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Conserved domains on  [gi|446080290|ref|WP_000158145|]
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MULTISPECIES: YaiI/YqxD family protein [Escherichia]

Protein Classification

YaiI/YqxD family protein( domain architecture ID 10004144)

YaiI/YqxD family protein is a PIN (PilT N terminus) domain-containing protein; similar to Escherichia coli YaiI and Bacillus subtilis YqxD

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YaiI COG1671
Uncharacterized conserved protein YaiI, UPF0178 family [Function unknown];
1-143 2.45e-88

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


:

Pssm-ID: 441277  Cd Length: 149  Bit Score: 253.87  E-value: 2.45e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446080290   1 MTIWVDADACPnVIKEILYRAAERMQLPLVLVANQSLRVPPSRFIRTLRVAAGFDVADNEIVRQCEAGDLVITADIPLAA 80
Cdd:COG1671    1 MKIWVDADACP-VVKEIIFRVAERYGIPVTLVANQSHRIPPSPYIETVVVDAGFDAADDYIVNRAEPGDLVITQDIPLAA 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446080290  81 EAIEKGAAALNPRGERYTPATIRERLTMRDFMDTLRASGIQTGGPDSLSQRDRQAFAAELEKW 143
Cdd:COG1671   80 RVLEKGALVLNPRGELYTEENIGELLAMRDLMAKLRRSGGRTGGPKPFSKEDRQRFANALDRL 142
 
Name Accession Description Interval E-value
YaiI COG1671
Uncharacterized conserved protein YaiI, UPF0178 family [Function unknown];
1-143 2.45e-88

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


Pssm-ID: 441277  Cd Length: 149  Bit Score: 253.87  E-value: 2.45e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446080290   1 MTIWVDADACPnVIKEILYRAAERMQLPLVLVANQSLRVPPSRFIRTLRVAAGFDVADNEIVRQCEAGDLVITADIPLAA 80
Cdd:COG1671    1 MKIWVDADACP-VVKEIIFRVAERYGIPVTLVANQSHRIPPSPYIETVVVDAGFDAADDYIVNRAEPGDLVITQDIPLAA 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446080290  81 EAIEKGAAALNPRGERYTPATIRERLTMRDFMDTLRASGIQTGGPDSLSQRDRQAFAAELEKW 143
Cdd:COG1671   80 RVLEKGALVLNPRGELYTEENIGELLAMRDLMAKLRRSGGRTGGPKPFSKEDRQRFANALDRL 142
PRK00124 PRK00124
YaiI/YqxD family protein;
1-151 1.69e-81

YaiI/YqxD family protein;


Pssm-ID: 178882 [Multi-domain]  Cd Length: 151  Bit Score: 236.68  E-value: 1.69e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446080290   1 MTIWVDADACPnvIKEILYRAAERMQLPLVLVA--NQSLRVPPSRFIRTLRVAAGFDVADNEIVRQCEAGDLVITADIPL 78
Cdd:PRK00124   1 MKIYVDADACP--VKDIIIRVAERHGIPVTLVAsfNHFLRVPYSPFIRTVYVDAGFDAADNEIVQLAEKGDIVITQDYGL 78

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446080290  79 AAEAIEKGAAALNPRGERYTPATIRERLTMRDFMDTLRASGIQTGGPDSLSQRDRQAFAAELEKWWLEVQRSR 151
Cdd:PRK00124  79 AALALEKGAIVLNPRGYIYTNDNIDQLLAMRDLMATLRRSGIRTGGPKPFTQEDRSRFEAELDKLIRRIKRLR 151
DUF188 pfam02639
Uncharacterized BCR, YaiI/YqxD family COG1671;
17-143 9.77e-67

Uncharacterized BCR, YaiI/YqxD family COG1671;


Pssm-ID: 426896  Cd Length: 130  Bit Score: 198.86  E-value: 9.77e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446080290   17 ILYRAAERMQLPLVLVANQSLRVPPSRFIRTLRVAAGFDVADNEIVRQCEAGDLVITADIPLAAEAIEKGAAALNPRGER 96
Cdd:pfam02639   1 EIFRVAERHGIPVTLVANQNHRVPSSPLIETVVVDAGFDAADDYIAELAEPGDLVITQDIPLAARVLGKGAYVLNPRGEL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 446080290   97 YTPATIRERLTMRDFMDTLRASGIQTGGPDSLSQRDRQAFAAELEKW 143
Cdd:pfam02639  81 YTEENIGELLAMRDLMAKLRRAGGRTGGPKPFSKEDRSRFANALDRL 127
PIN_YqxD-like cd18720
LabA-like PIN domain of uncharacterized Bacillus subtilis YqxD and related proteins; This ...
 2-97 5.98e-60

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: 180.36  E-value: 5.98e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446080290   2 TIWVDADACPNVIKEILYRAAERMQLPLVLVANQSLRVPPSRFIRTLRVAAGFDVADNEIVRQCEAGDLVITADIPLAAE 81
Cdd:cd18720    1 KIWVDADACPVKIKEILFRAAERLQIPVIFVANQPLRLPPSPLIRWIVVDSGFDAADDYIVEHVEPGDLVITADIPLAAL 80

                         90
                 ....*....|....*.
gi 446080290  82 AIEKGAAALNPRGERY 97
Cdd:cd18720   81 VVEKGAYVLNPRGELY 96
 
Name Accession Description Interval E-value
YaiI COG1671
Uncharacterized conserved protein YaiI, UPF0178 family [Function unknown];
1-143 2.45e-88

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


Pssm-ID: 441277  Cd Length: 149  Bit Score: 253.87  E-value: 2.45e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446080290   1 MTIWVDADACPnVIKEILYRAAERMQLPLVLVANQSLRVPPSRFIRTLRVAAGFDVADNEIVRQCEAGDLVITADIPLAA 80
Cdd:COG1671    1 MKIWVDADACP-VVKEIIFRVAERYGIPVTLVANQSHRIPPSPYIETVVVDAGFDAADDYIVNRAEPGDLVITQDIPLAA 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446080290  81 EAIEKGAAALNPRGERYTPATIRERLTMRDFMDTLRASGIQTGGPDSLSQRDRQAFAAELEKW 143
Cdd:COG1671   80 RVLEKGALVLNPRGELYTEENIGELLAMRDLMAKLRRSGGRTGGPKPFSKEDRQRFANALDRL 142
PRK00124 PRK00124
YaiI/YqxD family protein;
1-151 1.69e-81

YaiI/YqxD family protein;


Pssm-ID: 178882 [Multi-domain]  Cd Length: 151  Bit Score: 236.68  E-value: 1.69e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446080290   1 MTIWVDADACPnvIKEILYRAAERMQLPLVLVA--NQSLRVPPSRFIRTLRVAAGFDVADNEIVRQCEAGDLVITADIPL 78
Cdd:PRK00124   1 MKIYVDADACP--VKDIIIRVAERHGIPVTLVAsfNHFLRVPYSPFIRTVYVDAGFDAADNEIVQLAEKGDIVITQDYGL 78

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446080290  79 AAEAIEKGAAALNPRGERYTPATIRERLTMRDFMDTLRASGIQTGGPDSLSQRDRQAFAAELEKWWLEVQRSR 151
Cdd:PRK00124  79 AALALEKGAIVLNPRGYIYTNDNIDQLLAMRDLMATLRRSGIRTGGPKPFTQEDRSRFEAELDKLIRRIKRLR 151
DUF188 pfam02639
Uncharacterized BCR, YaiI/YqxD family COG1671;
17-143 9.77e-67

Uncharacterized BCR, YaiI/YqxD family COG1671;


Pssm-ID: 426896  Cd Length: 130  Bit Score: 198.86  E-value: 9.77e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446080290   17 ILYRAAERMQLPLVLVANQSLRVPPSRFIRTLRVAAGFDVADNEIVRQCEAGDLVITADIPLAAEAIEKGAAALNPRGER 96
Cdd:pfam02639   1 EIFRVAERHGIPVTLVANQNHRVPSSPLIETVVVDAGFDAADDYIAELAEPGDLVITQDIPLAARVLGKGAYVLNPRGEL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 446080290   97 YTPATIRERLTMRDFMDTLRASGIQTGGPDSLSQRDRQAFAAELEKW 143
Cdd:pfam02639  81 YTEENIGELLAMRDLMAKLRRAGGRTGGPKPFSKEDRSRFANALDRL 127
PIN_YqxD-like cd18720
LabA-like PIN domain of uncharacterized Bacillus subtilis YqxD and related proteins; This ...
 2-97 5.98e-60

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: 180.36  E-value: 5.98e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446080290   2 TIWVDADACPNVIKEILYRAAERMQLPLVLVANQSLRVPPSRFIRTLRVAAGFDVADNEIVRQCEAGDLVITADIPLAAE 81
Cdd:cd18720    1 KIWVDADACPVKIKEILFRAAERLQIPVIFVANQPLRLPPSPLIRWIVVDSGFDAADDYIVEHVEPGDLVITADIPLAAL 80

                         90
                 ....*....|....*.
gi 446080290  82 AIEKGAAALNPRGERY 97
Cdd:cd18720   81 VVEKGAYVLNPRGELY 96
PIN_LabA-like cd06167
PIN domain of Synechococcus elongatus LabA (low-amplitude and bright) and related proteins; ...
 2-97 1.87e-14

PIN domain of Synechococcus elongatus LabA (low-amplitude and bright) and related proteins; The LabA-like PIN domain family includes Synechococcus elongatus PCC 7942 LabA which participates in cyanobacterial circadian timing. It is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system. In particular, LabA seems necessary for KaiC-dependent repression of gene expression. This family also includes the N-terminal domain of limkain b1, a human autoantigen associated with cytoplasmic vesicles. Other members are the LabA-like PIN domains of 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 this family.


Pssm-ID: 350201  Cd Length: 113  Bit Score: 65.13  E-value: 1.87e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446080290   2 TIWVDADACPNVIK-EILYRAAERMQL----PLVLVANQSLRVPPSR--FIRTLRVAAGF-DVADNEIVRQCEAGD---- 69
Cdd:cd06167    1 GVLVDADNCSNGFGaLILRRYAGLFLQmgfeKYANINAQPLLVPPSNnrGFTVIRVAAKRkDAADVALVRQAGRLAytga 80

                         90       100       110
                 ....*....|....*....|....*....|...
gi 446080290  70 ----LVITADIPLAAEAIEKGAAA-LNPRGERY 97
Cdd:cd06167   81 pdtvVLVSGDKLDFSDLIEKAKEAgLNVIVVGP 113
PIN_VapC_like cd18702
uncharacterized subfamily of the VapC (virulence-associated protein C)-like family of the PIN ...
 41-91 7.87e-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. Matelska et al. recently classified PIN-like domains into distinct groups; this subgroup includes some sequences belonging to one of these, PIN_19


Pssm-ID: 350269  Cd Length: 139  Bit Score: 34.46  E-value: 7.87e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 446080290  41 PSRFIRTLRVAAGFDVADNEIVRQCEAGDLVITADIPLAAEAIEKGAAALN 91
Cdd:cd18702   89 PSKDIAASPEFFRLGLTDAGILELAKSGYLLLTDDLDLYLYAQKLGIDAIN 139
 
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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