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Conserved domains on  [gi|365260220|gb|EHM90184|]
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hypothetical protein HMPREF0975_02838 [Actinomyces sp. oral taxon 849 str. F0330]

Protein Classification

type II toxin-antitoxin system VapC family toxin( domain architecture ID 10177353)

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_Sll0205-like cd09872
VapC-like PIN domain of Sll0205 protein and homologs; Virulence associated protein C (VapC) ...
 5-130 5.34e-51

VapC-like PIN domain of Sll0205 protein and homologs; Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of the Synechocystis sp. (strain PCC 6803) Sll0205 protein and other uncharacterized 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: 350220  Cd Length: 125  Bit Score: 157.63  E-value: 5.34e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 365260220   5 LLDTHALMWAINEPSRLGDGAAEVLRDRGSLLVVSAASAWELYTKHRIGKLPGAGPWLEALEGHVRRLGAELLPIEWSHA 84
Cdd:cd09872    1 LLDTHALLWWLTDPPRLSPKARALIEDPANEVFVSAASLWEIAIKVSLGKLDLPGPLEEWLEELLAANGFEILPITPEHA 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 365260220  85 RLSGRLEWSHRDPFDRMLAAQAISESLVLVTRDPAFEELPsVKILW 130
Cdd:cd09872   81 LAAASLPLHHRDPFDRLLIAQAIVEGLTLVTADRKILAYG-VKTIW 125
 
Name Accession Description Interval E-value
PIN_Sll0205-like cd09872
VapC-like PIN domain of Sll0205 protein and homologs; Virulence associated protein C (VapC) ...
 5-130 5.34e-51

VapC-like PIN domain of Sll0205 protein and homologs; Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of the Synechocystis sp. (strain PCC 6803) Sll0205 protein and other uncharacterized 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: 350220  Cd Length: 125  Bit Score: 157.63  E-value: 5.34e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 365260220   5 LLDTHALMWAINEPSRLGDGAAEVLRDRGSLLVVSAASAWELYTKHRIGKLPGAGPWLEALEGHVRRLGAELLPIEWSHA 84
Cdd:cd09872    1 LLDTHALLWWLTDPPRLSPKARALIEDPANEVFVSAASLWEIAIKVSLGKLDLPGPLEEWLEELLAANGFEILPITPEHA 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 365260220  85 RLSGRLEWSHRDPFDRMLAAQAISESLVLVTRDPAFEELPsVKILW 130
Cdd:cd09872   81 LAAASLPLHHRDPFDRLLIAQAIVEGLTLVTADRKILAYG-VKTIW 125
COG3744 COG3744
PIN domain nuclease, a component of toxin-antitoxin system (PIN domain) [Defense mechanisms];
4-130 9.62e-50

PIN domain nuclease, a component of toxin-antitoxin system (PIN domain) [Defense mechanisms];


Pssm-ID: 442958  Cd Length: 128  Bit Score: 154.60  E-value: 9.62e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 365260220   4 YLLDTHALMWAINEPSRLGDGAAEVLRDRGSLLVVSAASAWELYTKHRIGKLPGAGPWLEALEGHVRRLGAELLPIEWSH 83
Cdd:COG3744    3 LLLDTHALLWWLLGDERLSPAARELIEDPANELYVSAASLWEIAIKVRLGKLDLPEDLDEWLEELLEELGFELLPITPEH 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 365260220  84 ARLSGRLEWSHRDPFDRMLAAQAISESLVLVTRDPAFEELPsVKILW 130
Cdd:COG3744   83 ALAAAQLPLHHRDPFDRLLIAQALVEGLPLVTADRKIAAYG-VKTIW 128
PIN pfam01850
PIN domain;
4-124 2.06e-11

PIN domain;


Pssm-ID: 426475  Cd Length: 121  Bit Score: 56.65  E-value: 2.06e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 365260220    4 YLLDTHALMWAInEPSRLGDGAAEVLrDRGSLLVVSAASAWELYtkHRIGKLPGAGPWLEALEGHVRRLGAELLPIEWSH 83
Cdd:pfam01850   1 IVLDTSVLIALL-RGEPLHEAARELL-EAAGELVTSAIVLAELL--YGLNRRLGLGKAAELVELLLLLSALEVLPIDAEL 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 365260220   84 ARLSGRLEWSHR--DPFDRMLAAQAISESLVLVTRDPAFEELP 124
Cdd:pfam01850  77 AEEAAELRLKYGklGPNDALIAATAKEHGAKLITFDEDFARVA 119
PRK13725 PRK13725
tRNA(fMet)-specific endonuclease VapC;
1-128 1.64e-04

tRNA(fMet)-specific endonuclease VapC;


Pssm-ID: 184277  Cd Length: 132  Bit Score: 38.86  E-value: 1.64e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 365260220   1 MSGYLLDTHALMWAI-NEPsrlgdgaaEVLRDRGSL----LVVSAASAWELYTKHRIGKLPGAGpwLEALEGHVRRLgaE 75
Cdd:PRK13725   1 MLKFMLDTNICIFTIkNKP--------EHVRERFNLntgrMCISSVTLMELIYGAEKSQMPERN--LAVIEGFVSRL--E 68

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 365260220  76 LLPIEWSHARLSG--RLEWSHRD----PFDRMLAAQAISESLVLVTRDP-AFEELPSVKI 128
Cdd:PRK13725  69 VLDYDTAAATHTGqiRAELARQGrpvgPFDQMIAGHARSRGLIVVTNNTrEFERVPGIRI 128
 
Name Accession Description Interval E-value
PIN_Sll0205-like cd09872
VapC-like PIN domain of Sll0205 protein and homologs; Virulence associated protein C (VapC) ...
 5-130 5.34e-51

VapC-like PIN domain of Sll0205 protein and homologs; Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of the Synechocystis sp. (strain PCC 6803) Sll0205 protein and other uncharacterized 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: 350220  Cd Length: 125  Bit Score: 157.63  E-value: 5.34e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 365260220   5 LLDTHALMWAINEPSRLGDGAAEVLRDRGSLLVVSAASAWELYTKHRIGKLPGAGPWLEALEGHVRRLGAELLPIEWSHA 84
Cdd:cd09872    1 LLDTHALLWWLTDPPRLSPKARALIEDPANEVFVSAASLWEIAIKVSLGKLDLPGPLEEWLEELLAANGFEILPITPEHA 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 365260220  85 RLSGRLEWSHRDPFDRMLAAQAISESLVLVTRDPAFEELPsVKILW 130
Cdd:cd09872   81 LAAASLPLHHRDPFDRLLIAQAIVEGLTLVTADRKILAYG-VKTIW 125
COG3744 COG3744
PIN domain nuclease, a component of toxin-antitoxin system (PIN domain) [Defense mechanisms];
4-130 9.62e-50

PIN domain nuclease, a component of toxin-antitoxin system (PIN domain) [Defense mechanisms];


Pssm-ID: 442958  Cd Length: 128  Bit Score: 154.60  E-value: 9.62e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 365260220   4 YLLDTHALMWAINEPSRLGDGAAEVLRDRGSLLVVSAASAWELYTKHRIGKLPGAGPWLEALEGHVRRLGAELLPIEWSH 83
Cdd:COG3744    3 LLLDTHALLWWLLGDERLSPAARELIEDPANELYVSAASLWEIAIKVRLGKLDLPEDLDEWLEELLEELGFELLPITPEH 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 365260220  84 ARLSGRLEWSHRDPFDRMLAAQAISESLVLVTRDPAFEELPsVKILW 130
Cdd:COG3744   83 ALAAAQLPLHHRDPFDRLLIAQALVEGLPLVTADRKIAAYG-VKTIW 128
PIN pfam01850
PIN domain;
4-124 2.06e-11

PIN domain;


Pssm-ID: 426475  Cd Length: 121  Bit Score: 56.65  E-value: 2.06e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 365260220    4 YLLDTHALMWAInEPSRLGDGAAEVLrDRGSLLVVSAASAWELYtkHRIGKLPGAGPWLEALEGHVRRLGAELLPIEWSH 83
Cdd:pfam01850   1 IVLDTSVLIALL-RGEPLHEAARELL-EAAGELVTSAIVLAELL--YGLNRRLGLGKAAELVELLLLLSALEVLPIDAEL 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 365260220   84 ARLSGRLEWSHR--DPFDRMLAAQAISESLVLVTRDPAFEELP 124
Cdd:pfam01850  77 AEEAAELRLKYGklGPNDALIAATAKEHGAKLITFDEDFARVA 119
PIN_VapC-FitB-like cd09875
VapC-like PIN domain of ribonucleases (toxins), VapC and FitB, of prokaryotic toxin/antitoxin ...
 5-130 3.69e-10

VapC-like PIN domain of ribonucleases (toxins), VapC and FitB, of prokaryotic toxin/antitoxin operons, Pyrococcus horikoshii protein PH0500, and other similar bacterial and archaeal homologs; PIN (PilT N terminus) domain-containing proteins of prokaryotic toxin/antitoxin (TA) operons, such as, Mycobacterium tuberculosis VapC of the VapBC (virulence associated proteins) TA operon, and Neisseria gonorrhoeae FitB of the FitAB (fast intracellular trafficking) TA operon, as well as, the archaeal Pyrococcus horikoshii protein PH0500 are included in this family. Toxins of TA operons are believed to be involved in growth inhibition by regulating translation and are nearly always co-expressed with an antitoxin, a cognate protein inhibitor, forming an inert protein complex. Disassociation of the complex activates the ribonuclease activity of the toxin. In N. gonorrhoeae, FitA and FitB form a heterodimer: FitA is the DNA binding subunit and FitB contains a ribonuclease activity that is blocked by the presence of FitA. A tetramer of FitAB heterodimers binds DNA from the fitAB upstream promoter region with high affinity. This results in both sequestration of FitAB and repression of fitAB transcription. It is thought that FitAB release from the DNA and subsequent dissociation both slows N. gonorrhoeae replication and transcytosis by an as yet undefined mechanism. The toxin M. tuberculosis VapC is a structural homolog of N. gonorrhoeae FitB, but their antitoxin partners, VapB and FitA, respectively, differ structurally. The M. tuberculosis VapC-5 is proposed to be both an endoribonuclease and an exoribonuclease that can act on free RNA in a similar manner to the endo and exonuclease Flap endonuclease-1 (FEN1). VapC-like toxins are structural homologs of FEN1-like PIN domains, but lack the extensive arch/clamp region and the H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region, seen in FEN1-like PIN domains. PIN domains within this group typically contain three or four conserved acidic residues that cluster at the C-terminal end of the beta-sheet and form a negatively charged pocket near the center of the molecule. These putative active site residues are thought to bind Mg2+ and/or Mn2+ ions and be essential for single-stranded ribonuclease activity. VapC-like PIN domains are single domain proteins that form dimers and dimerization configures the active sites in a groove along the long-axis of the structure.


Pssm-ID: 350223  Cd Length: 130  Bit Score: 53.73  E-value: 3.69e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 365260220   5 LLDTHALMWAINEPSRLgdgAAEVLRDR--GSLLVVSAASAWELytkhRIGKLPGAGPWLEALEGHVRRLGAELLPI--- 79
Cdd:cd09875    1 LLDTSVLIWLLDNDPKS---HLRSLADRieRGKVYVSIVSRWEL----AIGVNINKLRLNYAFADLENLLADLAIPVlpl 73

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 365260220  80 ------EWSHARLSGRLEWSHRDPFDRMLAAQAISESLVLVTRDPAFEELPSVKILW 130
Cdd:cd09875   74 tpriadEYLEACRNLPLRGRHRSPFDRMIAAQALQHGFTVAHRDEDFKAINAVNLEW 130
VapC COG1487
Ribonuclease/mRNA interferase VapC, contains PIN domain [Defense mechanisms];
4-129 1.07e-08

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


Pssm-ID: 441096  Cd Length: 128  Bit Score: 49.86  E-value: 1.07e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 365260220   4 YLLDTHALMWAINEPSrlgDGAAEVLRDRGS-LLVVSAASAWELYtkHRIGKLPgAGPWLEALEGHVRRLgaELLPIEWS 82
Cdd:COG1487    1 YLLDTNVLIDLLRGRP---PAVLAWLAELEAgELAISAITLAELL--YGARRSP-DAKRRAALEAFLEAF--PVLPFDAE 72

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 365260220  83 HARLSGRLEWSHR------DPFDRMLAAQAISESLVLVTRDPA-FEELPSVKIL 129
Cdd:COG1487   73 AARRAGELRAALRragrpiGLADLLIAATALAHGLTLVTRNTKdFERIPGLKVE 126
PIN_CcVapC1-like cd18736
VapC-like PIN domain of Caulobacter Crescentus VapC1-like and related proteins; This subfamily ...
 5-128 7.28e-07

VapC-like PIN domain of Caulobacter Crescentus VapC1-like and related proteins; This subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Caulobacter Crescentus VapC1, a ribonuclease toxin of the VapBC toxin/antitoxin (TA) system. This subfamily belongs to the PIN_VapC4-5_FitB-like subfamily of the VapC-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC TA systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. FitB is a toxin of the FitAB TA system. 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: 350303  Cd Length: 123  Bit Score: 44.86  E-value: 7.28e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 365260220   5 LLDTHALMWAInepsrlgDGAAEVLRDR------GSLlVVSAASAWELytkhRIGKLPGAGPWLEALEGHVRRLgaELLP 78
Cdd:cd18736    1 LLDTNICIYLL-------KGQPPALARRvaacepGEV-VISAITLAEL----AYGVRRSAPPRRAALDALLEVI--PVLP 66

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 365260220  79 IEWSHARLSGRLEWSH---RDPFDRMLAAQAISESLVLVTRDPA-FEELPSVKI 128
Cdd:cd18736   67 FDEAAAAAYARIRAAFpfrRASFDRLIAAHALALGLTLVTNNEAdFADIPGLRV 120
PIN_VapC-like cd18689
uncharacterized subfamily of the VapC-like nuclease family of the PIN domain superfamily; VapC ...
 5-130 5.29e-06

uncharacterized subfamily of the VapC-like nuclease 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: 350256  Cd Length: 125  Bit Score: 42.62  E-value: 5.29e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 365260220   5 LLDTHALM-WAINEPSRLGDGAAEVLRDRGSLLVVSAASAWELYtkHRIGKLPGAGPWLEALEgHVRRLGAELLPIEWSH 83
Cdd:cd18689    1 VLDSGALLaYFEGEPHKVAKKLIELIKEGKAELYISAINLGEVY--YITARKKGEEKAEEVLS-LLLALPIEVVEADEEL 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 365260220  84 ARLSGRLEWSHR----DPFdrmLAAQAISESLVLVTRDPAFEELPSVKILW 130
Cdd:cd18689   78 VEAAAKIKAKYGlsyaDCF---ALATAKELNAALVTGDPEFKKVKEIEIII 125
PRK13725 PRK13725
tRNA(fMet)-specific endonuclease VapC;
1-128 1.64e-04

tRNA(fMet)-specific endonuclease VapC;


Pssm-ID: 184277  Cd Length: 132  Bit Score: 38.86  E-value: 1.64e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 365260220   1 MSGYLLDTHALMWAI-NEPsrlgdgaaEVLRDRGSL----LVVSAASAWELYTKHRIGKLPGAGpwLEALEGHVRRLgaE 75
Cdd:PRK13725   1 MLKFMLDTNICIFTIkNKP--------EHVRERFNLntgrMCISSVTLMELIYGAEKSQMPERN--LAVIEGFVSRL--E 68

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 365260220  76 LLPIEWSHARLSG--RLEWSHRD----PFDRMLAAQAISESLVLVTRDP-AFEELPSVKI 128
Cdd:PRK13725  69 VLDYDTAAATHTGqiRAELARQGrpvgPFDQMIAGHARSRGLIVVTNNTrEFERVPGIRI 128
PIN_VapC4-5_FitB-like cd18740
uncharacterized subgroup of the PIN_VapC4-5_FitB-like subfamily of the PIN domain superfamily; ...
 97-128 1.96e-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: 350307  Cd Length: 126  Bit Score: 38.31  E-value: 1.96e-04
                         10        20        30
                 ....*....|....*....|....*....|..
gi 365260220  97 PFDRMLAAQAISESLVLVTRDPAFEELPSVKI 128
Cdd:cd18740   93 PLDMMIAAHALALGATLVTNDRAFRRVPGLAV 124
PIN_VapC4-5_FitB-like cd18741
uncharacterized subgroup of the PIN_VapC4-5_FitB-like subfamily of the PIN domain superfamily; ...
 5-116 4.10e-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: 37.48  E-value: 4.10e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 365260220   5 LLDTHALMWAInepsRLGDGAAEVLRD-RGSLLVVSAASAWELYTkhriGKLPGAGpwLEALEGHVRRLgaELLPIEWSH 83
Cdd:cd18741    1 LLDTDILIDFL----RGNPSAAEKLLElLGGNLAISVITVAELYA----GARNKKE--LEKLEKLLSLF--EVIPVDEEI 68

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 365260220  84 ARLSGRLEWSHR-----DPFDRMLAAQAISESLVLVTR 116
Cdd:cd18741   69 AELAGELRRKYRkshglGLPDALIAATALEHGLTLVTL 106
PIN_VapC4-5_FitB-like cd09881
VapC-like PIN domain of Mycobacterium tuberculosis VapC4 and VapC5, and Neisseria gonorrhoeae ...
 5-129 1.63e-03

VapC-like PIN domain of Mycobacterium tuberculosis VapC4 and VapC5, and Neisseria gonorrhoeae FitB and related proteins; This family 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 family 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: 350229  Cd Length: 127  Bit Score: 35.92  E-value: 1.63e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 365260220   5 LLDTHALMWAINEpsRLGDGAAEVLRDRGSLLVVSAASAWELYT-KHRIGKLPGAgpwLEALEGHVRRLgaELLPIEWSH 83
Cdd:cd09881    1 LLDTNICIDLLRG--RPPSVLERLEELLPEDLAISSITLAELLYgAEKSQRPEKN---LAALEAFLSRL--EVLPFDEEA 73

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 365260220  84 ARLSGRLEWSHR------DPFDRMLAAQAISESLVLVTRDPA-FEELPSVKIL 129
Cdd:cd09881   74 AEIYGEIRAELEkkgkpiGDNDLLIAATALAHGLTLVTNNTKhFERIPGLKVE 126
PIN_VapC4-5_FitB-like cd18746
uncharacterized subgroup of the PIN_VapC4-5_FitB-like subfamily of the PIN domain superfamily; ...
 61-117 2.20e-03

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: 350313 [Multi-domain]  Cd Length: 133  Bit Score: 35.49  E-value: 2.20e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 365260220  61 WLEA-LEGHVRRLGAELLPI------EWshARLSGRLEwSHRDPFDRMLAAQAISESLVLVTRD 117
Cdd:cd18746   58 RLEAwLDGLLLRFAGRILPVdaevarRW--GRLHAPAP-APLPVADALIAATALVHGLTLVTRN 118
PIN_VapC4-5_FitB-like cd18745
uncharacterized subgroup of the PIN_VapC4-5_FitB-like subfamily of the PIN domain superfamily; ...
 4-116 6.07e-03

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: 350312  Cd Length: 130  Bit Score: 34.39  E-value: 6.07e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 365260220   4 YLLDTHALMWAINepsrlgdGAAEVLRDR-----GSLLVVSAASAWELYTKhrIGKLPGAGPWLEALEGHVRrlGAELLP 78
Cdd:cd18745    1 YLLDTNTVIALFR-------GRGPVLRARlraaaPSDLALSSIVLYELEYG--AAKSARPERNRARLEELLS--LIEVLP 69

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 365260220  79 IEWSHARLSGRLewshR----------DPFDRMLAAQAISESLVLVTR 116
Cdd:cd18745   70 FDEEDARAAAEI----RadleragtpiGPYDTLIAGQALARGATLVTH 113
 
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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