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Conserved domains on  [gi|1125442188|gb|OLD69481|]
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MAG: twitching motility protein PilT [Candidatus Rokubacteria bacterium 13_1_20CM_70_15]

Protein Classification

type II toxin-antitoxin system VapC family toxin( domain architecture ID 10177354)

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PIN_Pae0151-like cd09873
VapC-like PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; ...
 4-129 3.36e-41

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: 133.43  E-value: 3.36e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125442188   4 VVDASVAIKWFLPELHDDAALRLL-RAEHRLVAPDLLFPEVGNVLWKRVRRREATASEAGAVLDALVAVPLEVHASQPMM 82
Cdd:cd09873     1 VVDASVAVKWLLPEEESEAADRLLeRLEEELVAPDLWLYEVANVLRKAVRRGRLTEEEAEEALEDLLDLPIEIDPDPELL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1125442188  83 PVAFEIACATGRTVYDSLYLALAVLRECPMVTADRKLHQALERGRFA 129
Cdd:cd09873    81 EEALELARRHGLTAYDAAYLALAERLGAPLVTADRKLARAAKAAGVK 127
 
Name Accession Description Interval E-value
PIN_Pae0151-like cd09873
VapC-like PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; ...
 4-129 3.36e-41

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: 133.43  E-value: 3.36e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125442188   4 VVDASVAIKWFLPELHDDAALRLL-RAEHRLVAPDLLFPEVGNVLWKRVRRREATASEAGAVLDALVAVPLEVHASQPMM 82
Cdd:cd09873     1 VVDASVAVKWLLPEEESEAADRLLeRLEEELVAPDLWLYEVANVLRKAVRRGRLTEEEAEEALEDLLDLPIEIDPDPELL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1125442188  83 PVAFEIACATGRTVYDSLYLALAVLRECPMVTADRKLHQALERGRFA 129
Cdd:cd09873    81 EEALELARRHGLTAYDAAYLALAERLGAPLVTADRKLARAAKAAGVK 127
VapC COG4113
RNA interferase (RNase) VapC, contains PIN domain [Defense mechanisms];
3-125 8.93e-36

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


Pssm-ID: 443289  Cd Length: 125  Bit Score: 119.62  E-value: 8.93e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125442188   3 VVVDASVAIKWFLPELHDDAALRLL-RAEHRLVAPDLLFPEVGNVLWKRVRRREATASEAGAVLDALVAVPLEVHASQPM 81
Cdd:COG4113     1 IVVDASALVKWLLPEEGSEEALRLLeRAADELVAPDLALYEVANVLWKAVRRGRLTEEEAEEALELLLELPIEVVPVTEL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1125442188  82 MPVAFEIACATGRTVYDSLYLALAVLRECPMVTADRKLHQALER 125
Cdd:COG4113    81 LERALELARRHGLTAYDAAYLALAERLGAPLVTADRRLARAARA 124
PIN pfam01850
PIN domain;
3-122 3.65e-07

PIN domain;


Pssm-ID: 426475  Cd Length: 121  Bit Score: 45.86  E-value: 3.65e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125442188   3 VVVDASVAIKWFLPELHDDAALRLLRAEHRLVAPDLLFPEVGNVLWKRVRR-REATASEAGAVLDALVAVPLEVHASqpm 81
Cdd:pfam01850   1 IVLDTSVLIALLRGEPLHEAARELLEAAGELVTSAIVLAELLYGLNRRLGLgKAAELVELLLLLSALEVLPIDAELA--- 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1125442188  82 mPVAFEIACATG-RTVYDSLYLALAVLRECPMVTADRKLHQA 122
Cdd:pfam01850  78 -EEAAELRLKYGkLGPNDALIAATAKEHGAKLITFDEDFARV 118
 
Name Accession Description Interval E-value
PIN_Pae0151-like cd09873
VapC-like PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; ...
 4-129 3.36e-41

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: 133.43  E-value: 3.36e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125442188   4 VVDASVAIKWFLPELHDDAALRLL-RAEHRLVAPDLLFPEVGNVLWKRVRRREATASEAGAVLDALVAVPLEVHASQPMM 82
Cdd:cd09873     1 VVDASVAVKWLLPEEESEAADRLLeRLEEELVAPDLWLYEVANVLRKAVRRGRLTEEEAEEALEDLLDLPIEIDPDPELL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1125442188  83 PVAFEIACATGRTVYDSLYLALAVLRECPMVTADRKLHQALERGRFA 129
Cdd:cd09873    81 EEALELARRHGLTAYDAAYLALAERLGAPLVTADRKLARAAKAAGVK 127
VapC COG4113
RNA interferase (RNase) VapC, contains PIN domain [Defense mechanisms];
3-125 8.93e-36

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


Pssm-ID: 443289  Cd Length: 125  Bit Score: 119.62  E-value: 8.93e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125442188   3 VVVDASVAIKWFLPELHDDAALRLL-RAEHRLVAPDLLFPEVGNVLWKRVRRREATASEAGAVLDALVAVPLEVHASQPM 81
Cdd:COG4113     1 IVVDASALVKWLLPEEGSEEALRLLeRAADELVAPDLALYEVANVLWKAVRRGRLTEEEAEEALELLLELPIEVVPVTEL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1125442188  82 MPVAFEIACATGRTVYDSLYLALAVLRECPMVTADRKLHQALER 125
Cdd:COG4113    81 LERALELARRHGLTAYDAAYLALAERLGAPLVTADRRLARAARA 124
PIN_MT3492-like cd09874
VapC-like PIN domain of the hypothetical protein MT3492 of Mycobacterium tuberculosis CDC1551 ...
 5-122 5.33e-08

VapC-like PIN domain of the hypothetical protein MT3492 of Mycobacterium tuberculosis CDC1551 and other uncharacterized, annotated PilT protein domain proteins; Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis CDC1551, hypothetical protein MT3492, and similar bacterial and archaeal proteins are included in this subfamily. They are PIN domain homologs 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: 350222  Cd Length: 134  Bit Score: 48.27  E-value: 5.33e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125442188   5 VDASVAIKWFLPELHDDAALRLLR-AEHRLVAPDLLFPEVGNVLWKRVRRREATASEAGAVLDALVAvplEVHASQPMMP 83
Cdd:cd09874     3 LDTSALVKLYVREPGSDAVRALLDaASDVLAISDLTRVEFASALARKVREGELSEEQARAALAAFER---DWASLLRVVP 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1125442188  84 VAFEIACATGRTV-------YDSLYLALA-VLRECPMVTADRKLHQA 122
Cdd:cd09874    80 VTDSLFRRAAELAerhglraLDALHLASAlRLGALTFVTADKRLAEA 126
PIN pfam01850
PIN domain;
3-122 3.65e-07

PIN domain;


Pssm-ID: 426475  Cd Length: 121  Bit Score: 45.86  E-value: 3.65e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125442188   3 VVVDASVAIKWFLPELHDDAALRLLRAEHRLVAPDLLFPEVGNVLWKRVRR-REATASEAGAVLDALVAVPLEVHASqpm 81
Cdd:pfam01850   1 IVLDTSVLIALLRGEPLHEAARELLEAAGELVTSAIVLAELLYGLNRRLGLgKAAELVELLLLLSALEVLPIDAELA--- 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1125442188  82 mPVAFEIACATG-RTVYDSLYLALAVLRECPMVTADRKLHQA 122
Cdd:pfam01850  78 -EEAAELRLKYGkLGPNDALIAATAKEHGAKLITFDEDFARV 118
PIN_VapC-like cd09854
VapC-like PIN domains of VapC and Smg6 ribonucleases, ribosome assembly factor NOB1, ...
 4-126 2.45e-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: 41.11  E-value: 2.45e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125442188   4 VVDASVAIKWFLPELHDDAALRLLR---AEHRLVAPDLLFPEVGNVLWKRVRRREATASEAgavLDALVAVPLEVHASQP 80
Cdd:cd09854     1 VLDTNVLIALLSSEPESEAAKELLAlllGDSELVIPPLVLAELLRLLARERGARRALEILE---LLRALEVVEEEPALAE 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1125442188  81 MMPVAFEIACATGRTVYDSLYLALA-VLRECPMVTADRKLHQALERG 126
Cdd:cd09854    78 IALEVLALGLERGLDFGDALILALAkELGGAVLVTNDRDFRRLAKLG 124
 
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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