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Conserved domains on  [gi|497293630|ref|WP_009607847|]
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MULTISPECIES: YbaK/EbsC family protein [Eggerthella]

Protein Classification

YbaK/EbsC family protein( domain architecture ID 10137841)

YbaK/EbsC family protein similar to Aeropyrum pernix Ape2540 YbaK a putative trans-editing enzyme for prolyl-tRNA synthetase

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
ProX_deacylase cd04333
This CD, composed mainly of bacterial single-domain proteins, includes the Thermus ...
 3-151 5.67e-66

This CD, composed mainly of bacterial single-domain proteins, includes the Thermus thermophilus (Tt) YbaK-like protein, a homolog of the trans-acting Escherichia coli YbaK Cys-tRNA(Pro) deacylase and the Agrobacterium tumefaciens ProX Ala-tRNA(Pro) deacylase and also the cis-acting prolyl-tRNA synthetase-editing domain (ProRS-INS). While ProX and ProRS-INS hydrolyze misacylated Ala-tRNA(Pro), the E. coli YbaK hydrolyzes misacylated Cys-tRNA(Pro). A few CD members are N-terminal, YbaK-ProX-like domains of an uncharacterized protein with a C-terminal, predicted Fe-S protein domain.


:

Pssm-ID: 239825 [Multi-domain]  Cd Length: 148  Bit Score: 197.34  E-value: 5.67e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497293630   3 IDKVKAFLRERGMEERVLEFETSSATVELAAQAVGCEPARIAKTLSFHVGDRVALVVAAGDARIDNPKYKARFGCKAKML 82
Cdd:cd04333    1 VERVRAFLAARGLDLEVIELPESTRTAALAAEALGCEPGQIAKSLVFRVDDEPVLVVTSGDARVDNKKFKALFGEKLKMA 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 497293630  83 AADEAEPLIGHGVGGVCPFALNEGVDVFLDESLRRFDTVYPAAGNAASAVRLTPDELERcAAPCTWVDV 151
Cdd:cd04333   81 DAEEVRELTGFAIGGVCPFGHPEPLPVYLDESLKRFDEVWAAAGTPNAAFRLTPDELER-LTGAEWVDV 148
 
Name Accession Description Interval E-value
ProX_deacylase cd04333
This CD, composed mainly of bacterial single-domain proteins, includes the Thermus ...
 3-151 5.67e-66

This CD, composed mainly of bacterial single-domain proteins, includes the Thermus thermophilus (Tt) YbaK-like protein, a homolog of the trans-acting Escherichia coli YbaK Cys-tRNA(Pro) deacylase and the Agrobacterium tumefaciens ProX Ala-tRNA(Pro) deacylase and also the cis-acting prolyl-tRNA synthetase-editing domain (ProRS-INS). While ProX and ProRS-INS hydrolyze misacylated Ala-tRNA(Pro), the E. coli YbaK hydrolyzes misacylated Cys-tRNA(Pro). A few CD members are N-terminal, YbaK-ProX-like domains of an uncharacterized protein with a C-terminal, predicted Fe-S protein domain.


Pssm-ID: 239825 [Multi-domain]  Cd Length: 148  Bit Score: 197.34  E-value: 5.67e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497293630   3 IDKVKAFLRERGMEERVLEFETSSATVELAAQAVGCEPARIAKTLSFHVGDRVALVVAAGDARIDNPKYKARFGCKAKML 82
Cdd:cd04333    1 VERVRAFLAARGLDLEVIELPESTRTAALAAEALGCEPGQIAKSLVFRVDDEPVLVVTSGDARVDNKKFKALFGEKLKMA 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 497293630  83 AADEAEPLIGHGVGGVCPFALNEGVDVFLDESLRRFDTVYPAAGNAASAVRLTPDELERcAAPCTWVDV 151
Cdd:cd04333   81 DAEEVRELTGFAIGGVCPFGHPEPLPVYLDESLKRFDEVWAAAGTPNAAFRLTPDELER-LTGAEWVDV 148
EbsC COG2606
Cys-tRNA(Pro) deacylase, prolyl-tRNA editing enzyme YbaK/EbsC [Translation, ribosomal ...
 4-153 1.56e-50

Cys-tRNA(Pro) deacylase, prolyl-tRNA editing enzyme YbaK/EbsC [Translation, ribosomal structure and biogenesis];


Pssm-ID: 442018 [Multi-domain]  Cd Length: 152  Bit Score: 158.33  E-value: 1.56e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497293630   4 DKVKAFLRERGMEERVLEFETSSATVELAAQAVGCEPARIAKTLSFHVGDRVALVVAAGDARIDNPKYKARFGC-KAKML 82
Cdd:COG2606    1 TPVRRALDAAGIPYEVVEHPEPAATAEEAAEALGVPPEQIAKTLVFRGDGGPVLAVVPGDRRLDLKKLAAALGAkKVEMA 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 497293630  83 AADEAEPLIGHGVGGVCPFALNEGVDVFLDESLRRFDTVYPAAGNAASAVRLTPDELERCAAPcTWVDVCK 153
Cdd:COG2606   81 DPEEVERLTGYEVGGVSPFGLKKGLPVYVDESLLEFDEVYVSAGDRGLLVELAPADLARLTGA-TVADIAR 150
tRNA_edit pfam04073
Aminoacyl-tRNA editing domain; This domain is found either on its own or in association with ...
 27-142 3.80e-25

Aminoacyl-tRNA editing domain; This domain is found either on its own or in association with the tRNA synthetase class II core domain (pfam00587). It is involved in the tRNA editing of mis-charged tRNAs including Cys-tRNA(Pro), Cys-tRNA(Cys), Ala-tRNA(Pro). The structure of this domain shows a novel fold.


Pssm-ID: 427693 [Multi-domain]  Cd Length: 123  Bit Score: 93.05  E-value: 3.80e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497293630   27 ATVELAAQAVGCEPARIAKTLSFHVGD-RVALVVAAGDARIDNPKYKARFGCK-AKMLAADEAEPLIGHGVGGVCPFALN 104
Cdd:pfam04073   5 ATIEELAAALGVPPGRIAKTLVLKDKKgKYVLVVVPGDREVDLKKLAKLLGVKrLRLASEEELLELTGVEPGGVTPFGLK 84

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 497293630  105 -EGVDVFLDESLRRFDTVYPAAGNAASAVRLTPDELERC 142
Cdd:pfam04073  85 aKGVPVLVDESLKDLPDVVVGAGENGATLRLSNADLRKL 123
PRK09194 PRK09194
prolyl-tRNA synthetase; Provisional
 3-116 1.28e-04

prolyl-tRNA synthetase; Provisional


Pssm-ID: 236405 [Multi-domain]  Cd Length: 565  Bit Score: 40.84  E-value: 1.28e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497293630   3 IDKVKAFLRERGMEERVLE-FETSSA-TVELAAQAVGCEPARIAKTLSFHVGDRVALVVAAGDARIDNPKYKARFGCKAK 80
Cdd:PRK09194 233 IEKAEALPPPRAAAEEALEkVDTPNAkTIEELAEFLNVPAEKTVKTLLVKADGELVAVLVRGDHELNEVKLENLLGAAPL 312

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 497293630  81 MLA-ADEAEPLIGHGVGGVCPFALNEGVDVFLDESLR 116
Cdd:PRK09194 313 ELAtEEEIRAALGAVPGFLGPVGLPKDVPIIADRSVA 349
 
Name Accession Description Interval E-value
ProX_deacylase cd04333
This CD, composed mainly of bacterial single-domain proteins, includes the Thermus ...
 3-151 5.67e-66

This CD, composed mainly of bacterial single-domain proteins, includes the Thermus thermophilus (Tt) YbaK-like protein, a homolog of the trans-acting Escherichia coli YbaK Cys-tRNA(Pro) deacylase and the Agrobacterium tumefaciens ProX Ala-tRNA(Pro) deacylase and also the cis-acting prolyl-tRNA synthetase-editing domain (ProRS-INS). While ProX and ProRS-INS hydrolyze misacylated Ala-tRNA(Pro), the E. coli YbaK hydrolyzes misacylated Cys-tRNA(Pro). A few CD members are N-terminal, YbaK-ProX-like domains of an uncharacterized protein with a C-terminal, predicted Fe-S protein domain.


Pssm-ID: 239825 [Multi-domain]  Cd Length: 148  Bit Score: 197.34  E-value: 5.67e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497293630   3 IDKVKAFLRERGMEERVLEFETSSATVELAAQAVGCEPARIAKTLSFHVGDRVALVVAAGDARIDNPKYKARFGCKAKML 82
Cdd:cd04333    1 VERVRAFLAARGLDLEVIELPESTRTAALAAEALGCEPGQIAKSLVFRVDDEPVLVVTSGDARVDNKKFKALFGEKLKMA 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 497293630  83 AADEAEPLIGHGVGGVCPFALNEGVDVFLDESLRRFDTVYPAAGNAASAVRLTPDELERcAAPCTWVDV 151
Cdd:cd04333   81 DAEEVRELTGFAIGGVCPFGHPEPLPVYLDESLKRFDEVWAAAGTPNAAFRLTPDELER-LTGAEWVDV 148
EbsC COG2606
Cys-tRNA(Pro) deacylase, prolyl-tRNA editing enzyme YbaK/EbsC [Translation, ribosomal ...
 4-153 1.56e-50

Cys-tRNA(Pro) deacylase, prolyl-tRNA editing enzyme YbaK/EbsC [Translation, ribosomal structure and biogenesis];


Pssm-ID: 442018 [Multi-domain]  Cd Length: 152  Bit Score: 158.33  E-value: 1.56e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497293630   4 DKVKAFLRERGMEERVLEFETSSATVELAAQAVGCEPARIAKTLSFHVGDRVALVVAAGDARIDNPKYKARFGC-KAKML 82
Cdd:COG2606    1 TPVRRALDAAGIPYEVVEHPEPAATAEEAAEALGVPPEQIAKTLVFRGDGGPVLAVVPGDRRLDLKKLAAALGAkKVEMA 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 497293630  83 AADEAEPLIGHGVGGVCPFALNEGVDVFLDESLRRFDTVYPAAGNAASAVRLTPDELERCAAPcTWVDVCK 153
Cdd:COG2606   81 DPEEVERLTGYEVGGVSPFGLKKGLPVYVDESLLEFDEVYVSAGDRGLLVELAPADLARLTGA-TVADIAR 150
YbaK_like cd04332
YbaK-like. The YbaK family of deacylase domains includes the INS amino acid-editing domain of ...
 16-149 9.67e-33

YbaK-like. The YbaK family of deacylase domains includes the INS amino acid-editing domain of the bacterial class II prolyl tRNA synthetase (ProRS), and it's trans-acting homologs, YbaK, ProX, and PrdX. The primary function of INS is to hydrolyze mischarged cysteinyl-tRNA(Pro)'s, thus helping ensure the fidelity of translation. Organisms whose ProRS lacks the INS domain express an INS homolog in trans (e.g. YbaK, ProX, or PrdX).


Pssm-ID: 239824 [Multi-domain]  Cd Length: 136  Bit Score: 112.64  E-value: 9.67e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497293630  16 EERVLEFETSSATVELAAQAVGCEPARIAKTLSFHV-GDRVALVVAAGDARIDNPKYKARFGC-KAKMLAADEAEPLIGH 93
Cdd:cd04332    1 EYLEYEHTPGAKTIEEAAEALGVPPGQIAKTLVLKDdKGGLVLVVVPGDHELDLKKLAKALGAkKLRLASEEELEELTGC 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 497293630  94 GVGGVCPFALNEGVDVFLDESLRRFDTVYPAAGNAASAVRLTPDELERCAAPCTWV 149
Cdd:cd04332   81 EPGGVGPFGLKKGVPVVVDESLLELEDVYVGAGERGADLHLSPADLLRLLGEAEVA 136
tRNA_edit pfam04073
Aminoacyl-tRNA editing domain; This domain is found either on its own or in association with ...
 27-142 3.80e-25

Aminoacyl-tRNA editing domain; This domain is found either on its own or in association with the tRNA synthetase class II core domain (pfam00587). It is involved in the tRNA editing of mis-charged tRNAs including Cys-tRNA(Pro), Cys-tRNA(Cys), Ala-tRNA(Pro). The structure of this domain shows a novel fold.


Pssm-ID: 427693 [Multi-domain]  Cd Length: 123  Bit Score: 93.05  E-value: 3.80e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497293630   27 ATVELAAQAVGCEPARIAKTLSFHVGD-RVALVVAAGDARIDNPKYKARFGCK-AKMLAADEAEPLIGHGVGGVCPFALN 104
Cdd:pfam04073   5 ATIEELAAALGVPPGRIAKTLVLKDKKgKYVLVVVPGDREVDLKKLAKLLGVKrLRLASEEELLELTGVEPGGVTPFGLK 84

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 497293630  105 -EGVDVFLDESLRRFDTVYPAAGNAASAVRLTPDELERC 142
Cdd:pfam04073  85 aKGVPVLVDESLKDLPDVVVGAGENGATLRLSNADLRKL 123
YbaK_deacylase cd00002
This CD includes cysteinyl-tRNA(Pro) deacylases from Haemophilus influenzae and Escherichia ...
 9-151 1.58e-12

This CD includes cysteinyl-tRNA(Pro) deacylases from Haemophilus influenzae and Escherichia coli and other related bacterial proteins. These trans-acting, single-domain proteins are homologs of ProX and also the cis-acting prolyl-tRNA synthetase (ProRS) inserted (INS) editing domain. The bacterial amino acid trans-editing enzyme YbaK is a deacylase that hydrolyzes cysteinyl-tRNA(Pro)'s mischarged by prolyl-tRNA synthetase. YbaK also hydrolyzes glycyl-tRNA's, alanyl-tRNA's, seryl-tRNA's, and prolyl-tRNA's. YbaK is homologous to the INS domain of prolyl-tRNA synthetase (ProRS) as well as the trans-editing enzyme ProX of Aeropyrum pernix which hydrolyzes alanyl-tRNA's and glycyl-tRNA's.


Pssm-ID: 237976 [Multi-domain]  Cd Length: 152  Bit Score: 61.31  E-value: 1.58e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497293630   9 FLRERGMEERVLEFETSSATV--ELAAQAVGCEPARIAKTLSFHvGDRVALVVAA--GDARIDNPKYKARFGCK-AKMLA 83
Cdd:cd00002    7 LLDKAKIPYELHEYEHDEDASdgLEAAEKLGLDPEQVFKTLVVE-GDKKGLVVAVvpVDEELDLKKLAKALGAKkVEMAP 85

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 497293630  84 ADEAEPLIGHGVGGVCPFALNEGVDVFLDESLRRFDTVYPAAGNAASAVRLTPDELERcAAPCTWVDV 151
Cdd:cd00002   86 PKDAERLTGYIRGGISPLGQKKRLPTVIDESALDLDTIYVSAGKRGLQIELAPQDLAK-LTGAKFADI 152
YeaK cd04336
YeaK is an uncharacterized Echerichia coli protein with a YbaK-like domain of unknown function. ...
 4-145 6.31e-08

YeaK is an uncharacterized Echerichia coli protein with a YbaK-like domain of unknown function. The YbaK-like domain family includes the INS amino acid-editing domain of the bacterial class II prolyl tRNA synthetase (ProRS), and it's trans-acting homologs, YbaK, and ProX. The primary function of INS is to hydrolyze mischarged cysteinyl-tRNA(Pro)'s, thus helping ensure the fidelity of translation. Organisms whose ProRS lacks the INS domain express a single-domain INS homolog such as YbaK, ProX, or PrdX which supplies the function of INS in trans.


Pssm-ID: 239828 [Multi-domain]  Cd Length: 153  Bit Score: 48.88  E-value: 6.31e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497293630   4 DKVKAFLRERGMEERVLEFETSSATVElAAQAVGCEPARIAKTLSFHV---GDRVALVVAAGDARIDNPKYKARFGC-KA 79
Cdd:cd04336    2 ERLQELLNTNGARFRVLDHPPEGTSEE-VAAIRGTELGQGAKALLCKVkdgSRRFVLAVLPADKKLDLKAVAAAVGGkKA 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 497293630  80 KMLAADEAEPLIGHGVGGVCPFALNEGVDVFLDESLR-RFDTVYPAAGNAASAVRLTPDELERCAAP 145
Cdd:cd04336   81 DLASPEEAEELTGCVIGAVPPFSFDPKLKLIADPSLLdRGDEIAFNAGRLDASVVLDTADYLRIARP 147
PRK09194 PRK09194
prolyl-tRNA synthetase; Provisional
 3-116 1.28e-04

prolyl-tRNA synthetase; Provisional


Pssm-ID: 236405 [Multi-domain]  Cd Length: 565  Bit Score: 40.84  E-value: 1.28e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497293630   3 IDKVKAFLRERGMEERVLE-FETSSA-TVELAAQAVGCEPARIAKTLSFHVGDRVALVVAAGDARIDNPKYKARFGCKAK 80
Cdd:PRK09194 233 IEKAEALPPPRAAAEEALEkVDTPNAkTIEELAEFLNVPAEKTVKTLLVKADGELVAVLVRGDHELNEVKLENLLGAAPL 312

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 497293630  81 MLA-ADEAEPLIGHGVGGVCPFALNEGVDVFLDESLR 116
Cdd:PRK09194 313 ELAtEEEIRAALGAVPGFLGPVGLPKDVPIIADRSVA 349
PRK10670 PRK10670
Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase YbaK;
32-141 6.04e-03

Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase YbaK;


Pssm-ID: 182634  Cd Length: 159  Bit Score: 35.11  E-value: 6.04e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497293630  32 AAQAVGCEPARIAKTLSFHV-GDRVALVVAAG--DARIDNPKYKARFGCKAkmlaADEAEPLI-----GHGVGGVCPFAL 103
Cdd:PRK10670  33 VVRKLGLNADQVYKTLLVAVnGDMKHLAVAVTpvAGQLDLKKVAKALGAKK----VEMADPMVaqrstGYLVGGISPLGQ 108

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 497293630 104 NEGVDVFLDESLRRFDTVYPAAGNAASAVRLTPDELER 141
Cdd:PRK10670 109 KKRLPTVIDAPAQEFATIYVSGGKRGLDIELAAGDLAK 146
 
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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