NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1818849326|ref|WP_164887687|]
View 

putative toxin-antitoxin system toxin component, PIN family [Sinirhodobacter populi]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
COG1569 COG1569
Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]; ...
 1-137 6.29e-36

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


:

Pssm-ID: 441177  Cd Length: 136  Bit Score: 120.33  E-value: 6.29e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1818849326   1 MRLVLDTNVIVAAFRSRNGASNLLLRAVDRGVLTPLCSTALFLEYEAVLSREETRkvtgHSLEDVAAVMSALAAVSEGVD 80
Cdd:COG1569     1 MRVVLDTNVLVSALLSPDGAPARLLRAALAGRFTLLVSAAILEELERVLARPKFK----LSPEEREELLAALLALAELVE 76

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1818849326  81 ISFRTRPMLSDVADEMVLEAALNGQAEAIVTHNvRDFRP-ALTLGVTVATPGEIVRRL 137
Cdd:COG1569    77 PTPLWRPICRDPDDNKFLELAVAGGADYLVTGD-KDLLSlARFFGIRILTPAEFLELL 133
 
Name Accession Description Interval E-value
COG1569 COG1569
Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]; ...
 1-137 6.29e-36

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


Pssm-ID: 441177  Cd Length: 136  Bit Score: 120.33  E-value: 6.29e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1818849326   1 MRLVLDTNVIVAAFRSRNGASNLLLRAVDRGVLTPLCSTALFLEYEAVLSREETRkvtgHSLEDVAAVMSALAAVSEGVD 80
Cdd:COG1569     1 MRVVLDTNVLVSALLSPDGAPARLLRAALAGRFTLLVSAAILEELERVLARPKFK----LSPEEREELLAALLALAELVE 76

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1818849326  81 ISFRTRPMLSDVADEMVLEAALNGQAEAIVTHNvRDFRP-ALTLGVTVATPGEIVRRL 137
Cdd:COG1569    77 PTPLWRPICRDPDDNKFLELAVAGGADYLVTGD-KDLLSlARFFGIRILTPAEFLELL 133
PIN_3 pfam13470
PIN domain; Members of this family of bacterial domains are predicted to be RNases (from ...
 2-115 7.39e-25

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: 91.63  E-value: 7.39e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1818849326   2 RLVLDTNVIVAA--FRSRNGASNLLLRAVDRGVLTPLCSTALFLEYEAVLSREETRKVTGHSLEDVAAVMSALAAVSEgV 79
Cdd:pfam13470   1 RVVLDTNVLLDAllFRSPFSASAKLLDLLARGRIQLVVSAAILDEYEYVLTRPLAKPRLALSIEERLLLLALVAAVVD-P 79

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1818849326  80 DISFRTRPMLSDVADEMVLEAALNGQAEAIVTHNVR 115
Cdd:pfam13470  80 DLPLAPVSACRDPEDAHFLEAAVAGQADFIVTRNRA 115
TIGR00305 TIGR00305
putative toxin-antitoxin system toxin component, PIN family; This uncharacterized protein ...
 2-111 1.49e-08

putative toxin-antitoxin system toxin component, PIN family; This uncharacterized protein family, part of the PIN domain superfamily, is restricted to bacteria and archaea. A comprehensive in silico study of toxin-antitoxin systems by Makarova, et al. (2009) finds evidence this family represents the toxin-like component of one class of type 2 toxin-antitoxin systems. [Cellular processes, Other, Transcription, Degradation of RNA]


Pssm-ID: 129405  Cd Length: 114  Bit Score: 49.39  E-value: 1.49e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1818849326   2 RLVLDTNVIVAAFRSRNGASNLLLRAVDRGVLTpLCSTALFLEYEAVLSREETRKVTGhsLEDVAAVMSALAAVSEGVDI 81
Cdd:TIGR00305   1 KVVIDTNVWISALIWKGLPGKLIKLIIDNKIVN-CTSVEILQEVEFVLLYPKLQKYFA--LETILEILLLLGEKSTIINP 77

                          90       100       110
                  ....*....|....*....|....*....|
gi 1818849326  82 SFRTRpMLSDVADEMVLEAALNGQAEAIVT 111
Cdd:TIGR00305  78 NPEFD-DCRDKKDNKFLNTAYASKANALIT 106
PIN_VapC-like cd09854
VapC-like PIN domains of VapC and Smg6 ribonucleases, ribosome assembly factor NOB1, ...
 4-127 3.42e-03

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: 35.33  E-value: 3.42e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1818849326   4 VLDTNVIVAAFRSRNGASNLLLRAVDRGVLTPL-CSTALFLEYEAVLSREETRKVTG---HSLEDVAAVMSALAAVSEGV 79
Cdd:cd09854     1 VLDTNVLIALLSSEPESEAAKELLALLLGDSELvIPPLVLAELLRLLARERGARRALeilELLRALEVVEEEPALAEIAL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1818849326  80 DISFRTRPMLSDVADEMVLEAALNGQAEAIVTHNvRDFRPALTLGVTV 127
Cdd:cd09854    81 EVLALGLERGLDFGDALILALAKELGGAVLVTND-RDFRRLAKLGLKV 127
PINc smart00670
Large family of predicted nucleotide-binding domains; From similarities to 5'-exonucleases, ...
 1-118 4.42e-03

Large family of predicted nucleotide-binding domains; From similarities to 5'-exonucleases, these domains are predicted to be RNases. PINc domains in nematode SMG-5 and yeast NMD4p are predicted to be involved in RNAi.


Pssm-ID: 214771 [Multi-domain]  Cd Length: 111  Bit Score: 34.71  E-value: 4.42e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1818849326    1 MRLVLDTNVIVAAFRSRngasnlLLRAVDRGVLTPLCSTALFLEYEAvLSREETRKVTGHSLEDVAAVMSALAAVSEGVD 80
Cdd:smart00670   1 MKVVLDTNVLIDGLIRD------ALEKLLEKKGEVYIPQTVLEELEY-LALRSLKKLEELALEGKIILKVLKEERIEEEI 73

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 1818849326   81 ISFRTRPMLSDVADEMVLEAALNGQAEAIVTHNvRDFR 118
Cdd:smart00670  74 LERLSLKLELLPNDALILATAKELGNVVLVTND-RDLR 110
 
Name Accession Description Interval E-value
COG1569 COG1569
Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]; ...
 1-137 6.29e-36

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


Pssm-ID: 441177  Cd Length: 136  Bit Score: 120.33  E-value: 6.29e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1818849326   1 MRLVLDTNVIVAAFRSRNGASNLLLRAVDRGVLTPLCSTALFLEYEAVLSREETRkvtgHSLEDVAAVMSALAAVSEGVD 80
Cdd:COG1569     1 MRVVLDTNVLVSALLSPDGAPARLLRAALAGRFTLLVSAAILEELERVLARPKFK----LSPEEREELLAALLALAELVE 76

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1818849326  81 ISFRTRPMLSDVADEMVLEAALNGQAEAIVTHNvRDFRP-ALTLGVTVATPGEIVRRL 137
Cdd:COG1569    77 PTPLWRPICRDPDDNKFLELAVAGGADYLVTGD-KDLLSlARFFGIRILTPAEFLELL 133
PIN_3 pfam13470
PIN domain; Members of this family of bacterial domains are predicted to be RNases (from ...
 2-115 7.39e-25

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: 91.63  E-value: 7.39e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1818849326   2 RLVLDTNVIVAA--FRSRNGASNLLLRAVDRGVLTPLCSTALFLEYEAVLSREETRKVTGHSLEDVAAVMSALAAVSEgV 79
Cdd:pfam13470   1 RVVLDTNVLLDAllFRSPFSASAKLLDLLARGRIQLVVSAAILDEYEYVLTRPLAKPRLALSIEERLLLLALVAAVVD-P 79

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1818849326  80 DISFRTRPMLSDVADEMVLEAALNGQAEAIVTHNVR 115
Cdd:pfam13470  80 DLPLAPVSACRDPEDAHFLEAAVAGQADFIVTRNRA 115
TIGR00305 TIGR00305
putative toxin-antitoxin system toxin component, PIN family; This uncharacterized protein ...
 2-111 1.49e-08

putative toxin-antitoxin system toxin component, PIN family; This uncharacterized protein family, part of the PIN domain superfamily, is restricted to bacteria and archaea. A comprehensive in silico study of toxin-antitoxin systems by Makarova, et al. (2009) finds evidence this family represents the toxin-like component of one class of type 2 toxin-antitoxin systems. [Cellular processes, Other, Transcription, Degradation of RNA]


Pssm-ID: 129405  Cd Length: 114  Bit Score: 49.39  E-value: 1.49e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1818849326   2 RLVLDTNVIVAAFRSRNGASNLLLRAVDRGVLTpLCSTALFLEYEAVLSREETRKVTGhsLEDVAAVMSALAAVSEGVDI 81
Cdd:TIGR00305   1 KVVIDTNVWISALIWKGLPGKLIKLIIDNKIVN-CTSVEILQEVEFVLLYPKLQKYFA--LETILEILLLLGEKSTIINP 77

                          90       100       110
                  ....*....|....*....|....*....|
gi 1818849326  82 SFRTRpMLSDVADEMVLEAALNGQAEAIVT 111
Cdd:TIGR00305  78 NPEFD-DCRDKKDNKFLNTAYASKANALIT 106
VapC COG1848
VapC family ribonuclease, toxin component of the VapBC toxin-antitoxin module, contains PIN ...
 2-132 1.43e-03

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


Pssm-ID: 441453  Cd Length: 134  Bit Score: 36.50  E-value: 1.43e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1818849326   2 RLVLDTNVIVAAFRSR---NGASNLLLRAVDRGVLTPLCSTALFLEYEAVLSREetrkvTGHSLEDVAAVMSALAAVSEG 78
Cdd:COG1848     1 MILLDTNVLIYALEGDspfHERARELLERAEEGEEELYTSPLVLAEVLYVLTRP-----GGLSLEEARELLEALLSNIEV 75

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1818849326  79 VDISFRTRPMLS--------DVADEMVLEAALNGQAEAIVTHNvRDFRPAltLGVTVATPGE 132
Cdd:COG1848    76 VPVDEEILEEAAellakyglRLNDALHLATALEHGADALVTFD-RDFARV--PGLEVVDPEE 134
PIN_VapC-like cd09854
VapC-like PIN domains of VapC and Smg6 ribonucleases, ribosome assembly factor NOB1, ...
 4-127 3.42e-03

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: 35.33  E-value: 3.42e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1818849326   4 VLDTNVIVAAFRSRNGASNLLLRAVDRGVLTPL-CSTALFLEYEAVLSREETRKVTG---HSLEDVAAVMSALAAVSEGV 79
Cdd:cd09854     1 VLDTNVLIALLSSEPESEAAKELLALLLGDSELvIPPLVLAELLRLLARERGARRALeilELLRALEVVEEEPALAEIAL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1818849326  80 DISFRTRPMLSDVADEMVLEAALNGQAEAIVTHNvRDFRPALTLGVTV 127
Cdd:cd09854    81 EVLALGLERGLDFGDALILALAKELGGAVLVTND-RDFRRLAKLGLKV 127
PINc smart00670
Large family of predicted nucleotide-binding domains; From similarities to 5'-exonucleases, ...
 1-118 4.42e-03

Large family of predicted nucleotide-binding domains; From similarities to 5'-exonucleases, these domains are predicted to be RNases. PINc domains in nematode SMG-5 and yeast NMD4p are predicted to be involved in RNAi.


Pssm-ID: 214771 [Multi-domain]  Cd Length: 111  Bit Score: 34.71  E-value: 4.42e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1818849326    1 MRLVLDTNVIVAAFRSRngasnlLLRAVDRGVLTPLCSTALFLEYEAvLSREETRKVTGHSLEDVAAVMSALAAVSEGVD 80
Cdd:smart00670   1 MKVVLDTNVLIDGLIRD------ALEKLLEKKGEVYIPQTVLEELEY-LALRSLKKLEELALEGKIILKVLKEERIEEEI 73

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 1818849326   81 ISFRTRPMLSDVADEMVLEAALNGQAEAIVTHNvRDFR 118
Cdd:smart00670  74 LERLSLKLELLPNDALILATAKELGNVVLVTND-RDLR 110
 
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