 71
Cdd:COG1487    1 YLLDTNVLIDLLRGRPPAVLAWlaeLEAGELAISAITLAELLYGARRSpdakrRAALEAFLEAFPVLPFdaEAARRAGEL 80

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 517056506  72 IDRHGIFSMGIGYTDAhLLASILLDRRAALWTRDKR 107
Cdd:COG1487   81 RAALRRAGRPIGLADL-LIAATALAHGLTLVTRNTK 115
 
Name Accession Description Interval E-value
VapC COG1487
Ribonuclease/mRNA interferase VapC, contains PIN domain [Defense mechanisms];
2-107 5.26e-07

Ribonuclease/mRNA interferase VapC, contains PIN domain [Defense mechanisms];


Pssm-ID: 441096  Cd Length: 128  Bit Score: 45.24  E-value: 5.26e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517056506   2 ILADTSIWIDHFRHVDAELRTI---IEDDRLLCHPAVVGELALGSLRD-----RGRVIAFLAAQRQAFV--ATHDEVMTM 71
Cdd:COG1487    1 YLLDTNVLIDLLRGRPPAVLAWlaeLEAGELAISAITLAELLYGARRSpdakrRAALEAFLEAFPVLPFdaEAARRAGEL 80

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 517056506  72 IDRHGIFSMGIGYTDAhLLASILLDRRAALWTRDKR 107
Cdd:COG1487   81 RAALRRAGRPIGLADL-LIAATALAHGLTLVTRNTK 115
PIN_VapC-like cd09854
VapC-like PIN domains of VapC and Smg6 ribonucleases, ribosome assembly factor NOB1, ...
 5-114 3.12e-05

VapC-like PIN domains of VapC and Smg6 ribonucleases, ribosome assembly factor NOB1, rRNA-processing protein Fcf1, Archaeoglobus fulgidus AF0591 protein, and homologs; PIN (PilT N terminus) domains of such ribonucleases as the toxins of prokaryotic toxin/antitoxin operons FitAB and VapBC, as well as, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1, are included in VapC-like this family. Also included are the PIN domains of the Pyrobaculum aerophilum Pea0151 and Archaeoglobus fulgidus AF0591 proteins and other similar archaeal homologs. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN 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 while some others 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: 350205  Cd Length: 129  Bit Score: 40.72  E-value: 3.12e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517056506   5 DTSIWIDHFR------HVDAELRTIIEDDRLLCHPAVVGELALGSLRDRGRVIAFLAAQRQAFVAT-----HDEVMTMID 73
Cdd:cd09854    3 DTNVLIALLSsepeseAAKELLALLLGDSELVIPPLVLAELLRLLARERGARRALEILELLRALEVveeepALAEIALEV 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 517056506  74 RHGIFSMGIGYTDAHLLASILLDRRAALWTRDKRLQAAAKK 114
Cdd:cd09854   83 LALGLERGLDFGDALILALAKELGGAVLVTNDRDFRRLAKL 123
 
Name Accession Description Interval E-value
VapC COG1487
Ribonuclease/mRNA interferase VapC, contains PIN domain [Defense mechanisms];
2-107 5.26e-07

Ribonuclease/mRNA interferase VapC, contains PIN domain [Defense mechanisms];


Pssm-ID: 441096  Cd Length: 128  Bit Score: 45.24  E-value: 5.26e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517056506   2 ILADTSIWIDHFRHVDAELRTI---IEDDRLLCHPAVVGELALGSLRD-----RGRVIAFLAAQRQAFV--ATHDEVMTM 71
Cdd:COG1487    1 YLLDTNVLIDLLRGRPPAVLAWlaeLEAGELAISAITLAELLYGARRSpdakrRAALEAFLEAFPVLPFdaEAARRAGEL 80

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 517056506  72 IDRHGIFSMGIGYTDAhLLASILLDRRAALWTRDKR 107
Cdd:COG1487   81 RAALRRAGRPIGLADL-LIAATALAHGLTLVTRNTK 115
PIN_VapC-like cd09854
VapC-like PIN domains of VapC and Smg6 ribonucleases, ribosome assembly factor NOB1, ...
 5-114 3.12e-05

VapC-like PIN domains of VapC and Smg6 ribonucleases, ribosome assembly factor NOB1, rRNA-processing protein Fcf1, Archaeoglobus fulgidus AF0591 protein, and homologs; PIN (PilT N terminus) domains of such ribonucleases as the toxins of prokaryotic toxin/antitoxin operons FitAB and VapBC, as well as, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1, are included in VapC-like this family. Also included are the PIN domains of the Pyrobaculum aerophilum Pea0151 and Archaeoglobus fulgidus AF0591 proteins and other similar archaeal homologs. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN 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 while some others 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: 350205  Cd Length: 129  Bit Score: 40.72  E-value: 3.12e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517056506   5 DTSIWIDHFR------HVDAELRTIIEDDRLLCHPAVVGELALGSLRDRGRVIAFLAAQRQAFVAT-----HDEVMTMID 73
Cdd:cd09854    3 DTNVLIALLSsepeseAAKELLALLLGDSELVIPPLVLAELLRLLARERGARRALEILELLRALEVveeepALAEIALEV 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 517056506  74 RHGIFSMGIGYTDAHLLASILLDRRAALWTRDKRLQAAAKK 114
Cdd:cd09854   83 LALGLERGLDFGDALILALAKELGGAVLVTNDRDFRRLAKL 123
PIN_MtVapC3-like cd18759
uncharacterized subgroup of the VapC3-like nuclease subfamily of the PIN domain superfamily; ...
 3-121 1.84e-04

uncharacterized subgroup of the VapC3-like nuclease subfamily of the PIN domain superfamily; The VapC3-like nuclease subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of various Mycobacterium tuberculosis VapC toxins including VapC3, VapC11, VapC15, VapC21, VapC25, VapC28, VapC29, VapC30, VapC32, VapC33, VapC37, and VapC39. It belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is a PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN 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 while some others 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: 350326  Cd Length: 126  Bit Score: 38.34  E-value: 1.84e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517056506   3 LADTSIWIDHFRHVDAE----LRTIIEDDRLLCHPAVVGELALG--SLRDRGRVIAFLAAQRqaFVATHDEVMTMIDRHG 76
Cdd:cd18759    1 LVDTSVWIEFFRGKSSPvsevVDELLDEDEVCTCGIVLAELLQGakSEKELSLLEDFLSALP--YLPITDELWIKAGELS 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 517056506  77 iFSM-----GIGYTDAhLLASILLDRRAALWTRDKRLQAAAKKAGASLHK 121
Cdd:cd18759   79 -FSLrkkgiTIPLSDL-YIAALAIENNLELFTLDKHFEIIPKHTGLKLYG 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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