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Conserved domains on  [gi|18414678|ref|NP_567502|]
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YbaK/aminoacyl-tRNA synthetase-associated domain-containing protein [Arabidopsis thaliana]

Protein Classification

YbaK/EbsC family protein( domain architecture ID 10137825)

YbaK/EbsC family protein hydrolyzes misacylated Cys-tRNA(Pro) or Ala-tRNA(Pro); similar to Bacillus thuringiensis aminoacyl-tRNA editing enzymes YbaK-like, ProX-like protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YbaK_like cd04332
YbaK-like. The YbaK family of deacylase domains includes the INS amino acid-editing domain of ...
 83-229 5.23e-21

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: 84.90  E-value: 5.23e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18414678  83 ESRRDVLGASsVDHLCKSIVLVNtqaasnildcsdpNNSKYYVVVVQYTARFNAEAVKQFLyslnegkipkKRFNLRLAP 162
Cdd:cd04332  15 EEAAEALGVP-PGQIAKTLVLKD-------------DKGGLVLVVVPGDHELDLKKLAKAL----------GAKKLRLAS 70

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 18414678 163 EETSIKLTGFEHNGVTCIGMKTNIPVILDEAITKLkpDFFWLGGGEIDLKLGVRTSEFLEFVKPFIV 229
Cdd:cd04332  71 EEELEELTGCEPGGVGPFGLKKGVPVVVDESLLEL--EDVYVGAGERGADLHLSPADLLRLLGEAEV 135
 
Name Accession Description Interval E-value
YbaK_like cd04332
YbaK-like. The YbaK family of deacylase domains includes the INS amino acid-editing domain of ...
 83-229 5.23e-21

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: 84.90  E-value: 5.23e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18414678  83 ESRRDVLGASsVDHLCKSIVLVNtqaasnildcsdpNNSKYYVVVVQYTARFNAEAVKQFLyslnegkipkKRFNLRLAP 162
Cdd:cd04332  15 EEAAEALGVP-PGQIAKTLVLKD-------------DKGGLVLVVVPGDHELDLKKLAKAL----------GAKKLRLAS 70

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 18414678 163 EETSIKLTGFEHNGVTCIGMKTNIPVILDEAITKLkpDFFWLGGGEIDLKLGVRTSEFLEFVKPFIV 229
Cdd:cd04332  71 EEELEELTGCEPGGVGPFGLKKGVPVVVDESLLEL--EDVYVGAGERGADLHLSPADLLRLLGEAEV 135
EbsC COG2606
Cys-tRNA(Pro) deacylase, prolyl-tRNA editing enzyme YbaK/EbsC [Translation, ribosomal ...
 122-232 2.33e-10

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: 57.02  E-value: 2.33e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18414678 122 KYYVVVVQYTARFNAEAVKQFLyslneGKipKKrfnLRLAPEETSIKLTGFEHNGVTCIGMKTNIPVILDEAITKLkpDF 201
Cdd:COG2606  51 GPVLAVVPGDRRLDLKKLAAAL-----GA--KK---VEMADPEEVERLTGYEVGGVSPFGLKKGLPVYVDESLLEF--DE 118

                        90       100       110
                ....*....|....*....|....*....|.
gi 18414678 202 FWLGGGEIDLKLGVRTSEFLEFVKPFIVPCS 232
Cdd:COG2606 119 VYVSAGDRGLLVELAPADLARLTGATVADIA 149
tRNA_edit pfam04073
Aminoacyl-tRNA editing domain; This domain is found either on its own or in association with ...
 97-223 4.96e-08

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: 49.91  E-value: 4.96e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18414678    97 LCKSIVLVNtqaasnildcsdpNNSKYYVVVVQYTARfnaeavkqflysLNEGKIpKKRFN---LRLAPEETSIKLTGFE 173
Cdd:pfam04073  21 IAKTLVLKD-------------KKGKYVLVVVPGDRE------------VDLKKL-AKLLGvkrLRLASEEELLELTGVE 74

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 18414678   174 HNGVTCIGMKT-NIPVILDEAITKLkpDFFWLGGGEIDLKLGVRTSEFLEF 223
Cdd:pfam04073  75 PGGVTPFGLKAkGVPVLVDESLKDL--PDVVVGAGENGATLRLSNADLRKL 123
 
Name Accession Description Interval E-value
YbaK_like cd04332
YbaK-like. The YbaK family of deacylase domains includes the INS amino acid-editing domain of ...
 83-229 5.23e-21

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: 84.90  E-value: 5.23e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18414678  83 ESRRDVLGASsVDHLCKSIVLVNtqaasnildcsdpNNSKYYVVVVQYTARFNAEAVKQFLyslnegkipkKRFNLRLAP 162
Cdd:cd04332  15 EEAAEALGVP-PGQIAKTLVLKD-------------DKGGLVLVVVPGDHELDLKKLAKAL----------GAKKLRLAS 70

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 18414678 163 EETSIKLTGFEHNGVTCIGMKTNIPVILDEAITKLkpDFFWLGGGEIDLKLGVRTSEFLEFVKPFIV 229
Cdd:cd04332  71 EEELEELTGCEPGGVGPFGLKKGVPVVVDESLLEL--EDVYVGAGERGADLHLSPADLLRLLGEAEV 135
EbsC COG2606
Cys-tRNA(Pro) deacylase, prolyl-tRNA editing enzyme YbaK/EbsC [Translation, ribosomal ...
 122-232 2.33e-10

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: 57.02  E-value: 2.33e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18414678 122 KYYVVVVQYTARFNAEAVKQFLyslneGKipKKrfnLRLAPEETSIKLTGFEHNGVTCIGMKTNIPVILDEAITKLkpDF 201
Cdd:COG2606  51 GPVLAVVPGDRRLDLKKLAAAL-----GA--KK---VEMADPEEVERLTGYEVGGVSPFGLKKGLPVYVDESLLEF--DE 118

                        90       100       110
                ....*....|....*....|....*....|.
gi 18414678 202 FWLGGGEIDLKLGVRTSEFLEFVKPFIVPCS 232
Cdd:COG2606 119 VYVSAGDRGLLVELAPADLARLTGATVADIA 149
tRNA_edit pfam04073
Aminoacyl-tRNA editing domain; This domain is found either on its own or in association with ...
 97-223 4.96e-08

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: 49.91  E-value: 4.96e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18414678    97 LCKSIVLVNtqaasnildcsdpNNSKYYVVVVQYTARfnaeavkqflysLNEGKIpKKRFN---LRLAPEETSIKLTGFE 173
Cdd:pfam04073  21 IAKTLVLKD-------------KKGKYVLVVVPGDRE------------VDLKKL-AKLLGvkrLRLASEEELLELTGVE 74

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 18414678   174 HNGVTCIGMKT-NIPVILDEAITKLkpDFFWLGGGEIDLKLGVRTSEFLEF 223
Cdd:pfam04073  75 PGGVTPFGLKAkGVPVLVDESLKDL--PDVVVGAGENGATLRLSNADLRKL 123
PA2301 cd04939
PA2301 is an uncharacterized Pseudomonas aeruginosa protein with a YbaK-like domain of unknown ...
 153-221 2.96e-03

PA2301 is an uncharacterized Pseudomonas aeruginosa 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: 240137  Cd Length: 139  Bit Score: 36.94  E-value: 2.96e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 18414678 153 KKRFNLR---LAPEETSIKLTGFEHNGVTCIGMKTNIPVILDEAItklkpdffwLGGGEIDLKLGVRTSEFL 221
Cdd:cd04939  62 KRRLGARkasFAPMETAVELTGMEYGGITPVGLPAGWPILVDSAV---------AERPAVVIGSGVRRSKLL 124
YbaK_deacylase cd00002
This CD includes cysteinyl-tRNA(Pro) deacylases from Haemophilus influenzae and Escherichia ...
 168-226 3.66e-03

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: 36.66  E-value: 3.66e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 18414678 168 KLTGFEHNGVTCIGMKTNIPVILDEAITKLkpDFFWLGGGEIDLKLGVRTSEFLEFVKP 226
Cdd:cd00002  91 RLTGYIRGGISPLGQKKRLPTVIDESALDL--DTIYVSAGKRGLQIELAPQDLAKLTGA 147
 
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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