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Conserved domains on  [gi|489498494|ref|WP_003403405|]
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MULTISPECIES: PIN domain-containing protein [Mycobacterium]

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
PIN_SF super family cl28905
PIN (PilT N terminus) domain: Superfamily; The PIN (PilT N terminus) domain belongs to a large ...
 10-108 5.64e-23

PIN (PilT N terminus) domain: Superfamily; The PIN (PilT N terminus) domain belongs to a large nuclease superfamily, and were originally named for their sequence similarity to the N-terminal domain of an annotated pili biogenesis protein, PilT, a domain fusion between a PIN-domain and a PilT ATPase domain. 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. The PIN domain superfamily includes: the FEN-like PIN domain family such as the PIN domains of Flap endonuclease-1 (FEN1), exonuclease-1 (EXO1), Mkt1, Gap Endonuclease 1 (GEN1), and Xeroderma pigmentosum complementation group G (XPG) nuclease, 5'-3' exonucleases of DNA polymerase I and bacteriophage T4- and T5-5' nucleases; the VapC-like PIN domain family which includes 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; the LabA-like PIN domain family which includes the PIN domains of Synechococcus elongatus LabA (low-amplitude and bright); the PRORP-Zc3h12a-like PIN domain family which includes the PIN domains of RNase P (PRORP), ribonuclease Zc3h12a; and Bacillus subtilis YacP/Rae1-like PIN domains. It also includes the Mut7-C PIN domain family, which is not represented here as it is a shortened version of the PIN fold and lacks a core strand and helix (H3 and S3). The Mut7-C PIN domain family includes the C-terminus of Caenorhabditis elegans exonuclease Mut-7.


The actual alignment was detected with superfamily member cd18768:

Pssm-ID: 475124  Cd Length: 123  Bit Score: 85.93  E-value: 5.64e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489498494  10 LLDTSVFIARESGGAIAD--LPERVALSVMTIGELQLGLLNAGDSATRSRRADTLALARTADQIPVSEAVMISLARLVAD 87
Cdd:cd18768    1 LADTSVFIAQESGRALDGdlLPDEIAVSVVTLAELRAGVLAARDLATRARRLATLQLAADLEPLPIDDAVAAAWARLRLE 80

                         90       100
                 ....*....|....*....|.
gi 489498494  88 CRAAGvrRSVKLTDALIAATA 108
Cdd:cd18768   81 LRESG--RRMRVNDSWIAATA 99
 
Name Accession Description Interval E-value
PIN_MtVapC4-C5-like cd18768
VapC-like PIN domain of Mycobacterium tuberculosis VapC4, VapC5, and related proteins; This ...
 10-108 5.64e-23

VapC-like PIN domain of Mycobacterium tuberculosis VapC4, VapC5, and related proteins; This subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis VapC4 and VapC5 toxin of the VapBC toxin/antitoxin (TA) system. This family belongs to the PIN_VapC4-5_FitB-like subfamily of 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. M. tuberculosis VapC4 interacts with, and cleaves tRNA44Cys-GCA. M. tuberculosis VapC5 has endonucleolytic activity with RNA, this activity is low with dsRNA, and no activity has been demonstrated on dsDNA. 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: 350335  Cd Length: 123  Bit Score: 85.93  E-value: 5.64e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489498494  10 LLDTSVFIARESGGAIAD--LPERVALSVMTIGELQLGLLNAGDSATRSRRADTLALARTADQIPVSEAVMISLARLVAD 87
Cdd:cd18768    1 LADTSVFIAQESGRALDGdlLPDEIAVSVVTLAELRAGVLAARDLATRARRLATLQLAADLEPLPIDDAVAAAWARLRLE 80

                         90       100
                 ....*....|....*....|.
gi 489498494  88 CRAAGvrRSVKLTDALIAATA 108
Cdd:cd18768   81 LRESG--RRMRVNDSWIAATA 99
VapC COG1487
Ribonuclease/mRNA interferase VapC, contains PIN domain [Defense mechanisms];
10-108 9.76e-13

Ribonuclease/mRNA interferase VapC, contains PIN domain [Defense mechanisms];


Pssm-ID: 441096  Cd Length: 128  Bit Score: 59.88  E-value: 9.76e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489498494  10 LLDTSVFIA---RESGGAIADL----PERVALSVMTIGELQLGLLNAGDSAtrsRRADTLALARTADQIPVSEAVMISLA 82
Cdd:COG1487    2 LLDTNVLIDllrGRPPAVLAWLaeleAGELAISAITLAELLYGARRSPDAK---RRAALEAFLEAFPVLPFDAEAARRAG 78

                         90       100
                 ....*....|....*....|....*.
gi 489498494  83 RLVADCRAAGvrRSVKLTDALIAATA 108
Cdd:COG1487   79 ELRAALRRAG--RPIGLADLLIAATA 102
 
Name Accession Description Interval E-value
PIN_MtVapC4-C5-like cd18768
VapC-like PIN domain of Mycobacterium tuberculosis VapC4, VapC5, and related proteins; This ...
 10-108 5.64e-23

VapC-like PIN domain of Mycobacterium tuberculosis VapC4, VapC5, and related proteins; This subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis VapC4 and VapC5 toxin of the VapBC toxin/antitoxin (TA) system. This family belongs to the PIN_VapC4-5_FitB-like subfamily of 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. M. tuberculosis VapC4 interacts with, and cleaves tRNA44Cys-GCA. M. tuberculosis VapC5 has endonucleolytic activity with RNA, this activity is low with dsRNA, and no activity has been demonstrated on dsDNA. 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: 350335  Cd Length: 123  Bit Score: 85.93  E-value: 5.64e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489498494  10 LLDTSVFIARESGGAIAD--LPERVALSVMTIGELQLGLLNAGDSATRSRRADTLALARTADQIPVSEAVMISLARLVAD 87
Cdd:cd18768    1 LADTSVFIAQESGRALDGdlLPDEIAVSVVTLAELRAGVLAARDLATRARRLATLQLAADLEPLPIDDAVAAAWARLRLE 80

                         90       100
                 ....*....|....*....|.
gi 489498494  88 CRAAGvrRSVKLTDALIAATA 108
Cdd:cd18768   81 LRESG--RRMRVNDSWIAATA 99
PIN_MtVapC4-C5_like cd18732
VapC-like PIN domain of Mycobacterium tuberculosis VapC4, VapC5, and related proteins; This ...
 10-108 1.59e-16

VapC-like PIN domain of Mycobacterium tuberculosis VapC4, VapC5, and related proteins; This subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis VapC4 and VapC5 toxin of the VapBC toxin/antitoxin (TA) system. This family belongs to the PIN_VapC4-5_FitB-like subfamily of 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. M. tuberculosis VapC4 interacts with, and cleaves tRNA44Cys-GCA. M. tuberculosis VapC5 has endonucleolytic activity with RNA, this activity is low with dsRNA, and no activity has been demonstrated on dsDNA. 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: 350299  Cd Length: 124  Bit Score: 69.22  E-value: 1.59e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489498494  10 LLDTSVFIAREsGGAIADLPERVALSVMTIGELQLGLLNAGDSATRSRRADTLALARTADQIPVSEAVMISLARLVADCR 89
Cdd:cd18732    1 LLDTSVVIDLE-RGDPADLPDEVAISAITLAELAFGVLAADTRAERAQRLQRLLQAEDFDPLPFDAEAARAYGRLAAAVR 79

                         90
                 ....*....|....*....
gi 489498494  90 AAGVRRSVKLTDALIAATA 108
Cdd:cd18732   80 AAGRKPRPRANDLLIAATA 98
VapC COG1487
Ribonuclease/mRNA interferase VapC, contains PIN domain [Defense mechanisms];
10-108 9.76e-13

Ribonuclease/mRNA interferase VapC, contains PIN domain [Defense mechanisms];


Pssm-ID: 441096  Cd Length: 128  Bit Score: 59.88  E-value: 9.76e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489498494  10 LLDTSVFIA---RESGGAIADL----PERVALSVMTIGELQLGLLNAGDSAtrsRRADTLALARTADQIPVSEAVMISLA 82
Cdd:COG1487    2 LLDTNVLIDllrGRPPAVLAWLaeleAGELAISAITLAELLYGARRSPDAK---RRAALEAFLEAFPVLPFDAEAARRAG 78

                         90       100
                 ....*....|....*....|....*.
gi 489498494  83 RLVADCRAAGvrRSVKLTDALIAATA 108
Cdd:COG1487   79 ELRAALRRAG--RPIGLADLLIAATA 102
PIN_VapC4-5_FitB-like cd09881
VapC-like PIN domain of Mycobacterium tuberculosis VapC4 and VapC5, and Neisseria gonorrhoeae ...
 10-108 8.69e-08

VapC-like PIN domain of Mycobacterium tuberculosis VapC4 and VapC5, and Neisseria gonorrhoeae FitB and related proteins; This family includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis VapC4 and VapC5 ribonuclease toxins of the VapBC toxin/antitoxin (TA) system, and Neisseria gonorrhoeae FitB toxin of the FitAB TA system. This family belongs to the VapC-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 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: 350229  Cd Length: 127  Bit Score: 46.71  E-value: 8.69e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489498494  10 LLDTSVFIA--RESGGAIAD-----LPERVALSVMTIGELQLGLLNAGDSAtrSRRADTLALARTADQIPVSEAVMISLA 82
Cdd:cd09881    1 LLDTNICIDllRGRPPSVLErleelLPEDLAISSITLAELLYGAEKSQRPE--KNLAALEAFLSRLEVLPFDEEAAEIYG 78

                         90       100
                 ....*....|....*....|....*.
gi 489498494  83 RLVADCRAAGvrRSVKLTDALIAATA 108
Cdd:cd09881   79 EIRAELEKKG--KPIGDNDLLIAATA 102
PIN_VapC4-5_FitB-like cd18746
uncharacterized subgroup of the PIN_VapC4-5_FitB-like subfamily of the PIN domain superfamily; ...
 10-108 1.15e-07

uncharacterized subgroup of the PIN_VapC4-5_FitB-like subfamily of the PIN domain superfamily; The PIN_VapC4-5_FitB-like subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis VapC4 and VapC5 ribonuclease toxins of the VapBC toxin/antitoxin (TA) system, and Neisseria gonorrhoeae FitB toxin of the FitAB TA system. This subfamily belongs to the VapC-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 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: 350313 [Multi-domain]  Cd Length: 133  Bit Score: 46.66  E-value: 1.15e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489498494  10 LLDTSV---FIARESGGAIADL-----PERVALSVMTIGELQLG--LLNAGDsatrSRRADTLA------LARTADQI-P 72
Cdd:cd18746    1 LLDTNViseLRKPRPDPGVVAWlaavdEDDLFLSVITIGEIRKGieRLRRRD----PARAARLEawldglLLRFAGRIlP 76

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 489498494  73 VSEAVMISLARLVADcraagVRRSVKLTDALIAATA 108
Cdd:cd18746   77 VDAEVARRWGRLHAP-----APAPLPVADALIAATA 107
PIN_VapC4-5_FitB-like cd18738
uncharacterized subgroup of the PIN_VapC4-5_FitB-like subfamily of the PIN domain superfamily; ...
 10-108 1.77e-06

uncharacterized subgroup of the PIN_VapC4-5_FitB-like subfamily of the PIN domain superfamily; The PIN_VapC4-5_FitB-like subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis VapC4 and VapC5 ribonuclease toxins of the VapBC toxin/antitoxin (TA) system, and Neisseria gonorrhoeae FitB toxin of the FitAB TA system. This subfamily belongs to the VapC-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 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: 350305  Cd Length: 118  Bit Score: 43.29  E-value: 1.77e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489498494  10 LLDTSVFI------ARESGGAIADLPERVALSVMTIGELqLGLlnagDSATRSRRADTLALARTADQIPVSEAVmislAR 83
Cdd:cd18738    1 LLDTNIIIyylkgeLPESLEELLEELNEPAISVITKIEL-LGW----PKLTPEEEEEIEDFLSLAEVIPLDDEI----AR 71

                         90       100
                 ....*....|....*....|....*
gi 489498494  84 LVADCRAagvRRSVKLTDALIAATA 108
Cdd:cd18738   72 KTIELRK---QYKIKLPDAIIAATA 93
PIN_VapC4-5_FitB-like cd18741
uncharacterized subgroup of the PIN_VapC4-5_FitB-like subfamily of the PIN domain superfamily; ...
 10-110 6.54e-06

uncharacterized subgroup of the PIN_VapC4-5_FitB-like subfamily of the PIN domain superfamily; The PIN_VapC4-5_FitB-like subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis VapC4 and VapC5 ribonuclease toxins of the VapBC toxin/antitoxin (TA) system, and Neisseria gonorrhoeae FitB toxin of the FitAB TA system. This subfamily belongs to the VapC-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 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: 350308  Cd Length: 120  Bit Score: 41.71  E-value: 6.54e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489498494  10 LLDTSVFI--ARESGGAIADL----PERVALSVMTIGELQLGLLNAgdsatrSRRADTLALARTADQIPVSEAVMISLAR 83
Cdd:cd18741    1 LLDTDILIdfLRGNPSAAEKLlellGGNLAISVITVAELYAGARNK------KELEKLEKLLSLFEVIPVDEEIAELAGE 74

                         90       100
                 ....*....|....*....|....*..
gi 489498494  84 LVADCRAagvRRSVKLTDALIAATAEI 110
Cdd:cd18741   75 LRRKYRK---SHGLGLPDALIAATALE 98
VapC COG1848
VapC family ribonuclease, toxin component of the VapBC toxin-antitoxin module, contains PIN ...
 10-108 2.93e-05

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


Pssm-ID: 441453  Cd Length: 134  Bit Score: 40.35  E-value: 2.93e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489498494  10 LLDTSVFIA---RESGG---------AIADLPERVALSVMTIGELQLGLLNAGDSATRSRRADTLALARTADQIPVSEAV 77
Cdd:COG1848    3 LLDTNVLIYaleGDSPFherarelleRAEEGEEELYTSPLVLAEVLYVLTRPGGLSLEEARELLEALLSNIEVVPVDEEI 82

                         90       100       110
                 ....*....|....*....|....*....|.
gi 489498494  78 MISLARLVAdcraagvRRSVKLTDALIAATA 108
Cdd:COG1848   83 LEEAAELLA-------KYGLRLNDALHLATA 106
PIN_VapC4-5_FitB-like cd18740
uncharacterized subgroup of the PIN_VapC4-5_FitB-like subfamily of the PIN domain superfamily; ...
 10-108 5.82e-05

uncharacterized subgroup of the PIN_VapC4-5_FitB-like subfamily of the PIN domain superfamily; The PIN_VapC4-5_FitB-like subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis VapC4 and VapC5 ribonuclease toxins of the VapBC toxin/antitoxin (TA) system, and Neisseria gonorrhoeae FitB toxin of the FitAB TA system. This subfamily belongs to the VapC-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 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: 350307  Cd Length: 126  Bit Score: 39.46  E-value: 5.82e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489498494  10 LLDT---SVFIARESGGAIADL----PERVALSVMTIGELQLGLLNAGDSATRSRRADtlALARTADQIPVSEAVMISLA 82
Cdd:cd18740    1 MLDTntvSHIIKGRPPAVRERLravpMASICISSITEAELLYGLAKRPEAKRLHAAVR--EFLLRVDVLPWDSSVARTYG 78

                         90       100
                 ....*....|....*....|....*.
gi 489498494  83 RLVADCRAAGvrRSVKLTDALIAATA 108
Cdd:cd18740   79 DLRAALEAQG--KTLGPLDMMIAAHA 102
PIN_RfVapC1-like cd18733
VapC-like PIN domain of Rickettsia felis VapC1 and related proteins; This subfamily includes ...
 10-108 1.61e-04

VapC-like PIN domain of Rickettsia felis VapC1 and related proteins; This subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Rickettsia felis VapC1, a ribonuclease toxin of the VapBC toxin/antitoxin (TA) system. This subfamily belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC TA systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include 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: 350300  Cd Length: 131  Bit Score: 38.35  E-value: 1.61e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489498494  10 LLDTSVFIARESGG------AIADLPERVALSVMTIGELQLGLLNAGDSATRSRRAdtlALARTA-DQIPV---SEAVMI 79
Cdd:cd18733    3 IIDTSVFIAAERGRldlealQQERPDEDVYISAITASELLHGVHRAKTPERRARRE---AFVEAIlEAFPVldfDLEVAR 79

                         90       100
                 ....*....|....*....|....*....
gi 489498494  80 SLARLVADCRAAGVrrSVKLTDALIAATA 108
Cdd:cd18733   80 THARLWAELAKRGI--TIGAHDLLIAATA 106
PIN_MtVapC3_VapC21-like cd18755
VapC-like PIN domain of Mycobacterium tuberculosis VapC3, VapC21 and related proteins; This ...
 10-109 4.04e-03

VapC-like PIN domain of Mycobacterium tuberculosis VapC3, VapC21 and related proteins; This subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis VapC3 and VapC21 toxins. It belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is a 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 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: 350322  Cd Length: 127  Bit Score: 34.46  E-value: 4.04e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489498494  10 LLDTSVFIAR---ESGGAIADLPERVALSVMTIGELQLgLLNAGDSATRSRRADTLalaRTADQIPVSEAVM---ISLAR 83
Cdd:cd18755    1 LIDTSALVRLlrpAVAARWEPLIERGLVAICGPTELEI-LYSARSAADRDRLLRLL---RAFPWLPVPDEAWrraLEVQR 76

                         90       100
                 ....*....|....*....|....*.
gi 489498494  84 LVADcraAGVRRSVKLTDALIAATAE 109
Cdd:cd18755   77 LLAR---RGQHRAASIPDLLIAATAE 99
PIN_VapC4-5_FitB-like cd18750
uncharacterized subgroup of the PIN_VapC4-5_FitB-like subfamily of the PIN domain superfamily; ...
 10-108 4.15e-03

uncharacterized subgroup of the PIN_VapC4-5_FitB-like subfamily of the PIN domain superfamily; The PIN_VapC4-5_FitB-like subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis VapC4 and VapC5 ribonuclease toxins of the VapBC toxin/antitoxin (TA) system, and Neisseria gonorrhoeae FitB toxin of the FitAB TA system. This subfamily belongs to the VapC-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 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: 350317  Cd Length: 127  Bit Score: 34.52  E-value: 4.15e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489498494  10 LLDTSV--FIARESGGAIADL----PERVALSVMTIGELQLGL-LNAgdSATRSRRADTLALARTADQIPVSEAVMISLA 82
Cdd:cd18750    1 LLDTCTisDFVRGNPNTLERLkstsPSLIAISSITVMEIEYGLrLNP--QRAKKLRPILEAFLSSITILPFDEEDAIAAA 78

                         90       100
                 ....*....|....*....|....*.
gi 489498494  83 RLVADCRAAGvrRSVKLTDALIAATA 108
Cdd:cd18750   79 AIRAALKKQG--TPIGAYDVLIAGTA 102
PIN_NgFitB-like cd18731
VapC-like PIN domain of Neisseria gonorrhoeae FitB and related proteins; This subfamily ...
 29-108 5.63e-03

VapC-like PIN domain of Neisseria gonorrhoeae FitB and related proteins; This subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Neisseria gonorrhoeae FitB toxin of the FitAB toxin/antitoxin (TA) system. This subfamily belongs to the VapC-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. In N. gonorrhoeae, FitA and FitB form a heterodimer: FitA is the DNA binding subunit and FitB contains a ribonuclease activity that is blocked by the presence of FitA. A tetramer of FitAB heterodimers binds DNA from the fitAB upstream promoter region with high affinity. This results in both sequestration of FitAB and repression of fitAB transcription. It is thought that FitAB release from the DNA and subsequent dissociation both slows N. gonorrhoeae replication and transcytosis by an as yet undefined mechanism. The toxin M. tuberculosis VapC is a structural homolog of N. gonorrhoeae FitB, but their antitoxin partners, VapB and FitA, respectively, differ structurally. 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: 350298  Cd Length: 136  Bit Score: 33.93  E-value: 5.63e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489498494  29 PERVALSVMTIGELQLGLLNAGDSATRSR---RADTLALARTADQI-PVSEAVMISLARLVADCRAAGvrRSVKLTDALI 104
Cdd:cd18731   29 AEDLYLTAITVAELLYGIALLPDGRRRDAleaAAEALLAEDFAGRIlPFDAAAAEAYAEIVAARRRAG--RPISVADAQI 106


                 ....
gi 489498494 105 AATA 108
Cdd:cd18731  107 AAIA 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.
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