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Conserved domains on  [gi|2524725010|ref|WP_286746196|]
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MULTISPECIES: putative toxin-antitoxin system toxin component, PIN family [Roseivirga]

Protein Classification

PIN domain-containing protein( domain architecture ID 1000090)

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
COG5378 COG5378
Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]; ...
 1-139 1.60e-40

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


:

Pssm-ID: 444143  Cd Length: 141  Bit Score: 132.33  E-value: 1.60e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524725010   1 MNVVVDTNIIFSAILSSKGKIGNLLLNSvnRFEFFTTSYLLEELDTHHDKLKKISGINDSDIKYLKRILFNHIEFIdPNL 80
Cdd:COG5378     2 MKLVVDANILFSALLGGKSRIRRLLLNL--ELELYTPEYALDELEKHLEKIAKKSGLSEDELAQALDLLLSRINIV-PEE 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2524725010  81 IHPDNWQNAYNLVKDIDENDTPFVALSLEIQAYLWTGDKKLnraLKQKGVNWILTTNEL 139
Cdd:COG5378    79 IYNDYLEEAYELIPDRDPDDTPFVALALALDAPIWTGDKDL---FGGLGFVKTWTTDEL 134
 
Name Accession Description Interval E-value
COG5378 COG5378
Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]; ...
 1-139 1.60e-40

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


Pssm-ID: 444143  Cd Length: 141  Bit Score: 132.33  E-value: 1.60e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524725010   1 MNVVVDTNIIFSAILSSKGKIGNLLLNSvnRFEFFTTSYLLEELDTHHDKLKKISGINDSDIKYLKRILFNHIEFIdPNL 80
Cdd:COG5378     2 MKLVVDANILFSALLGGKSRIRRLLLNL--ELELYTPEYALDELEKHLEKIAKKSGLSEDELAQALDLLLSRINIV-PEE 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2524725010  81 IHPDNWQNAYNLVKDIDENDTPFVALSLEIQAYLWTGDKKLnraLKQKGVNWILTTNEL 139
Cdd:COG5378    79 IYNDYLEEAYELIPDRDPDDTPFVALALALDAPIWTGDKDL---FGGLGFVKTWTTDEL 134
PIN_2 pfam10130
PIN domain; Members of this family of bacterial domains are predicted to be RNases (from ...
 4-121 8.85e-27

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


Pssm-ID: 370825  Cd Length: 132  Bit Score: 97.09  E-value: 8.85e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524725010   4 VVDTNIIFSAILsskGKIGNLLLNSVNRFEFFTTSYLLEELDTHHDKLKKISGINDSDIKYLKRILFNHIEFIDPNLIhP 83
Cdd:pfam10130   1 VVDANIVISALL---SRIKRRLLFFAPNLELFVPEFAVDELEKHLEALVRKSKLSEEELQELLDLLFTKIHIVNESLY-E 76

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 2524725010  84 DNWQNAYNLVKDIDENDTPFVALSLEIQAYLWTGDKKL 121
Cdd:pfam10130  77 PKEKEARERIPRRDPDDWPFVALALLLDAPIWTEDKDF 114
PIN_VapC-like cd18715
uncharacterized subfamily of the VapC (virulence-associated protein C)-like family of the PIN ...
 3-120 2.33e-05

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: 41.13  E-value: 2.33e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524725010   3 VVVDTNIIFSAILSSKGKIGNLL-LNSVNRFEFFTTSYLLEELD--THHDKLKKI-----SG--INDsdikyLKRILFnh 72
Cdd:cd18715     2 VVLDTNILISALISPHSPPDLIYrAWRAGRFELVTSEEQLDELRrvSRYPKLQARlqpaeAGtmVNN-----LRRLAV-- 74

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 2524725010  73 ieFIDPNLIhpdnwqnaYNLVKDIDENdtPFVALSLEIQA-YLWTGDKK 120
Cdd:cd18715    75 --MLERLPI--------VEESPDPDDN--FLLAMALAGDAdYLVTGDKR 111
 
Name Accession Description Interval E-value
COG5378 COG5378
Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]; ...
 1-139 1.60e-40

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


Pssm-ID: 444143  Cd Length: 141  Bit Score: 132.33  E-value: 1.60e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524725010   1 MNVVVDTNIIFSAILSSKGKIGNLLLNSvnRFEFFTTSYLLEELDTHHDKLKKISGINDSDIKYLKRILFNHIEFIdPNL 80
Cdd:COG5378     2 MKLVVDANILFSALLGGKSRIRRLLLNL--ELELYTPEYALDELEKHLEKIAKKSGLSEDELAQALDLLLSRINIV-PEE 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2524725010  81 IHPDNWQNAYNLVKDIDENDTPFVALSLEIQAYLWTGDKKLnraLKQKGVNWILTTNEL 139
Cdd:COG5378    79 IYNDYLEEAYELIPDRDPDDTPFVALALALDAPIWTGDKDL---FGGLGFVKTWTTDEL 134
PIN_2 pfam10130
PIN domain; Members of this family of bacterial domains are predicted to be RNases (from ...
 4-121 8.85e-27

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


Pssm-ID: 370825  Cd Length: 132  Bit Score: 97.09  E-value: 8.85e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524725010   4 VVDTNIIFSAILsskGKIGNLLLNSVNRFEFFTTSYLLEELDTHHDKLKKISGINDSDIKYLKRILFNHIEFIDPNLIhP 83
Cdd:pfam10130   1 VVDANIVISALL---SRIKRRLLFFAPNLELFVPEFAVDELEKHLEALVRKSKLSEEELQELLDLLFTKIHIVNESLY-E 76

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 2524725010  84 DNWQNAYNLVKDIDENDTPFVALSLEIQAYLWTGDKKL 121
Cdd:pfam10130  77 PKEKEARERIPRRDPDDWPFVALALLLDAPIWTEDKDF 114
COG1569 COG1569
Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]; ...
 1-142 2.15e-10

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


Pssm-ID: 441177  Cd Length: 136  Bit Score: 54.85  E-value: 2.15e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524725010   1 MNVVVDTNIIFSAILSSKGKIGnLLLNSV--NRFEFFTTSYLLEELdthHDKLKKIS-GINDSDIKYLKRILFNHIEFID 77
Cdd:COG1569     1 MRVVLDTNVLVSALLSPDGAPA-RLLRAAlaGRFTLLVSAAILEEL---ERVLARPKfKLSPEEREELLAALLALAELVE 76

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2524725010  78 PnlihPDNWqnaynLVKDIDENDTPFVALSLEIQA-YLWTGDKKLNRALKQKGVNwILTTNELMEI 142
Cdd:COG1569    77 P----TPLW-----RPICRDPDDNKFLELAVAGGAdYLVTGDKDLLSLARFFGIR-ILTPAEFLEL 132
PIN_VapC-like cd18715
uncharacterized subfamily of the VapC (virulence-associated protein C)-like family of the PIN ...
 3-120 2.33e-05

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: 41.13  E-value: 2.33e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524725010   3 VVVDTNIIFSAILSSKGKIGNLL-LNSVNRFEFFTTSYLLEELD--THHDKLKKI-----SG--INDsdikyLKRILFnh 72
Cdd:cd18715     2 VVLDTNILISALISPHSPPDLIYrAWRAGRFELVTSEEQLDELRrvSRYPKLQARlqpaeAGtmVNN-----LRRLAV-- 74

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 2524725010  73 ieFIDPNLIhpdnwqnaYNLVKDIDENdtPFVALSLEIQA-YLWTGDKK 120
Cdd:cd18715    75 --MLERLPI--------VEESPDPDDN--FLLAMALAGDAdYLVTGDKR 111
PIN_3 pfam13470
PIN domain; Members of this family of bacterial domains are predicted to be RNases (from ...
 3-120 2.98e-04

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: 38.09  E-value: 2.98e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524725010   3 VVVDTNIIFSAILSSK-----GKIGNLLLNsvNRFEFFTTSYLLEELDT--HHDKLKKISGINDSDIKYLKRILFNHIEF 75
Cdd:pfam13470   2 VVLDTNVLLDALLFRSpfsasAKLLDLLAR--GRIQLVVSAAILDEYEYvlTRPLAKPRLALSIEERLLLLALVAAVVDP 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2524725010  76 IDPNLIHPdNWQnaynlvkdiDENDTPFVALSLEIQA-YLWTGDKK 120
Cdd:pfam13470  80 DLPLAPVS-ACR---------DPEDAHFLEAAVAGQAdFIVTRNRA 115
PIN_Pae0151-like cd09873
VapC-like PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; ...
 103-132 8.04e-04

VapC-like PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of the Pyrobaculum aerophilum proteins, Pae0151 and Pae2754, and 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: 350221  Cd Length: 128  Bit Score: 37.13  E-value: 8.04e-04
                          10        20        30
                  ....*....|....*....|....*....|
gi 2524725010 103 FVALSLEIQAYLWTGDKKLNRALKQKGVNW 132
Cdd:cd09873    99 YLALAERLGAPLVTADRKLARAAKAAGVKL 128
 
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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