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Conserved domains on  [gi|2556158967|ref|WP_303937210|]
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PIN domain-containing protein [Rothia mucilaginosa]

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 super family cl46324
PIN domain; Members of this family of bacterial domains are predicted to be RNases (from ...
 8-146 2.32e-08

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


The actual alignment was detected with superfamily member COG1569:

Pssm-ID: 480664  Cd Length: 136  Bit Score: 51.00  E-value: 2.32e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556158967   8 VLLDTNILMS-----KTLRDWILLLAVKseyEFFTPHVSSGVMDEFGYHVRRANPAISDAVLENWKQQIIRSCVsCISGF 82
Cdd:COG1569     3 VVLDTNVLVSallspDGAPARLLRAALA---GRFTLLVSAAILEELERVLARPKFKLSPEEREELLAALLALAE-LVEPT 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2556158967  83 PVEAPVSfPDTDDLHVHAAAQHGAMHALVTDDRKLLDyasteeAHNIQNYETLSADDFLMQLTE 146
Cdd:COG1569    79 PLWRPIC-RDPDDNKFLELAVAGGADYLVTGDKDLLS------LARFFGIRILTPAEFLELLRP 135
 
Name Accession Description Interval E-value
COG1569 COG1569
Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]; ...
 8-146 2.32e-08

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


Pssm-ID: 441177  Cd Length: 136  Bit Score: 51.00  E-value: 2.32e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556158967   8 VLLDTNILMS-----KTLRDWILLLAVKseyEFFTPHVSSGVMDEFGYHVRRANPAISDAVLENWKQQIIRSCVsCISGF 82
Cdd:COG1569     3 VVLDTNVLVSallspDGAPARLLRAALA---GRFTLLVSAAILEELERVLARPKFKLSPEEREELLAALLALAE-LVEPT 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2556158967  83 PVEAPVSfPDTDDLHVHAAAQHGAMHALVTDDRKLLDyasteeAHNIQNYETLSADDFLMQLTE 146
Cdd:COG1569    79 PLWRPIC-RDPDDNKFLELAVAGGADYLVTGDKDLLS------LARFFGIRILTPAEFLELLRP 135
PIN_3 pfam13470
PIN domain; Members of this family of bacterial domains are predicted to be RNases (from ...
 8-116 3.56e-08

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: 50.03  E-value: 3.56e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556158967   8 VLLDTNILMSKTLRD------WILLLAVKSEyeFFTPHVSSGVMDE----FGYHVRRANPAISDAVLEnwkQQIIRSCVS 77
Cdd:pfam13470   2 VVLDTNVLLDALLFRspfsasAKLLDLLARG--RIQLVVSAAILDEyeyvLTRPLAKPRLALSIEERL---LLLALVAAV 76

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 2556158967  78 CISGFPVEAPVSFPDTDDLHVHAAAQHGAMHALVTDDRK 116
Cdd:pfam13470  77 VDPDLPLAPVSACRDPEDAHFLEAAVAGQADFIVTRNRA 115
PINc smart00670
Large family of predicted nucleotide-binding domains; From similarities to 5'-exonucleases, ...
 8-117 7.88e-04

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: 37.79  E-value: 7.88e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556158967    8 VLLDTNILMSKTLRDwillLAVKSEYEFFTPHVSSGVMDEFGYHVRRANPAISDAVLENWKQQIIRSCVSCIsGFPVEAP 87
Cdd:smart00670   3 VVLDTNVLIDGLIRD----ALEKLLEKKGEVYIPQTVLEELEYLALRSLKKLEELALEGKIILKVLKEERIE-EEILERL 77

                           90       100       110
                   ....*....|....*....|....*....|..
gi 2556158967   88 V--SFPDTDDLHVHAAAQHGAMHALVTDDRKL 117
Cdd:smart00670  78 SlkLELLPNDALILATAKELGNVVLVTNDRDL 109
PIN_VapC-like cd18715
uncharacterized subfamily of the VapC (virulence-associated protein C)-like family of the PIN ...
 8-116 9.71e-04

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: 37.67  E-value: 9.71e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556158967   8 VLLDTNILMS-----KTLRDWILLLAVKSEYEFFTphvSSGVMDEFgyhvRRA----------NPAISDAVLENwkqqiI 72
Cdd:cd18715     2 VVLDTNILISalispHSPPDLIYRAWRAGRFELVT---SEEQLDEL----RRVsrypklqarlQPAEAGTMVNN-----L 69

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 2556158967  73 RSCVSCISGFPVEAPVsfPDTDDLHVHAAAQHGAMHALVTDDRK 116
Cdd:cd18715    70 RRLAVMLERLPIVEES--PDPDDNFLLAMALAGDADYLVTGDKR 111
 
Name Accession Description Interval E-value
COG1569 COG1569
Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]; ...
 8-146 2.32e-08

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


Pssm-ID: 441177  Cd Length: 136  Bit Score: 51.00  E-value: 2.32e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556158967   8 VLLDTNILMS-----KTLRDWILLLAVKseyEFFTPHVSSGVMDEFGYHVRRANPAISDAVLENWKQQIIRSCVsCISGF 82
Cdd:COG1569     3 VVLDTNVLVSallspDGAPARLLRAALA---GRFTLLVSAAILEELERVLARPKFKLSPEEREELLAALLALAE-LVEPT 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2556158967  83 PVEAPVSfPDTDDLHVHAAAQHGAMHALVTDDRKLLDyasteeAHNIQNYETLSADDFLMQLTE 146
Cdd:COG1569    79 PLWRPIC-RDPDDNKFLELAVAGGADYLVTGDKDLLS------LARFFGIRILTPAEFLELLRP 135
PIN_3 pfam13470
PIN domain; Members of this family of bacterial domains are predicted to be RNases (from ...
 8-116 3.56e-08

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: 50.03  E-value: 3.56e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556158967   8 VLLDTNILMSKTLRD------WILLLAVKSEyeFFTPHVSSGVMDE----FGYHVRRANPAISDAVLEnwkQQIIRSCVS 77
Cdd:pfam13470   2 VVLDTNVLLDALLFRspfsasAKLLDLLARG--RIQLVVSAAILDEyeyvLTRPLAKPRLALSIEERL---LLLALVAAV 76

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 2556158967  78 CISGFPVEAPVSFPDTDDLHVHAAAQHGAMHALVTDDRK 116
Cdd:pfam13470  77 VDPDLPLAPVSACRDPEDAHFLEAAVAGQADFIVTRNRA 115
PINc smart00670
Large family of predicted nucleotide-binding domains; From similarities to 5'-exonucleases, ...
 8-117 7.88e-04

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: 37.79  E-value: 7.88e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556158967    8 VLLDTNILMSKTLRDwillLAVKSEYEFFTPHVSSGVMDEFGYHVRRANPAISDAVLENWKQQIIRSCVSCIsGFPVEAP 87
Cdd:smart00670   3 VVLDTNVLIDGLIRD----ALEKLLEKKGEVYIPQTVLEELEYLALRSLKKLEELALEGKIILKVLKEERIE-EEILERL 77

                           90       100       110
                   ....*....|....*....|....*....|..
gi 2556158967   88 V--SFPDTDDLHVHAAAQHGAMHALVTDDRKL 117
Cdd:smart00670  78 SlkLELLPNDALILATAKELGNVVLVTNDRDL 109
PIN_VapC-like cd18715
uncharacterized subfamily of the VapC (virulence-associated protein C)-like family of the PIN ...
 8-116 9.71e-04

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: 37.67  E-value: 9.71e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556158967   8 VLLDTNILMS-----KTLRDWILLLAVKSEYEFFTphvSSGVMDEFgyhvRRA----------NPAISDAVLENwkqqiI 72
Cdd:cd18715     2 VVLDTNILISalispHSPPDLIYRAWRAGRFELVT---SEEQLDEL----RRVsrypklqarlQPAEAGTMVNN-----L 69

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 2556158967  73 RSCVSCISGFPVEAPVsfPDTDDLHVHAAAQHGAMHALVTDDRK 116
Cdd:cd18715    70 RRLAVMLERLPIVEES--PDPDDNFLLAMALAGDADYLVTGDKR 111
PIN_VapC-like cd09854
VapC-like PIN domains of VapC and Smg6 ribonucleases, ribosome assembly factor NOB1, ...
 9-122 2.68e-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: 36.87  E-value: 2.68e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556158967   9 LLDTNILMS-------KTLRDWILLLaVKSEYEFFTPHVssgVMDEFGYHVRRANPA----ISDAVLENWKQQIIRSCVS 77
Cdd:cd09854     1 VLDTNVLIAllssepeSEAAKELLAL-LLGDSELVIPPL---VLAELLRLLARERGArralEILELLRALEVVEEEPALA 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2556158967  78 CIS-GFPVEAPVSFPDTDDLHVHAAAQHGAMHALVTDDRKLLDYAS 122
Cdd:cd09854    77 EIAlEVLALGLERGLDFGDALILALAKELGGAVLVTNDRDFRRLAK 122
 
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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