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Conserved domains on  [gi|488762512|ref|WP_002685712|]
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PIN domain-containing protein [Treponema denticola]

Protein Classification

PIN domain-containing protein( domain architecture ID 10604431)

PIN (PilT N terminus) domain-containing protein may function as a nuclease

Gene Ontology:  GO:0004540
PubMed:  28508407|28575517|21036780

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PIN_3 pfam13470
PIN domain; Members of this family of bacterial domains are predicted to be RNases (from ...
 3-116 3.82e-14

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: 63.90  E-value: 3.82e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488762512    3 KVLIDLNIILDFLNKRNFHEEAANIINMCVEKKLFGFIAAHEITTLSYFLLKEKKDKNKAADIISALLDMFNIIPIDEKI 82
Cdd:pfam13470   1 RVVLDTNVLLDALLFRSPFSASAKLLDLLARGRIQLVVSAAILDEYEYVLTRPLAKPRLALSIEERLLLLALVAAVVDPD 80

                          90       100       110
                  ....*....|....*....|....*....|....
gi 488762512   83 LREALFSPVKDYEDAVIEVSSVKNSIDYIISRNL 116
Cdd:pfam13470  81 LPLAPVSACRDPEDAHFLEAAVAGQADFIVTRNR 114
 
Name Accession Description Interval E-value
PIN_3 pfam13470
PIN domain; Members of this family of bacterial domains are predicted to be RNases (from ...
 3-116 3.82e-14

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: 63.90  E-value: 3.82e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488762512    3 KVLIDLNIILDFLNKRNFHEEAANIINMCVEKKLFGFIAAHEITTLSYFLLKEKKDKNKAADIISALLDMFNIIPIDEKI 82
Cdd:pfam13470   1 RVVLDTNVLLDALLFRSPFSASAKLLDLLARGRIQLVVSAAILDEYEYVLTRPLAKPRLALSIEERLLLLALVAAVVDPD 80

                          90       100       110
                  ....*....|....*....|....*....|....
gi 488762512   83 LREALFSPVKDYEDAVIEVSSVKNSIDYIISRNL 116
Cdd:pfam13470  81 LPLAPVSACRDPEDAHFLEAAVAGQADFIVTRNR 114
VapC COG1848
VapC family ribonuclease, toxin component of the VapBC toxin-antitoxin module, contains PIN ...
 3-131 8.77e-13

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


Pssm-ID: 441453  Cd Length: 134  Bit Score: 60.77  E-value: 8.77e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488762512   3 KVLIDLNIILDFLNKRN-FHEEAANIINMCVEKKLFGFIAAHEITTLSYFLLKEKK-DKNKAADIISALLDMFNIIPIDE 80
Cdd:COG1848    1 MILLDTNVLIYALEGDSpFHERARELLERAEEGEEELYTSPLVLAEVLYVLTRPGGlSLEEARELLEALLSNIEVVPVDE 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 488762512  81 KILREALFSPVK---DYEDAVIEVSSVKNSIDYIISRNlGDFKSAR-VQVFTPEQ 131
Cdd:COG1848   81 EILEEAAELLAKyglRLNDALHLATALEHGADALVTFD-RDFARVPgLEVVDPEE 134
PIN_VapC-like cd18684
uncharacterized subfamily of the VapC (virulence-associated protein C)-like family of the PIN ...
 4-99 5.15e-03

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: 350251  Cd Length: 131  Bit Score: 34.90  E-value: 5.15e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488762512   4 VLIDLNIIL-DFLNKRNFHEEAANIINMcVEKKLFGFIAAHEITtlsYFLLKEKKDKNKAADIISALLD--MFNIIPIDE 80
Cdd:cd18684    1 AVVDTNVLIyDTVEDSEYHKEARELLDS-LEKWVIPTIVVHELV---WFLRKLGLSPDDAKEKVEEYLEdpRFEVVCEDR 76

                         90       100
                 ....*....|....*....|....*
gi 488762512  81 KILREAL------FSPVKDYEDAVI 99
Cdd:cd18684   77 EDIKSALellleeGLSLSRYNDYVI 101
 
Name Accession Description Interval E-value
PIN_3 pfam13470
PIN domain; Members of this family of bacterial domains are predicted to be RNases (from ...
 3-116 3.82e-14

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: 63.90  E-value: 3.82e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488762512    3 KVLIDLNIILDFLNKRNFHEEAANIINMCVEKKLFGFIAAHEITTLSYFLLKEKKDKNKAADIISALLDMFNIIPIDEKI 82
Cdd:pfam13470   1 RVVLDTNVLLDALLFRSPFSASAKLLDLLARGRIQLVVSAAILDEYEYVLTRPLAKPRLALSIEERLLLLALVAAVVDPD 80

                          90       100       110
                  ....*....|....*....|....*....|....
gi 488762512   83 LREALFSPVKDYEDAVIEVSSVKNSIDYIISRNL 116
Cdd:pfam13470  81 LPLAPVSACRDPEDAHFLEAAVAGQADFIVTRNR 114
VapC COG1848
VapC family ribonuclease, toxin component of the VapBC toxin-antitoxin module, contains PIN ...
 3-131 8.77e-13

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


Pssm-ID: 441453  Cd Length: 134  Bit Score: 60.77  E-value: 8.77e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488762512   3 KVLIDLNIILDFLNKRN-FHEEAANIINMCVEKKLFGFIAAHEITTLSYFLLKEKK-DKNKAADIISALLDMFNIIPIDE 80
Cdd:COG1848    1 MILLDTNVLIYALEGDSpFHERARELLERAEEGEEELYTSPLVLAEVLYVLTRPGGlSLEEARELLEALLSNIEVVPVDE 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 488762512  81 KILREALFSPVK---DYEDAVIEVSSVKNSIDYIISRNlGDFKSAR-VQVFTPEQ 131
Cdd:COG1848   81 EILEEAAELLAKyglRLNDALHLATALEHGADALVTFD-RDFARVPgLEVVDPEE 134
PIN_VapC-like cd18684
uncharacterized subfamily of the VapC (virulence-associated protein C)-like family of the PIN ...
 4-99 5.15e-03

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: 350251  Cd Length: 131  Bit Score: 34.90  E-value: 5.15e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488762512   4 VLIDLNIIL-DFLNKRNFHEEAANIINMcVEKKLFGFIAAHEITtlsYFLLKEKKDKNKAADIISALLD--MFNIIPIDE 80
Cdd:cd18684    1 AVVDTNVLIyDTVEDSEYHKEARELLDS-LEKWVIPTIVVHELV---WFLRKLGLSPDDAKEKVEEYLEdpRFEVVCEDR 76

                         90       100
                 ....*....|....*....|....*
gi 488762512  81 KILREAL------FSPVKDYEDAVI 99
Cdd:cd18684   77 EDIKSALellleeGLSLSRYNDYVI 101
PIN_MjVapC2-VapC6_like cd18677
VapC-like PIN domain of Methanocaldococcus jannaschii VapC2, and VapC6, and related proteins; ...
 5-122 6.87e-03

VapC-like PIN domain of Methanocaldococcus jannaschii VapC2, and VapC6, and related proteins; This subfamily includes Methanocaldococcus jannaschii VapC2 and VapC6. It belongs to the VapC (virulence-associated protein C)-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 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 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: 350244  Cd Length: 136  Bit Score: 34.48  E-value: 6.87e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488762512   5 LIDLNIILDFLNK--------RNFHEEAANIIN-MCVEKKLFGFIAAheITTLSYFLLKEKKDKNK--AADIISALLDMF 73
Cdd:cd18677    1 FIDSNVFIEYLKGnelakellEKLENEFELFINpIVFSEVLYVYLRL--KTGKSPYTLKKKPEIIEklELEDVLELLELF 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 488762512  74 NIIPIDEKILREAlFSPVKDY----EDAVIEVSSVKNSIDYIISRNlGDFKSA 122
Cdd:cd18677   79 KILEINEEILELA-LELIEKYgllpNDALILATCKYYGIKKIATFD-SDFKRV 129
 
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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