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Conserved domains on  [gi|1084716070|gb|OGP61160|]
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putative toxin-antitoxin system toxin component, PIN family [Deltaproteobacteria bacterium RBG_13_52_11b]

Protein Classification

putative toxin-antitoxin system toxin component, PIN family( domain architecture ID 10003974)

putative toxin-antitoxin system toxin component, PIN (PilT N terminus) family, might function as a nuclease; similar to Methanocaldococcus jannaschii uncharacterized protein MJ1680

Gene Ontology:  GO:0004540
PubMed:  21036780

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
COG1569 COG1569
Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]; ...
 1-135 3.20e-43

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


:

Pssm-ID: 441177  Cd Length: 136  Bit Score: 138.82  E-value: 3.20e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084716070   1 MIIVLETNVVVSGILKPYSKTAAILRLVADGAIQLAYDLRILSEYRDVLSRPKFNFVKENIEAFLDQVEQEGVLVSVKPL 80
Cdd:COG1569     1 MRVVLDTNVLVSALLSPDGAPARLLRAALAGRFTLLVSAAILEELERVLARPKFKLSPEEREELLAALLALAELVEPTPL 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1084716070  81 KN-HLPDSDDEPFLEVALSGGVKAVVTGNKRHFPRKDYQGVKILSPVEFLEAMKEK 135
Cdd:COG1569    81 WRpICRDPDDNKFLELAVAGGADYLVTGDKDLLSLARFFGIRILTPAEFLELLRPK 136
 
Name Accession Description Interval E-value
COG1569 COG1569
Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]; ...
 1-135 3.20e-43

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


Pssm-ID: 441177  Cd Length: 136  Bit Score: 138.82  E-value: 3.20e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084716070   1 MIIVLETNVVVSGILKPYSKTAAILRLVADGAIQLAYDLRILSEYRDVLSRPKFNFVKENIEAFLDQVEQEGVLVSVKPL 80
Cdd:COG1569     1 MRVVLDTNVLVSALLSPDGAPARLLRAALAGRFTLLVSAAILEELERVLARPKFKLSPEEREELLAALLALAELVEPTPL 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1084716070  81 KN-HLPDSDDEPFLEVALSGGVKAVVTGNKRHFPRKDYQGVKILSPVEFLEAMKEK 135
Cdd:COG1569    81 WRpICRDPDDNKFLELAVAGGADYLVTGDKDLLSLARFFGIRILTPAEFLELLRPK 136
PIN_3 pfam13470
PIN domain; Members of this family of bacterial domains are predicted to be RNases (from ...
 3-110 1.08e-19

PIN domain; Members of this family of bacterial domains are predicted to be RNases (from similarities to 5'-exonucleases).


Pssm-ID: 463888  Cd Length: 115  Bit Score: 78.15  E-value: 1.08e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084716070   3 IVLETNVVVSGIL--KPYSKTAAILRLVADGAIQLAYDLRILSEYRDVLSRPKFNF-----VKENIEAFLDQVEQEGVLV 75
Cdd:pfam13470   2 VVLDTNVLLDALLfrSPFSASAKLLDLLARGRIQLVVSAAILDEYEYVLTRPLAKPrlalsIEERLLLLALVAAVVDPDL 81

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1084716070  76 SVKPLKNhLPDSDDEPFLEVALSGGVKAVVTGNKR 110
Cdd:pfam13470  82 PLAPVSA-CRDPEDAHFLEAAVAGQADFIVTRNRA 115
PIN_VapC-like cd18715
uncharacterized subfamily of the VapC (virulence-associated protein C)-like family of the PIN ...
 3-110 1.70e-07

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: 350282  Cd Length: 125  Bit Score: 46.91  E-value: 1.70e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084716070   3 IVLETNVVVSGILKPYSKTAAILRLVADGAIQLAYDLRILSEYRDVLSRPKFNFVKENIEA--FLDQVEQEGVLVSVKPL 80
Cdd:cd18715     2 VVLDTNILISALISPHSPPDLIYRAWRAGRFELVTSEEQLDELRRVSRYPKLQARLQPAEAgtMVNNLRRLAVMLERLPI 81

                          90       100       110
                  ....*....|....*....|....*....|
gi 1084716070  81 KNHLPDSDDEPFLEVALSGGVKAVVTGNKR 110
Cdd:cd18715    82 VEESPDPDDNFLLAMALAGDADYLVTGDKR 111
 
Name Accession Description Interval E-value
COG1569 COG1569
Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]; ...
 1-135 3.20e-43

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


Pssm-ID: 441177  Cd Length: 136  Bit Score: 138.82  E-value: 3.20e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084716070   1 MIIVLETNVVVSGILKPYSKTAAILRLVADGAIQLAYDLRILSEYRDVLSRPKFNFVKENIEAFLDQVEQEGVLVSVKPL 80
Cdd:COG1569     1 MRVVLDTNVLVSALLSPDGAPARLLRAALAGRFTLLVSAAILEELERVLARPKFKLSPEEREELLAALLALAELVEPTPL 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1084716070  81 KN-HLPDSDDEPFLEVALSGGVKAVVTGNKRHFPRKDYQGVKILSPVEFLEAMKEK 135
Cdd:COG1569    81 WRpICRDPDDNKFLELAVAGGADYLVTGDKDLLSLARFFGIRILTPAEFLELLRPK 136
PIN_3 pfam13470
PIN domain; Members of this family of bacterial domains are predicted to be RNases (from ...
 3-110 1.08e-19

PIN domain; Members of this family of bacterial domains are predicted to be RNases (from similarities to 5'-exonucleases).


Pssm-ID: 463888  Cd Length: 115  Bit Score: 78.15  E-value: 1.08e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084716070   3 IVLETNVVVSGIL--KPYSKTAAILRLVADGAIQLAYDLRILSEYRDVLSRPKFNF-----VKENIEAFLDQVEQEGVLV 75
Cdd:pfam13470   2 VVLDTNVLLDALLfrSPFSASAKLLDLLARGRIQLVVSAAILDEYEYVLTRPLAKPrlalsIEERLLLLALVAAVVDPDL 81

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1084716070  76 SVKPLKNhLPDSDDEPFLEVALSGGVKAVVTGNKR 110
Cdd:pfam13470  82 PLAPVSA-CRDPEDAHFLEAAVAGQADFIVTRNRA 115
PIN_VapC-like cd18715
uncharacterized subfamily of the VapC (virulence-associated protein C)-like family of the PIN ...
 3-110 1.70e-07

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: 350282  Cd Length: 125  Bit Score: 46.91  E-value: 1.70e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084716070   3 IVLETNVVVSGILKPYSKTAAILRLVADGAIQLAYDLRILSEYRDVLSRPKFNFVKENIEA--FLDQVEQEGVLVSVKPL 80
Cdd:cd18715     2 VVLDTNILISALISPHSPPDLIYRAWRAGRFELVTSEEQLDELRRVSRYPKLQARLQPAEAgtMVNNLRRLAVMLERLPI 81

                          90       100       110
                  ....*....|....*....|....*....|
gi 1084716070  81 KNHLPDSDDEPFLEVALSGGVKAVVTGNKR 110
Cdd:cd18715    82 VEESPDPDDNFLLAMALAGDADYLVTGDKR 111
 
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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