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Conserved domains on  [gi|487750223|ref|WP_001832102|]
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MULTISPECIES: YaiI/YqxD family protein [Staphylococcus]

Protein Classification

DUF188 domain-containing protein( domain architecture ID 10011261)

uncharacterized DUF188 domain-containing protein similar to Escherichia coli YaiI

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK00124 PRK00124
YaiI/YqxD family protein;
3-149 7.12e-76

YaiI/YqxD family protein;


:

Pssm-ID: 178882 [Multi-domain]  Cd Length: 151  Bit Score: 222.43  E-value: 7.12e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487750223   3 TNVIIDGDACPVVNSVIELTKGTGIFVTILRSFSHFSQQIQPEHVKIVYVDDGPDAVDYKIVELASNNDIVITQDYGLAS 82
Cdd:PRK00124   1 MKIYVDADACPVKDIIIRVAERHGIPVTLVASFNHFLRVPYSPFIRTVYVDAGFDAADNEIVQLAEKGDIVITQDYGLAA 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 487750223  83 LLIDKVHTVMHHKGNIYHSNNIQSLLDQRYLNAQIRRRGGRHKGPPPFTTEDRLKFEHAFRKIINQI 149
Cdd:PRK00124  81 LALEKGAIVLNPRGYIYTNDNIDQLLAMRDLMATLRRSGIRTGGPKPFTQEDRSRFEAELDKLIRRI 147
 
Name Accession Description Interval E-value
PRK00124 PRK00124
YaiI/YqxD family protein;
3-149 7.12e-76

YaiI/YqxD family protein;


Pssm-ID: 178882 [Multi-domain]  Cd Length: 151  Bit Score: 222.43  E-value: 7.12e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487750223   3 TNVIIDGDACPVVNSVIELTKGTGIFVTILRSFSHFSQQIQPEHVKIVYVDDGPDAVDYKIVELASNNDIVITQDYGLAS 82
Cdd:PRK00124   1 MKIYVDADACPVKDIIIRVAERHGIPVTLVASFNHFLRVPYSPFIRTVYVDAGFDAADNEIVQLAEKGDIVITQDYGLAA 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 487750223  83 LLIDKVHTVMHHKGNIYHSNNIQSLLDQRYLNAQIRRRGGRHKGPPPFTTEDRLKFEHAFRKIINQI 149
Cdd:PRK00124  81 LALEKGAIVLNPRGYIYTNDNIDQLLAMRDLMATLRRSGIRTGGPKPFTQEDRSRFEAELDKLIRRI 147
YaiI COG1671
Uncharacterized conserved protein YaiI, UPF0178 family [Function unknown];
1-149 4.79e-60

Uncharacterized conserved protein YaiI, UPF0178 family [Function unknown];


Pssm-ID: 441277  Cd Length: 149  Bit Score: 182.23  E-value: 4.79e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487750223   1 MKtnVIIDGDACPVV-NSVIELTKGTGIFVTILRSFSHFSQQiqPEHVKIVYVDDGPDAVDYKIVELASNNDIVITQDYG 79
Cdd:COG1671    1 MK--IWVDADACPVVkEIIFRVAERYGIPVTLVANQSHRIPP--SPYIETVVVDAGFDAADDYIVNRAEPGDLVITQDIP 76

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487750223  80 LASLLIDKVHTVMHHKGNIYHSNNIQSLLDQRYLNAQIRRRGGRHKGPPPFTTEDRLKFEHAFRKIINQI 149
Cdd:COG1671   77 LAARVLEKGALVLNPRGELYTEENIGELLAMRDLMAKLRRSGGRTGGPKPFSKEDRQRFANALDRLLARA 146
DUF188 pfam02639
Uncharacterized BCR, YaiI/YqxD family COG1671;
18-147 1.96e-53

Uncharacterized BCR, YaiI/YqxD family COG1671;


Pssm-ID: 426896  Cd Length: 130  Bit Score: 164.96  E-value: 1.96e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487750223   18 VIELTKGTGIFVTILRSFSHFSQQiqPEHVKIVYVDDGPDAVDYKIVELASNNDIVITQDYGLASLLIDKVHTVMHHKGN 97
Cdd:pfam02639   2 IFRVAERHGIPVTLVANQNHRVPS--SPLIETVVVDAGFDAADDYIAELAEPGDLVITQDIPLAARVLGKGAYVLNPRGE 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 487750223   98 IYHSNNIQSLLDQRYLNAQIRRRGGRHKGPPPFTTEDRLKFEHAFRKIIN 147
Cdd:pfam02639  80 LYTEENIGELLAMRDLMAKLRRAGGRTGGPKPFSKEDRSRFANALDRLLA 129
PIN_YqxD-like cd18720
LabA-like PIN domain of uncharacterized Bacillus subtilis YqxD and related proteins; This ...
 7-99 1.42e-21

LabA-like PIN domain of uncharacterized Bacillus subtilis YqxD and related proteins; This subfamily includes the PIN domain of uncharacterized Bacillus subtilis YqxD (also known as YqfM) and Escherichia coli YaiI. Firmicute, such as Bacillus and Listeria, YqxD proteins are encoded within RNA polymerase major sigma43 operons, whereas E. coli YaiL is transcribed as a mono cistron. This subfamily belongs to LabA-like PIN domain family which includes Synechococcus elongatus PCC 7942 LabA, human ZNF451, uncharacterized Bacillus subtilis YqxD and Escherichia coli YaiI, and the N-terminal domain of a well-conserved group of mainly bacterial proteins with no defined function, which contain a C-terminal LabA_like_C domain. Curiously, a gene labeled NicB from Pseudomonas putida S16, which is described as a putative NADH-dependent hydroxylase involved in the microbial degradation of nicotine also falls into the LabA-like PIN family. The PIN (PilT N terminus) 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: 350287  Cd Length: 96  Bit Score: 82.90  E-value: 1.42e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487750223   7 IDGDACPVVNSVI-----ELTKGTGIFVTilrsfSHFSQQIQPEHVKIVYVDDGPDAVDYKIVELASNNDIVITQDYGLA 81
Cdd:cd18720    4 VDADACPVKIKEIlfraaERLQIPVIFVA-----NQPLRLPPSPLIRWIVVDSGFDAADDYIVEHVEPGDLVITADIPLA 78

                         90
                 ....*....|....*...
gi 487750223  82 SLLIDKVHTVMHHKGNIY 99
Cdd:cd18720   79 ALVVEKGAYVLNPRGELY 96
 
Name Accession Description Interval E-value
PRK00124 PRK00124
YaiI/YqxD family protein;
3-149 7.12e-76

YaiI/YqxD family protein;


Pssm-ID: 178882 [Multi-domain]  Cd Length: 151  Bit Score: 222.43  E-value: 7.12e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487750223   3 TNVIIDGDACPVVNSVIELTKGTGIFVTILRSFSHFSQQIQPEHVKIVYVDDGPDAVDYKIVELASNNDIVITQDYGLAS 82
Cdd:PRK00124   1 MKIYVDADACPVKDIIIRVAERHGIPVTLVASFNHFLRVPYSPFIRTVYVDAGFDAADNEIVQLAEKGDIVITQDYGLAA 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 487750223  83 LLIDKVHTVMHHKGNIYHSNNIQSLLDQRYLNAQIRRRGGRHKGPPPFTTEDRLKFEHAFRKIINQI 149
Cdd:PRK00124  81 LALEKGAIVLNPRGYIYTNDNIDQLLAMRDLMATLRRSGIRTGGPKPFTQEDRSRFEAELDKLIRRI 147
YaiI COG1671
Uncharacterized conserved protein YaiI, UPF0178 family [Function unknown];
1-149 4.79e-60

Uncharacterized conserved protein YaiI, UPF0178 family [Function unknown];


Pssm-ID: 441277  Cd Length: 149  Bit Score: 182.23  E-value: 4.79e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487750223   1 MKtnVIIDGDACPVV-NSVIELTKGTGIFVTILRSFSHFSQQiqPEHVKIVYVDDGPDAVDYKIVELASNNDIVITQDYG 79
Cdd:COG1671    1 MK--IWVDADACPVVkEIIFRVAERYGIPVTLVANQSHRIPP--SPYIETVVVDAGFDAADDYIVNRAEPGDLVITQDIP 76

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487750223  80 LASLLIDKVHTVMHHKGNIYHSNNIQSLLDQRYLNAQIRRRGGRHKGPPPFTTEDRLKFEHAFRKIINQI 149
Cdd:COG1671   77 LAARVLEKGALVLNPRGELYTEENIGELLAMRDLMAKLRRSGGRTGGPKPFSKEDRQRFANALDRLLARA 146
DUF188 pfam02639
Uncharacterized BCR, YaiI/YqxD family COG1671;
18-147 1.96e-53

Uncharacterized BCR, YaiI/YqxD family COG1671;


Pssm-ID: 426896  Cd Length: 130  Bit Score: 164.96  E-value: 1.96e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487750223   18 VIELTKGTGIFVTILRSFSHFSQQiqPEHVKIVYVDDGPDAVDYKIVELASNNDIVITQDYGLASLLIDKVHTVMHHKGN 97
Cdd:pfam02639   2 IFRVAERHGIPVTLVANQNHRVPS--SPLIETVVVDAGFDAADDYIAELAEPGDLVITQDIPLAARVLGKGAYVLNPRGE 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 487750223   98 IYHSNNIQSLLDQRYLNAQIRRRGGRHKGPPPFTTEDRLKFEHAFRKIIN 147
Cdd:pfam02639  80 LYTEENIGELLAMRDLMAKLRRAGGRTGGPKPFSKEDRSRFANALDRLLA 129
PIN_YqxD-like cd18720
LabA-like PIN domain of uncharacterized Bacillus subtilis YqxD and related proteins; This ...
 7-99 1.42e-21

LabA-like PIN domain of uncharacterized Bacillus subtilis YqxD and related proteins; This subfamily includes the PIN domain of uncharacterized Bacillus subtilis YqxD (also known as YqfM) and Escherichia coli YaiI. Firmicute, such as Bacillus and Listeria, YqxD proteins are encoded within RNA polymerase major sigma43 operons, whereas E. coli YaiL is transcribed as a mono cistron. This subfamily belongs to LabA-like PIN domain family which includes Synechococcus elongatus PCC 7942 LabA, human ZNF451, uncharacterized Bacillus subtilis YqxD and Escherichia coli YaiI, and the N-terminal domain of a well-conserved group of mainly bacterial proteins with no defined function, which contain a C-terminal LabA_like_C domain. Curiously, a gene labeled NicB from Pseudomonas putida S16, which is described as a putative NADH-dependent hydroxylase involved in the microbial degradation of nicotine also falls into the LabA-like PIN family. The PIN (PilT N terminus) 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: 350287  Cd Length: 96  Bit Score: 82.90  E-value: 1.42e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487750223   7 IDGDACPVVNSVI-----ELTKGTGIFVTilrsfSHFSQQIQPEHVKIVYVDDGPDAVDYKIVELASNNDIVITQDYGLA 81
Cdd:cd18720    4 VDADACPVKIKEIlfraaERLQIPVIFVA-----NQPLRLPPSPLIRWIVVDSGFDAADDYIVEHVEPGDLVITADIPLA 78

                         90
                 ....*....|....*...
gi 487750223  82 SLLIDKVHTVMHHKGNIY 99
Cdd:cd18720   79 ALVVEKGAYVLNPRGELY 96
 
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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