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Conserved domains on  [gi|873899426|ref|WP_048605859|]
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MULTISPECIES: aminoacyl-tRNA deacylase [Vibrio]

Protein Classification

aminoacyl-tRNA deacylase( domain architecture ID 10006507)

aminoacyl-tRNA deacylase of the YbaK/EbsC family, such as Haemophilus influenzae cysteinyl-tRNA(Pro) deacylase

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
EbsC COG2606
Cys-tRNA(Pro) deacylase, prolyl-tRNA editing enzyme YbaK/EbsC [Translation, ribosomal ...
 3-153 1.40e-42

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: 138.30  E-value: 1.40e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873899426   3 TLITQWLDQQQVNYRLLMQSKPTTSIEETAQERGIDASQMVKCILLKDMGnQYALACTAGDRSVDPKKVRSVLNCRRMTC 82
Cdd:COG2606    1 TPVRRALDAAGIPYEVVEHPEPAATAEEAAEALGVPPEQIAKTLVFRGDG-GPVLAVVPGDRRLDLKKLAAALGAKKVEM 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 873899426  83 VSLADVEAITGFKVGCVGPLALKRHMPIIFDPSIQNNSTVTISSGDRMAGVALDLNDLMALCAPTVADISR 153
Cdd:COG2606   80 ADPEEVERLTGYEVGGVSPFGLKKGLPVYVDESLLEFDEVYVSAGDRGLLVELAPADLARLTGATVADIAR 150
 
Name Accession Description Interval E-value
EbsC COG2606
Cys-tRNA(Pro) deacylase, prolyl-tRNA editing enzyme YbaK/EbsC [Translation, ribosomal ...
 3-153 1.40e-42

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: 138.30  E-value: 1.40e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873899426   3 TLITQWLDQQQVNYRLLMQSKPTTSIEETAQERGIDASQMVKCILLKDMGnQYALACTAGDRSVDPKKVRSVLNCRRMTC 82
Cdd:COG2606    1 TPVRRALDAAGIPYEVVEHPEPAATAEEAAEALGVPPEQIAKTLVFRGDG-GPVLAVVPGDRRLDLKKLAAALGAKKVEM 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 873899426  83 VSLADVEAITGFKVGCVGPLALKRHMPIIFDPSIQNNSTVTISSGDRMAGVALDLNDLMALCAPTVADISR 153
Cdd:COG2606   80 ADPEEVERLTGYEVGGVSPFGLKKGLPVYVDESLLEFDEVYVSAGDRGLLVELAPADLARLTGATVADIAR 150
YbaK_like cd04332
YbaK-like. The YbaK family of deacylase domains includes the INS amino acid-editing domain of ...
 25-149 5.78e-38

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: 126.12  E-value: 5.78e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873899426  25 TTSIEETAQERGIDASQMVKCILLKDMGNQYALACTAGDRSVDPKKVRSVLNCRRMTCVSLADVEAITGFKVGCVGPLAL 104
Cdd:cd04332   11 AKTIEEAAEALGVPPGQIAKTLVLKDDKGGLVLVVVPGDHELDLKKLAKALGAKKLRLASEEELEELTGCEPGGVGPFGL 90

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 873899426 105 KRHMPIIFDPSIQNNSTVTISSGDRMAGVALDLNDLMALCA-PTVA 149
Cdd:cd04332   91 KKGVPVVVDESLLELEDVYVGAGERGADLHLSPADLLRLLGeAEVA 136
tRNA_edit pfam04073
Aminoacyl-tRNA editing domain; This domain is found either on its own or in association with ...
 23-143 1.89e-33

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: 114.24  E-value: 1.89e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873899426   23 KPTTSIEETAQERGIDASQMVKCILLKDMGNQYALACTAGDRSVDPKKVRSVLNCRRMTCVSLADVEAITGFKVGCVGPL 102
Cdd:pfam04073   2 PPAATIEELAAALGVPPGRIAKTLVLKDKKGKYVLVVVPGDREVDLKKLAKLLGVKRLRLASEEELLELTGVEPGGVTPF 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 873899426  103 ALKRH-MPIIFDPSIQNNSTVTISSGDRMAGVALDLNDLMAL 143
Cdd:pfam04073  82 GLKAKgVPVLVDESLKDLPDVVVGAGENGATLRLSNADLRKL 123
PRK09194 PRK09194
prolyl-tRNA synthetase; Provisional
 25-118 2.09e-16

prolyl-tRNA synthetase; Provisional


Pssm-ID: 236405 [Multi-domain]  Cd Length: 565  Bit Score: 74.74  E-value: 2.09e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873899426  25 TTSIEETAQERGIDASQMVKCILLKDmGNQYALACTAGDRSVDPKKVRSVLNCRRMTCVSLADVEAITGFKVGCVGPLAL 104
Cdd:PRK09194 258 AKTIEELAEFLNVPAEKTVKTLLVKA-DGELVAVLVRGDHELNEVKLENLLGAAPLELATEEEIRAALGAVPGFLGPVGL 336

                         90
                 ....*....|....
gi 873899426 105 KRHMPIIFDPSIQN 118
Cdd:PRK09194 337 PKDVPIIADRSVAD 350
 
Name Accession Description Interval E-value
EbsC COG2606
Cys-tRNA(Pro) deacylase, prolyl-tRNA editing enzyme YbaK/EbsC [Translation, ribosomal ...
 3-153 1.40e-42

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: 138.30  E-value: 1.40e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873899426   3 TLITQWLDQQQVNYRLLMQSKPTTSIEETAQERGIDASQMVKCILLKDMGnQYALACTAGDRSVDPKKVRSVLNCRRMTC 82
Cdd:COG2606    1 TPVRRALDAAGIPYEVVEHPEPAATAEEAAEALGVPPEQIAKTLVFRGDG-GPVLAVVPGDRRLDLKKLAAALGAKKVEM 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 873899426  83 VSLADVEAITGFKVGCVGPLALKRHMPIIFDPSIQNNSTVTISSGDRMAGVALDLNDLMALCAPTVADISR 153
Cdd:COG2606   80 ADPEEVERLTGYEVGGVSPFGLKKGLPVYVDESLLEFDEVYVSAGDRGLLVELAPADLARLTGATVADIAR 150
YbaK_like cd04332
YbaK-like. The YbaK family of deacylase domains includes the INS amino acid-editing domain of ...
 25-149 5.78e-38

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: 126.12  E-value: 5.78e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873899426  25 TTSIEETAQERGIDASQMVKCILLKDMGNQYALACTAGDRSVDPKKVRSVLNCRRMTCVSLADVEAITGFKVGCVGPLAL 104
Cdd:cd04332   11 AKTIEEAAEALGVPPGQIAKTLVLKDDKGGLVLVVVPGDHELDLKKLAKALGAKKLRLASEEELEELTGCEPGGVGPFGL 90

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 873899426 105 KRHMPIIFDPSIQNNSTVTISSGDRMAGVALDLNDLMALCA-PTVA 149
Cdd:cd04332   91 KKGVPVVVDESLLELEDVYVGAGERGADLHLSPADLLRLLGeAEVA 136
tRNA_edit pfam04073
Aminoacyl-tRNA editing domain; This domain is found either on its own or in association with ...
 23-143 1.89e-33

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: 114.24  E-value: 1.89e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873899426   23 KPTTSIEETAQERGIDASQMVKCILLKDMGNQYALACTAGDRSVDPKKVRSVLNCRRMTCVSLADVEAITGFKVGCVGPL 102
Cdd:pfam04073   2 PPAATIEELAAALGVPPGRIAKTLVLKDKKGKYVLVVVPGDREVDLKKLAKLLGVKRLRLASEEELLELTGVEPGGVTPF 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 873899426  103 ALKRH-MPIIFDPSIQNNSTVTISSGDRMAGVALDLNDLMAL 143
Cdd:pfam04073  82 GLKAKgVPVLVDESLKDLPDVVVGAGENGATLRLSNADLRKL 123
YbaK_deacylase cd00002
This CD includes cysteinyl-tRNA(Pro) deacylases from Haemophilus influenzae and Escherichia ...
 3-151 3.14e-24

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: 91.36  E-value: 3.14e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873899426   3 TLITQWLDQQQVNYRLL-MQSKPTTSI-EETAQERGIDASQMVKCILLKDMGNQYALACTAGDRSVDPKKVRSVLNCRRM 80
Cdd:cd00002    2 TPAIRLLDKAKIPYELHeYEHDEDASDgLEAAEKLGLDPEQVFKTLVVEGDKKGLVVAVVPVDEELDLKKLAKALGAKKV 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 873899426  81 TCVSLADVEAITGFKVGCVGPLALKRHMPIIFDPSIQNNSTVTISSGDRMAGVALDLNDLMALCAPTVADI 151
Cdd:cd00002   82 EMAPPKDAERLTGYIRGGISPLGQKKRLPTVIDESALDLDTIYVSAGKRGLQIELAPQDLAKLTGAKFADI 152
YeaK cd04336
YeaK is an uncharacterized Echerichia coli protein with a YbaK-like domain of unknown function. ...
 5-151 8.64e-22

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: 85.09  E-value: 8.64e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873899426   5 ITQWLDQQQVNYRLLMQsKPTTSIEETAQERGIDASQMVKCILL--KDMGNQYALACTAGDRSVDPKKVRSVLNCRRMTC 82
Cdd:cd04336    4 LQELLNTNGARFRVLDH-PPEGTSEEVAAIRGTELGQGAKALLCkvKDGSRRFVLAVLPADKKLDLKAVAAAVGGKKADL 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873899426  83 VSLADVEAITGFKVGCVGPLALKRHMPIIFDPS-IQNNSTVTISSGDRMAGVALDLNDLMALCAPTVADI 151
Cdd:cd04336   83 ASPEEAEELTGCVIGAVPPFSFDPKLKLIADPSlLDRGDEIAFNAGRLDASVVLDTADYLRIARPLVLQF 152
ProX_deacylase cd04333
This CD, composed mainly of bacterial single-domain proteins, includes the Thermus ...
 7-151 2.54e-17

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: 73.69  E-value: 2.54e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873899426   7 QWLDQQQVNYRLLMQSKPTTSIEETAQERGIDASQMVKCILLKDMGnQYALACTAGDRSVDPKKVRSVLNCR-RMtcVSL 85
Cdd:cd04333    6 AFLAARGLDLEVIELPESTRTAALAAEALGCEPGQIAKSLVFRVDD-EPVLVVTSGDARVDNKKFKALFGEKlKM--ADA 82

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 873899426  86 ADVEAITGFKVGCVGPLALKRHMPIIFDPSIQNNSTVTISSGDRMAGVALDLNDLMALCAPTVADI 151
Cdd:cd04333   83 EEVRELTGFAIGGVCPFGHPEPLPVYLDESLKRFDEVWAAAGTPNAAFRLTPDELERLTGAEWVDV 148
PRK09194 PRK09194
prolyl-tRNA synthetase; Provisional
 25-118 2.09e-16

prolyl-tRNA synthetase; Provisional


Pssm-ID: 236405 [Multi-domain]  Cd Length: 565  Bit Score: 74.74  E-value: 2.09e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873899426  25 TTSIEETAQERGIDASQMVKCILLKDmGNQYALACTAGDRSVDPKKVRSVLNCRRMTCVSLADVEAITGFKVGCVGPLAL 104
Cdd:PRK09194 258 AKTIEELAEFLNVPAEKTVKTLLVKA-DGELVAVLVRGDHELNEVKLENLLGAAPLELATEEEIRAALGAVPGFLGPVGL 336

                         90
                 ....*....|....
gi 873899426 105 KRHMPIIFDPSIQN 118
Cdd:PRK09194 337 PKDVPIIADRSVAD 350
ProRS-INS cd04334
INS is an amino acid-editing domain inserted (INS) into the bacterial class II prolyl-tRNA ...
 25-118 1.51e-14

INS is an amino acid-editing domain inserted (INS) into the bacterial class II prolyl-tRNA synthetase (ProRS) however, this CD is not exclusively bacterial. It is also found at the N-terminus of the eukaryotic/archaea-like ProRS's of yeasts and single-celled parasites. ProRS catalyzes the attachment of proline to tRNA(Pro); proline is first activated by ATP, and then transferred to the acceptor end of tRNA(Pro). ProRS can inadvertently process noncognate amino acids such as alanine and cysteine, and to avoid such errors, in post-transfer editing, the INS domain deacylates mischarged Ala-tRNA(Pro), thus ensuring the fidelity of translation. Misacylated Cys-tRNA(Pro) is not edited by ProRS. In addition to the INS editing domain, the prokaryote-like ProRS protein contains catalytic and anticodon-binding domains which form a dimeric interface.


Pssm-ID: 239826 [Multi-domain]  Cd Length: 160  Bit Score: 66.38  E-value: 1.51e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873899426  25 TTSIEETAQERGIDASQMVKCILLKDMGN-QYALACTAGDRSVDPKKVRSVLNCRRMTCVSLADVEAITGFKVGCVGPLA 103
Cdd:cd04334   35 QKTIEELAEFLGVPPSQTVKTLLVKADGEeELVAVLLRGDHELNEVKLENLLGAAPLELASEEEIEAATGAPPGFIGPVG 114

                         90
                 ....*....|....*
gi 873899426 104 LKrHMPIIFDPSIQN 118
Cdd:cd04334  115 LK-KIPIIADRSVAD 128
PrdX_deacylase cd04335
This CD includes bacterial (Agrobacterium tumefaciens and Caulobacter crescentus ProX, and ...
 7-147 7.85e-09

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: 51.36  E-value: 7.85e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873899426   7 QWLDQQQVNYRLLmQSKPTTSIEETAQERGIDASQMVKCILLKDMGNQYALACTAGDRSVDPKKVRSVLNCRRMtcvSLA 86
Cdd:cd04335    6 ALLDELGIAYETV-EHPPVFTVEEADEVLGELPGAHTKNLFLKDKKGRLYLVTALHDKKVDLKALSKQLGASRL---SFA 81

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 873899426  87 DVEAIT---GFKVGCVGPLALK----RHMPIIFDPSIQNNSTVTISSGDRMAGVALDLNDLMALCAPT 147
Cdd:cd04335   82 SEERLEeklGVTPGSVTPFALIndkeNDVQVVLDKDLLEEERVGFHPLTNTATVGISTEDLLKFLEAT 149
 
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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