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Conserved domains on  [gi|1817152827|ref|WP_164042455|]
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putative toxin-antitoxin system toxin component, PIN family [Spirosoma agri]

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]; ...
 1-130 6.31e-31

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


:

Pssm-ID: 441177  Cd Length: 136  Bit Score: 107.62  E-value: 6.31e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1817152827   1 MRVIIDTNVLLAALPKV-SRFRTIITALVLGKFELAVSTAILLEYQEILSRKTNEIVATNFLEFLTKL-PGVIRVDTPFI 78
Cdd:COG1569     1 MRVVLDTNVLVSALLSPdGAPARLLRAALAGRFTLLVSAAILEELERVLARPKFKLSPEEREELLAALlALAELVEPTPL 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1817152827  79 WNIIEADPDDNKFVDAGLMAGADYIITYDSHFNVVKsqPFPAIGVLTPDDFL 130
Cdd:COG1569    81 WRPICRDPDDNKFLELAVAGGADYLVTGDKDLLSLA--RFFGIRILTPAEFL 130
 
Name Accession Description Interval E-value
COG1569 COG1569
Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]; ...
 1-130 6.31e-31

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


Pssm-ID: 441177  Cd Length: 136  Bit Score: 107.62  E-value: 6.31e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1817152827   1 MRVIIDTNVLLAALPKV-SRFRTIITALVLGKFELAVSTAILLEYQEILSRKTNEIVATNFLEFLTKL-PGVIRVDTPFI 78
Cdd:COG1569     1 MRVVLDTNVLVSALLSPdGAPARLLRAALAGRFTLLVSAAILEELERVLARPKFKLSPEEREELLAALlALAELVEPTPL 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1817152827  79 WNIIEADPDDNKFVDAGLMAGADYIITYDSHFNVVKsqPFPAIGVLTPDDFL 130
Cdd:COG1569    81 WRPICRDPDDNKFLELAVAGGADYLVTGDKDLLSLA--RFFGIRILTPAEFL 130
PIN_3 pfam13470
PIN domain; Members of this family of bacterial domains are predicted to be RNases (from ...
 2-109 1.17e-18

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: 75.45  E-value: 1.17e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1817152827   2 RVIIDTNVLLAALPKVSRF---RTIITALVLGKFELAVSTAILLEYQEILSRKTNEI-VATNFLEFLTKLPGVIRVDTP- 76
Cdd:pfam13470   1 RVVLDTNVLLDALLFRSPFsasAKLLDLLARGRIQLVVSAAILDEYEYVLTRPLAKPrLALSIEERLLLLALVAAVVDPd 80

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1817152827  77 FIWNIIE--ADPDDNKFVDAGLMAGADYIITYDSH 109
Cdd:pfam13470  81 LPLAPVSacRDPEDAHFLEAAVAGQADFIVTRNRA 115
TIGR00305 TIGR00305
putative toxin-antitoxin system toxin component, PIN family; This uncharacterized protein ...
 2-108 1.28e-06

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: 44.38  E-value: 1.28e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1817152827   2 RVIIDTNVLLAALPKVSRFRTIITALVLGKFELAVSTAILLEYQEILS--RKTNEIVATNFLEFLTKLPGVIRVDTPFIW 79
Cdd:TIGR00305   1 KVVIDTNVWISALIWKGLPGKLIKLIIDNKIVNCTSVEILQEVEFVLLypKLQKYFALETILEILLLLGEKSTIINPNPE 80

                          90       100
                  ....*....|....*....|....*....
gi 1817152827  80 NIIEADPDDNKFVDAGLMAGADYIITYDS 108
Cdd:TIGR00305  81 FDDCRDKKDNKFLNTAYASKANALITGDT 109
PIN_VapC-like cd18715
uncharacterized subfamily of the VapC (virulence-associated protein C)-like family of the PIN ...
 2-107 3.74e-06

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: 43.45  E-value: 3.74e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1817152827   2 RVIIDTNVLLAAL-PKVSRFRTIITALVLGKFELAVSTAILLE---------YQEILS-----RKTNEIVATNFLefLTK 66
Cdd:cd18715     1 RVVLDTNILISALiSPHSPPDLIYRAWRAGRFELVTSEEQLDElrrvsrypkLQARLQpaeagTMVNNLRRLAVM--LER 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1817152827  67 LPGVIRVDtpfiwniieaDPDDNKFVDAGLMAGADYIITYD 107
Cdd:cd18715    79 LPIVEESP----------DPDDNFLLAMALAGDADYLVTGD 109
PINc smart00670
Large family of predicted nucleotide-binding domains; From similarities to 5'-exonucleases, ...
 1-112 2.58e-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: 35.48  E-value: 2.58e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1817152827    1 MRVIIDTNVLLAALpkvsrFRTIITALVLGKFELAVSTAILLEYQEILSRKTN---EIVATNFLEFL-TKLPGVIRVDTP 76
Cdd:smart00670   1 MKVVLDTNVLIDGL-----IRDALEKLLEKKGEVYIPQTVLEELEYLALRSLKkleELALEGKIILKvLKEERIEEEILE 75

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1817152827   77 FIWNIIEADPDDNKFVDAGLMAGADYIITYDSHFNV 112
Cdd:smart00670  76 RLSLKLELLPNDALILATAKELGNVVLVTNDRDLRR 111
 
Name Accession Description Interval E-value
COG1569 COG1569
Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]; ...
 1-130 6.31e-31

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


Pssm-ID: 441177  Cd Length: 136  Bit Score: 107.62  E-value: 6.31e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1817152827   1 MRVIIDTNVLLAALPKV-SRFRTIITALVLGKFELAVSTAILLEYQEILSRKTNEIVATNFLEFLTKL-PGVIRVDTPFI 78
Cdd:COG1569     1 MRVVLDTNVLVSALLSPdGAPARLLRAALAGRFTLLVSAAILEELERVLARPKFKLSPEEREELLAALlALAELVEPTPL 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1817152827  79 WNIIEADPDDNKFVDAGLMAGADYIITYDSHFNVVKsqPFPAIGVLTPDDFL 130
Cdd:COG1569    81 WRPICRDPDDNKFLELAVAGGADYLVTGDKDLLSLA--RFFGIRILTPAEFL 130
PIN_3 pfam13470
PIN domain; Members of this family of bacterial domains are predicted to be RNases (from ...
 2-109 1.17e-18

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: 75.45  E-value: 1.17e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1817152827   2 RVIIDTNVLLAALPKVSRF---RTIITALVLGKFELAVSTAILLEYQEILSRKTNEI-VATNFLEFLTKLPGVIRVDTP- 76
Cdd:pfam13470   1 RVVLDTNVLLDALLFRSPFsasAKLLDLLARGRIQLVVSAAILDEYEYVLTRPLAKPrLALSIEERLLLLALVAAVVDPd 80

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1817152827  77 FIWNIIE--ADPDDNKFVDAGLMAGADYIITYDSH 109
Cdd:pfam13470  81 LPLAPVSacRDPEDAHFLEAAVAGQADFIVTRNRA 115
VapC COG1848
VapC family ribonuclease, toxin component of the VapBC toxin-antitoxin module, contains PIN ...
 2-128 1.83e-09

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


Pssm-ID: 441453  Cd Length: 134  Bit Score: 52.29  E-value: 1.83e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1817152827   2 RVIIDTNVLLAAL----PKVSRFRTIITALVLGKFELAVSTAILLEYQEILSRKTN--EIVATNFLEFLTKLPGVIRVDT 75
Cdd:COG1848     1 MILLDTNVLIYALegdsPFHERARELLERAEEGEEELYTSPLVLAEVLYVLTRPGGlsLEEARELLEALLSNIEVVPVDE 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1817152827  76 PFIWNIIEADPDDN-KFVDAGLMA-----GADYIITYDSHFNVvksqpFPAIGVLTPDD 128
Cdd:COG1848    81 EILEEAAELLAKYGlRLNDALHLAtalehGADALVTFDRDFAR-----VPGLEVVDPEE 134
COG2402 COG2402
Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]; ...
 2-113 4.93e-08

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


Pssm-ID: 441958  Cd Length: 135  Bit Score: 48.35  E-value: 4.93e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1817152827   2 RVIIDTNVLLAAL----PKVSRFRTIITALVLGKFELAVSTAILLEYQEILSRKTNEIVATNFLEFLTKLPG--VIRVDT 75
Cdd:COG2402     1 MIFVDTGALIALFnrrdQYHEAAVELLESLLEGELPLVTTDYVLTETLTLLSRRLGREAAVKFLDRLRESGGleIVPLTE 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1817152827  76 PF---IWNIIEADPDDNK-FVDAGLMA-----GADYIITYDSHFNVV 113
Cdd:COG2402    81 EDferALELFEKYADKPLsLTDASSVAlmerlGIDEILTFDRDFDQY 127
TIGR00305 TIGR00305
putative toxin-antitoxin system toxin component, PIN family; This uncharacterized protein ...
 2-108 1.28e-06

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: 44.38  E-value: 1.28e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1817152827   2 RVIIDTNVLLAALPKVSRFRTIITALVLGKFELAVSTAILLEYQEILS--RKTNEIVATNFLEFLTKLPGVIRVDTPFIW 79
Cdd:TIGR00305   1 KVVIDTNVWISALIWKGLPGKLIKLIIDNKIVNCTSVEILQEVEFVLLypKLQKYFALETILEILLLLGEKSTIINPNPE 80

                          90       100
                  ....*....|....*....|....*....
gi 1817152827  80 NIIEADPDDNKFVDAGLMAGADYIITYDS 108
Cdd:TIGR00305  81 FDDCRDKKDNKFLNTAYASKANALITGDT 109
PIN_VapC-like cd18715
uncharacterized subfamily of the VapC (virulence-associated protein C)-like family of the PIN ...
 2-107 3.74e-06

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: 43.45  E-value: 3.74e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1817152827   2 RVIIDTNVLLAAL-PKVSRFRTIITALVLGKFELAVSTAILLE---------YQEILS-----RKTNEIVATNFLefLTK 66
Cdd:cd18715     1 RVVLDTNILISALiSPHSPPDLIYRAWRAGRFELVTSEEQLDElrrvsrypkLQARLQpaeagTMVNNLRRLAVM--LER 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1817152827  67 LPGVIRVDtpfiwniieaDPDDNKFVDAGLMAGADYIITYD 107
Cdd:cd18715    79 LPIVEESP----------DPDDNFLLAMALAGDADYLVTGD 109
COG5378 COG5378
Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]; ...
 1-135 2.51e-05

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


Pssm-ID: 444143  Cd Length: 141  Bit Score: 41.42  E-value: 2.51e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1817152827   1 MRVIIDTNVLLAAL-PKVSRFRTIItalVLGKFELAVSTAILLE---YQEILSRKT--NEIVATNFLEFLTKLPGVIRVD 74
Cdd:COG5378     2 MKLVVDANILFSALlGGKSRIRRLL---LNLELELYTPEYALDElekHLEKIAKKSglSEDELAQALDLLLSRINIVPEE 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1817152827  75 TPF-----IWNII-EADPDDNKFVDAGLMAGADyIITYDSHF----NVVKsqpfpaigVLTPDDFLFLLST 135
Cdd:COG5378    79 IYNdyleeAYELIpDRDPDDTPFVALALALDAP-IWTGDKDLfgglGFVK--------TWTTDELLRLLDG 140
PINc smart00670
Large family of predicted nucleotide-binding domains; From similarities to 5'-exonucleases, ...
 1-112 2.58e-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: 35.48  E-value: 2.58e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1817152827    1 MRVIIDTNVLLAALpkvsrFRTIITALVLGKFELAVSTAILLEYQEILSRKTN---EIVATNFLEFL-TKLPGVIRVDTP 76
Cdd:smart00670   1 MKVVLDTNVLIDGL-----IRDALEKLLEKKGEVYIPQTVLEELEYLALRSLKkleELALEGKIILKvLKEERIEEEILE 75

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1817152827   77 FIWNIIEADPDDNKFVDAGLMAGADYIITYDSHFNV 112
Cdd:smart00670  76 RLSLKLELLPNDALILATAKELGNVVLVTNDRDLRR 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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