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Conserved domains on  [gi|754692835|ref|WP_042070318|]
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YbaK/EbsC family protein [Aeromonas enteropelogenes]

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 ...
 18-148 4.01e-30

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: 106.47  E-value: 4.01e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754692835  18 PHQRYQHEPilDYATDEQVKARLGWQAE-FSKTLFLKFKDGRFALLLTHRDGRLDNKAVKATLGAKP-SICTAEEMQAQI 95
Cdd:cd04332    1 EYLEYEHTP--GAKTIEEAAEALGVPPGqIAKTLVLKDDKGGLVLVVVPGDHELDLKKLAKALGAKKlRLASEEELEELT 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 754692835  96 GCLPGAVCPFLPRADIPLLIDPQLLAHHAFTWTPGHPEQTFLLETAHLPRVLA 148
Cdd:cd04332   79 GCEPGGVGPFGLKKGVPVVVDESLLELEDVYVGAGERGADLHLSPADLLRLLG 131
 
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 ...
 18-148 4.01e-30

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: 106.47  E-value: 4.01e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754692835  18 PHQRYQHEPilDYATDEQVKARLGWQAE-FSKTLFLKFKDGRFALLLTHRDGRLDNKAVKATLGAKP-SICTAEEMQAQI 95
Cdd:cd04332    1 EYLEYEHTP--GAKTIEEAAEALGVPPGqIAKTLVLKDDKGGLVLVVVPGDHELDLKKLAKALGAKKlRLASEEELEELT 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 754692835  96 GCLPGAVCPFLPRADIPLLIDPQLLAHHAFTWTPGHPEQTFLLETAHLPRVLA 148
Cdd:cd04332   79 GCEPGGVGPFGLKKGVPVVVDESLLELEDVYVGAGERGADLHLSPADLLRLLG 131
EbsC COG2606
Cys-tRNA(Pro) deacylase, prolyl-tRNA editing enzyme YbaK/EbsC [Translation, ribosomal ...
 15-155 1.92e-22

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: 87.07  E-value: 1.92e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754692835  15 ADLPHQRYQHEPilDYATDEQVKARLGWQAE-FSKTLFLKFkDGRFALLLTHRDGRLDNKAVKATLGA-KPSICTAEEMQ 92
Cdd:COG2606   10 AGIPYEVVEHPE--PAATAEEAAEALGVPPEqIAKTLVFRG-DGGPVLAVVPGDRRLDLKKLAAALGAkKVEMADPEEVE 86

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 754692835  93 AQIGCLPGAVCPFLPRADIPLLIDPQLLAHHAFTWTPGHPEQTFLLETAHLPRVLAQLPCEVS 155
Cdd:COG2606   87 RLTGYEVGGVSPFGLKKGLPVYVDESLLEFDEVYVSAGDRGLLVELAPADLARLTGATVADIA 149
tRNA_edit pfam04073
Aminoacyl-tRNA editing domain; This domain is found either on its own or in association with ...
 24-145 3.49e-20

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: 80.34  E-value: 3.49e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754692835   24 HEPIldyATDEQVKARLGWQAE-FSKTLFLKFKDGRFALLLTHRDGRLDNKAVKATLGAKP-SICTAEEMQAQIGCLPGA 101
Cdd:pfam04073   1 HPPA---ATIEELAAALGVPPGrIAKTLVLKDKKGKYVLVVVPGDREVDLKKLAKLLGVKRlRLASEEELLELTGVEPGG 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 754692835  102 VCPF-LPRADIPLLIDPQLLAHHAFTWTPGHPEQTFLLETAHLPR 145
Cdd:pfam04073  78 VTPFgLKAKGVPVLVDESLKDLPDVVVGAGENGATLRLSNADLRK 122
 
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 ...
 18-148 4.01e-30

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: 106.47  E-value: 4.01e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754692835  18 PHQRYQHEPilDYATDEQVKARLGWQAE-FSKTLFLKFKDGRFALLLTHRDGRLDNKAVKATLGAKP-SICTAEEMQAQI 95
Cdd:cd04332    1 EYLEYEHTP--GAKTIEEAAEALGVPPGqIAKTLVLKDDKGGLVLVVVPGDHELDLKKLAKALGAKKlRLASEEELEELT 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 754692835  96 GCLPGAVCPFLPRADIPLLIDPQLLAHHAFTWTPGHPEQTFLLETAHLPRVLA 148
Cdd:cd04332   79 GCEPGGVGPFGLKKGVPVVVDESLLELEDVYVGAGERGADLHLSPADLLRLLG 131
EbsC COG2606
Cys-tRNA(Pro) deacylase, prolyl-tRNA editing enzyme YbaK/EbsC [Translation, ribosomal ...
 15-155 1.92e-22

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: 87.07  E-value: 1.92e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754692835  15 ADLPHQRYQHEPilDYATDEQVKARLGWQAE-FSKTLFLKFkDGRFALLLTHRDGRLDNKAVKATLGA-KPSICTAEEMQ 92
Cdd:COG2606   10 AGIPYEVVEHPE--PAATAEEAAEALGVPPEqIAKTLVFRG-DGGPVLAVVPGDRRLDLKKLAAALGAkKVEMADPEEVE 86

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 754692835  93 AQIGCLPGAVCPFLPRADIPLLIDPQLLAHHAFTWTPGHPEQTFLLETAHLPRVLAQLPCEVS 155
Cdd:COG2606   87 RLTGYEVGGVSPFGLKKGLPVYVDESLLEFDEVYVSAGDRGLLVELAPADLARLTGATVADIA 149
tRNA_edit pfam04073
Aminoacyl-tRNA editing domain; This domain is found either on its own or in association with ...
 24-145 3.49e-20

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: 80.34  E-value: 3.49e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754692835   24 HEPIldyATDEQVKARLGWQAE-FSKTLFLKFKDGRFALLLTHRDGRLDNKAVKATLGAKP-SICTAEEMQAQIGCLPGA 101
Cdd:pfam04073   1 HPPA---ATIEELAAALGVPPGrIAKTLVLKDKKGKYVLVVVPGDREVDLKKLAKLLGVKRlRLASEEELLELTGVEPGG 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 754692835  102 VCPF-LPRADIPLLIDPQLLAHHAFTWTPGHPEQTFLLETAHLPR 145
Cdd:pfam04073  78 VTPFgLKAKGVPVLVDESLKDLPDVVVGAGENGATLRLSNADLRK 122
YeaK cd04336
YeaK is an uncharacterized Echerichia coli protein with a YbaK-like domain of unknown function. ...
 48-124 1.46e-12

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: 61.59  E-value: 1.46e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754692835  48 KTLFLKFKDG--RFALLLTHRDGRLDNKAVKATLGA-KPSICTAEEMQAQIGCLPGAVCPFLPRADIPLLIDPQLLAHHA 124
Cdd:cd04336   42 KALLCKVKDGsrRFVLAVLPADKKLDLKAVAAAVGGkKADLASPEEAEELTGCVIGAVPPFSFDPKLKLIADPSLLDRGD 121
ProX_deacylase cd04333
This CD, composed mainly of bacterial single-domain proteins, includes the Thermus ...
 48-122 4.82e-12

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: 59.82  E-value: 4.82e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 754692835  48 KTLFLKFkDGRFALLLTHRDGRLDNKAVKATLGAKPSICTAEEMQAQIGCLPGAVCPFLPRADIPLLIDPQLLAH 122
Cdd:cd04333   43 KSLVFRV-DDEPVLVVTSGDARVDNKKFKALFGEKLKMADAEEVRELTGFAIGGVCPFGHPEPLPVYLDESLKRF 116
PrdX_deacylase cd04335
This CD includes bacterial (Agrobacterium tumefaciens and Caulobacter crescentus ProX, and ...
 11-147 4.30e-11

This CD includes bacterial (Agrobacterium tumefaciens and Caulobacter crescentus ProX, and Clostridium sticklandii PrdX) and eukaryotic (Plasmodium falciparum N-terminal ProRS editing domain) sequences. The C. sticklandii PrdX protein, a homolog of the YbaK and ProX proteins, and the prolyl-tRNA synthetase-editing domain (ProRS-INS), specifically hydrolyzes Ala-tRNA(Pro). In this CD, many of the eukaryotic editing domains are N-terminal and cis-acting, expressed from a multidomain ProRS, however, similar to the bacterial PrdX, the mammalian, amphibian, and echinoderm PrdX-like proteins are trans-acting, single-domain proteins.


Pssm-ID: 239827  Cd Length: 156  Bit Score: 57.53  E-value: 4.30e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754692835  11 CQLLADL--PHQRYQHEPIldYATDEQVKARLGWQAEFSKTLFLKFKDGRFALLLTHRDGRLDNKAVKATLGAKP-SICT 87
Cdd:cd04335    5 LALLDELgiAYETVEHPPV--FTVEEADEVLGELPGAHTKNLFLKDKKGRLYLVTALHDKKVDLKALSKQLGASRlSFAS 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 754692835  88 AEEMQAQIGCLPGAVCPFL----PRADIPLLIDPQLLAHHAFTWTPGHPEQT----------FLLETAHLPRVL 147
Cdd:cd04335   83 EERLEEKLGVTPGSVTPFAlindKENDVQVVLDKDLLEEERVGFHPLTNTATvgistedllkFLEATGHEPTVV 156
PA2301 cd04939
PA2301 is an uncharacterized Pseudomonas aeruginosa protein with a YbaK-like domain of unknown ...
 58-154 1.74e-05

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: 42.33  E-value: 1.74e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754692835  58 RFALLLTHRDGRLD-NKAVKATLGA-KPSICTAEEMQAQIGCLPGAVCPF-LPrADIPLLIDPQLLAHHAFTWTPGHPEQ 134
Cdd:cd04939   43 RYAACVVLATTRADvNGVVKRRLGArKASFAPMETAVELTGMEYGGITPVgLP-AGWPILVDSAVAERPAVVIGSGVRRS 121

                         90       100
                 ....*....|....*....|.
gi 754692835 135 TFLLEtahlPRVLAQLP-CEV 154
Cdd:cd04939  122 KLLLP----GAALAELPgAEV 138
 
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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