NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2321365147|gb|UYP80199|]
View 

type II toxin-antitoxin system VapC family toxin (plasmid) [Xanthomonas campestris pv. campestris]

Protein Classification

type II toxin-antitoxin system VapC family toxin( domain architecture ID 13036743)

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

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PIN_VapC-like cd18683
Uncharacterized subfamily of the VapC (virulence-associated protein C)-like family of the PIN ...
 2-111 8.01e-36

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: 350250  Cd Length: 125  Bit Score: 118.75  E-value: 8.01e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321365147   2 RDDPAQADVAAAVLTDAELIAVASPCLCEFVWVLLRVYGFQQADAASAIRALLAAANVEVNRP-AVEAGLLVLDAGGDFA 80
Cdd:cd18683    14 NDDPEQAARARALLEEAEPVFVPLTVLLELEWVLRSAYKFSRAEIAAALRALLGLPNVVVEDPeAVEAALDWYRAGADFA 93

                          90       100       110
                  ....*....|....*....|....*....|.
gi 2321365147  81 DGVIAYEGNWLGGETFVSFDKKAVVLLTAQG 111
Cdd:cd18683    94 DALHLAAARRAGCETFVTFDRKAARRAGALG 124
 
Name Accession Description Interval E-value
PIN_VapC-like cd18683
Uncharacterized subfamily of the VapC (virulence-associated protein C)-like family of the PIN ...
 2-111 8.01e-36

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: 350250  Cd Length: 125  Bit Score: 118.75  E-value: 8.01e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321365147   2 RDDPAQADVAAAVLTDAELIAVASPCLCEFVWVLLRVYGFQQADAASAIRALLAAANVEVNRP-AVEAGLLVLDAGGDFA 80
Cdd:cd18683    14 NDDPEQAARARALLEEAEPVFVPLTVLLELEWVLRSAYKFSRAEIAAALRALLGLPNVVVEDPeAVEAALDWYRAGADFA 93

                          90       100       110
                  ....*....|....*....|....*....|.
gi 2321365147  81 DGVIAYEGNWLGGETFVSFDKKAVVLLTAQG 111
Cdd:cd18683    94 DALHLAAARRAGCETFVTFDRKAARRAGALG 124
COG5611 COG5611
Predicted nucleic-acid-binding protein, contains PIN domain [General function prediction only]; ...
 1-110 1.15e-31

Predicted nucleic-acid-binding protein, contains PIN domain [General function prediction only];


Pssm-ID: 444342  Cd Length: 128  Bit Score: 108.41  E-value: 1.15e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321365147   1 MRDDPAQADVAAAVL---TDAELIAVASPCLCEFVWVLLRVYGFQQADAASAIRALLAAANVEV-NRPAVEAGL-LVLDA 75
Cdd:COG5611    14 TQDDPEQAAKARRLLeqlTGEEPLFVPLVVLAETVWVLRSVYKLPREEIAEALEALLGLPNVVVeDREAVEAALaLYAEG 93

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 2321365147  76 GGDFADGVIAYEGNWLGGETFVSFDKKAVVLLTAQ 110
Cdd:COG5611    94 GADFADALIAARARAAGCEPVVTFDRKAAKLAGVR 128
 
Name Accession Description Interval E-value
PIN_VapC-like cd18683
Uncharacterized subfamily of the VapC (virulence-associated protein C)-like family of the PIN ...
 2-111 8.01e-36

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: 350250  Cd Length: 125  Bit Score: 118.75  E-value: 8.01e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321365147   2 RDDPAQADVAAAVLTDAELIAVASPCLCEFVWVLLRVYGFQQADAASAIRALLAAANVEVNRP-AVEAGLLVLDAGGDFA 80
Cdd:cd18683    14 NDDPEQAARARALLEEAEPVFVPLTVLLELEWVLRSAYKFSRAEIAAALRALLGLPNVVVEDPeAVEAALDWYRAGADFA 93

                          90       100       110
                  ....*....|....*....|....*....|.
gi 2321365147  81 DGVIAYEGNWLGGETFVSFDKKAVVLLTAQG 111
Cdd:cd18683    94 DALHLAAARRAGCETFVTFDRKAARRAGALG 124
COG5611 COG5611
Predicted nucleic-acid-binding protein, contains PIN domain [General function prediction only]; ...
 1-110 1.15e-31

Predicted nucleic-acid-binding protein, contains PIN domain [General function prediction only];


Pssm-ID: 444342  Cd Length: 128  Bit Score: 108.41  E-value: 1.15e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321365147   1 MRDDPAQADVAAAVL---TDAELIAVASPCLCEFVWVLLRVYGFQQADAASAIRALLAAANVEV-NRPAVEAGL-LVLDA 75
Cdd:COG5611    14 TQDDPEQAAKARRLLeqlTGEEPLFVPLVVLAETVWVLRSVYKLPREEIAEALEALLGLPNVVVeDREAVEAALaLYAEG 93

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 2321365147  76 GGDFADGVIAYEGNWLGGETFVSFDKKAVVLLTAQ 110
Cdd:COG5611    94 GADFADALIAARARAAGCEPVVTFDRKAAKLAGVR 128
VapC COG1848
VapC family ribonuclease, toxin component of the VapBC toxin-antitoxin module, contains PIN ...
 2-102 4.69e-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: 42.66  E-value: 4.69e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321365147   2 RDDPAQADVAAAVLTDAE----LIAVASPCLCEFVWVLLRVYGFQQADAASAIRALLAAAN-VEVNRP-AVEAGLLVLDA 75
Cdd:COG1848    14 EGDSPFHERARELLERAEegeeELYTSPLVLAEVLYVLTRPGGLSLEEARELLEALLSNIEvVPVDEEiLEEAAELLAKY 93

                          90       100
                  ....*....|....*....|....*..
gi 2321365147  76 GGDFADGVIAYEGNWLGGETFVSFDKK 102
Cdd:COG1848    94 GLRLNDALHLATALEHGADALVTFDRD 120
 
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