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Conserved domains on  [gi|753822357|ref|WP_041577981|]
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MULTISPECIES: type II toxin-antitoxin system VapC family toxin [Xanthobacter]

Protein Classification

type II toxin-antitoxin system VapC family toxin( domain architecture ID 10007939)

type II toxin-antitoxin (TA) system VapC family toxin functions as a ribonuclease that is neutralized by its cognate antitoxin VapB; similar to Mycolicibacterium smegmatis ribonuclease VapC

Gene Ontology:  GO:0004540
PubMed:  28279904|21036780

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
VapC COG3742
VapC family ribonuclease, contains PIN domain [Defense mechanisms];
1-132 1.01e-58

VapC family ribonuclease, contains PIN domain [Defense mechanisms];


:

Pssm-ID: 442956  Cd Length: 129  Bit Score: 177.69  E-value: 1.01e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 753822357   1 MFVDTSVIVSILADEPDAVVFANKLTDAPRRYTSGLVILEAAMRLSTLLKVDpvdVEVRIQQVLEEARISVIPINASIAK 80
Cdd:COG3742    1 MVVDTSALVAILLGEPEAEALAAALEAAPPRLISAVTVLEAAIVLARRRGPE---ARRELDALLAELGIEVVPVDAAQAR 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 753822357  81 RAVAAFATFGKGRGHPAQLNLADCMSYACARAYRVPLLFKGNDFSQTDIEVA 132
Cdd:COG3742   78 LAREAYRRYGKGRGHPARLNFGDCFAYALAKALGAPLLFKGDDFSHTDIEPA 129
 
Name Accession Description Interval E-value
VapC COG3742
VapC family ribonuclease, contains PIN domain [Defense mechanisms];
1-132 1.01e-58

VapC family ribonuclease, contains PIN domain [Defense mechanisms];


Pssm-ID: 442956  Cd Length: 129  Bit Score: 177.69  E-value: 1.01e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 753822357   1 MFVDTSVIVSILADEPDAVVFANKLTDAPRRYTSGLVILEAAMRLSTLLKVDpvdVEVRIQQVLEEARISVIPINASIAK 80
Cdd:COG3742    1 MVVDTSALVAILLGEPEAEALAAALEAAPPRLISAVTVLEAAIVLARRRGPE---ARRELDALLAELGIEVVPVDAAQAR 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 753822357  81 RAVAAFATFGKGRGHPAQLNLADCMSYACARAYRVPLLFKGNDFSQTDIEVA 132
Cdd:COG3742   78 LAREAYRRYGKGRGHPARLNFGDCFAYALAKALGAPLLFKGDDFSHTDIEPA 129
PIN_MtVapC28-VapC30-like cd09871
VapC-like PIN domain of Mycobacterium tuberculosis VapC28 and 30 and related proteins; This ...
 1-132 1.09e-53

VapC-like PIN domain of Mycobacterium tuberculosis VapC28 and 30 and related proteins; This subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis VapC28 and VapC30 toxins. M. tuberculosis VapC28 and VapC30 both cleave tRNA25Ser-TGA and tRNA28Ser-CGA. 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: 350219  Cd Length: 128  Bit Score: 164.57  E-value: 1.09e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 753822357   1 MFVDTSVIVSILADEPDAVVFANKLTDAPRRYTSGLVILEAAMRLSTLLKVDPVDvevRIQQVLEEARISVIPINASIAK 80
Cdd:cd09871    1 MVVDTSALVAILLGEPEAERFLAALAAAPRRLISAATLVEAAIVLERRRGPEARS---ELDELLAELGIEIVPVDAEQAR 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 753822357  81 RAVAAFATFGKGRgHPAQLNLADCMSYACARAYRVPLLFKGNDFSQTDIEVA 132
Cdd:cd09871   78 LAREAYRRFGKGR-HPARLNFGDCFAYALAKELGEPLLFKGDDFAHTDIRSA 128
PIN pfam01850
PIN domain;
1-130 8.65e-15

PIN domain;


Pssm-ID: 426475  Cd Length: 121  Bit Score: 65.51  E-value: 8.65e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 753822357    1 MFVDTSVIVSILADEPDAVVFANKLTDAPRRYTSGLVILEAAMRLSTLLKVDPVDVEVRIQQVLeeARISVIPINASIAK 80
Cdd:pfam01850   1 IVLDTSVLIALLRGEPLHEAARELLEAAGELVTSAIVLAELLYGLNRRLGLGKAAELVELLLLL--SALEVLPIDAELAE 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 753822357   81 RAVAAFATFGKgrghpaqLNLADCMSYACARAYRVPLLFKGNDFSQTDIE 130
Cdd:pfam01850  79 EAAELRLKYGK-------LGPNDALIAATAKEHGAKLITFDEDFARVAKL 121
 
Name Accession Description Interval E-value
VapC COG3742
VapC family ribonuclease, contains PIN domain [Defense mechanisms];
1-132 1.01e-58

VapC family ribonuclease, contains PIN domain [Defense mechanisms];


Pssm-ID: 442956  Cd Length: 129  Bit Score: 177.69  E-value: 1.01e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 753822357   1 MFVDTSVIVSILADEPDAVVFANKLTDAPRRYTSGLVILEAAMRLSTLLKVDpvdVEVRIQQVLEEARISVIPINASIAK 80
Cdd:COG3742    1 MVVDTSALVAILLGEPEAEALAAALEAAPPRLISAVTVLEAAIVLARRRGPE---ARRELDALLAELGIEVVPVDAAQAR 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 753822357  81 RAVAAFATFGKGRGHPAQLNLADCMSYACARAYRVPLLFKGNDFSQTDIEVA 132
Cdd:COG3742   78 LAREAYRRYGKGRGHPARLNFGDCFAYALAKALGAPLLFKGDDFSHTDIEPA 129
PIN_MtVapC28-VapC30-like cd09871
VapC-like PIN domain of Mycobacterium tuberculosis VapC28 and 30 and related proteins; This ...
 1-132 1.09e-53

VapC-like PIN domain of Mycobacterium tuberculosis VapC28 and 30 and related proteins; This subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis VapC28 and VapC30 toxins. M. tuberculosis VapC28 and VapC30 both cleave tRNA25Ser-TGA and tRNA28Ser-CGA. 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: 350219  Cd Length: 128  Bit Score: 164.57  E-value: 1.09e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 753822357   1 MFVDTSVIVSILADEPDAVVFANKLTDAPRRYTSGLVILEAAMRLSTLLKVDPVDvevRIQQVLEEARISVIPINASIAK 80
Cdd:cd09871    1 MVVDTSALVAILLGEPEAERFLAALAAAPRRLISAATLVEAAIVLERRRGPEARS---ELDELLAELGIEIVPVDAEQAR 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 753822357  81 RAVAAFATFGKGRgHPAQLNLADCMSYACARAYRVPLLFKGNDFSQTDIEVA 132
Cdd:cd09871   78 LAREAYRRFGKGR-HPARLNFGDCFAYALAKELGEPLLFKGDDFAHTDIRSA 128
PIN pfam01850
PIN domain;
1-130 8.65e-15

PIN domain;


Pssm-ID: 426475  Cd Length: 121  Bit Score: 65.51  E-value: 8.65e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 753822357    1 MFVDTSVIVSILADEPDAVVFANKLTDAPRRYTSGLVILEAAMRLSTLLKVDPVDVEVRIQQVLeeARISVIPINASIAK 80
Cdd:pfam01850   1 IVLDTSVLIALLRGEPLHEAARELLEAAGELVTSAIVLAELLYGLNRRLGLGKAAELVELLLLL--SALEVLPIDAELAE 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 753822357   81 RAVAAFATFGKgrghpaqLNLADCMSYACARAYRVPLLFKGNDFSQTDIE 130
Cdd:pfam01850  79 EAAELRLKYGK-------LGPNDALIAATAKEHGAKLITFDEDFARVAKL 121
VapC COG1848
VapC family ribonuclease, toxin component of the VapBC toxin-antitoxin module, contains PIN ...
 1-118 2.85e-06

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


Pssm-ID: 441453  Cd Length: 134  Bit Score: 43.43  E-value: 2.85e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 753822357   1 MFVDTSVIVSILADEPDAVVFANKLTDAPRR-----YTSGLVILEAAMRLSTLLKVDPVDVEVRIQQVLeeARISVIPIN 75
Cdd:COG1848    2 ILLDTNVLIYALEGDSPFHERARELLERAEEgeeelYTSPLVLAEVLYVLTRPGGLSLEEARELLEALL--SNIEVVPVD 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 753822357  76 ASIAKRAVAAFATFGkgrghpaqLNLADCMSYACARAYRVPLL 118
Cdd:COG1848   80 EEILEEAAELLAKYG--------LRLNDALHLATALEHGADAL 114
VapC COG1487
Ribonuclease/mRNA interferase VapC, contains PIN domain [Defense mechanisms];
3-118 1.20e-05

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


Pssm-ID: 441096  Cd Length: 128  Bit Score: 41.77  E-value: 1.20e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 753822357   3 VDTSVIVSILADEPDAVVFANKLTDAPRRYTSGLVILEaaMRLSTLLKVDPVDVEvRIQQVLEeaRISVIPINASIAKRA 82
Cdd:COG1487    3 LDTNVLIDLLRGRPPAVLAWLAELEAGELAISAITLAE--LLYGARRSPDAKRRA-ALEAFLE--AFPVLPFDAEAARRA 77

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 753822357  83 VAAFATFGKgRGHPaqLNLADCMSYACARAYRVPLL 118
Cdd:COG1487   78 GELRAALRR-AGRP--IGLADLLIAATALAHGLTLV 110
PIN_VapC4-5_FitB-like cd18741
uncharacterized subgroup of the PIN_VapC4-5_FitB-like subfamily of the PIN domain superfamily; ...
 3-118 6.62e-04

uncharacterized subgroup of the PIN_VapC4-5_FitB-like subfamily of the PIN domain superfamily; The PIN_VapC4-5_FitB-like subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis VapC4 and VapC5 ribonuclease toxins of the VapBC toxin/antitoxin (TA) system, and Neisseria gonorrhoeae FitB toxin of the FitAB TA system. This subfamily belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is the 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 eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. 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: 350308  Cd Length: 120  Bit Score: 37.09  E-value: 6.62e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 753822357   3 VDTSVIVSILADEPDAVVFANKLTDApRRYTSGLVILE--AAMRlstllkvdpvdvEVRIQQVLEE--ARISVIPINASI 78
Cdd:cd18741    2 LDTDILIDFLRGNPSAAEKLLELLGG-NLAISVITVAElyAGAR------------NKKELEKLEKllSLFEVIPVDEEI 68

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 753822357  79 AKRAVAAFATFGKGRGhpaqLNLADCMSYACARAYRVPLL 118
Cdd:cd18741   69 AELAGELRRKYRKSHG----LGLPDALIAATALEHGLTLV 104
PIN_VapC-like cd18686
uncharacterized subfamily of the VapC (virulence-associated protein C)-like family of the PIN ...
 3-121 2.26e-03

uncharacterized subfamily of the VapC (virulence-associated protein C)-like family of the PIN domain superfamily; VapC is the 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 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: 350253  Cd Length: 119  Bit Score: 35.55  E-value: 2.26e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 753822357   3 VDTSVIVSILADEPDAVVFANKLTDAPRRYTSGLVILEaamrLSTLLKVDpVDVEVRIQQVLEEARISVIPINASIAKRA 82
Cdd:cd18686    2 VDSSGWIEYFADGPLADEFAPAIEDPEELIVPTIVLYE----VYKKILRE-RGEEAALEAVALMQQGRVVPLDESLALAA 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 753822357  83 vaafATFGKGRGhpaqLNLADCMSYACARAYRVPLL-----FKG 121
Cdd:cd18686   77 ----ADLSLEHK----LPMADSIIYATARRHGATLWtqdahFKG 112
 
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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