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Conserved domains on  [gi|499656893|ref|WP_011337627|]
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YbaK/EbsC family protein [Cereibacter sphaeroides]

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 ...
 5-150 5.10e-50

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: 157.28  E-value: 5.10e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499656893   5 LARVRSALEAAGVAAEIREMPAETRTAEQAAAAAGCALDQIVKSILFLGAesGQLHLFLTAGGNQVSVEKAGALAGEALG 84
Cdd:cd04333    1 VERVRAFLAARGLDLEVIELPESTRTAALAAEALGCEPGQIAKSLVFRVD--DEPVLVVTSGDARVDNKKFKALFGEKLK 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 499656893  85 RADAATVRAQSGFAIGGVAPVGHLVPLPVWLDPRLMEFREVWAAGGTPRHIFAVAPDILQRLTGAQ 150
Cdd:cd04333   79 MADAEEVRELTGFAIGGVCPFGHPEPLPVYLDESLKRFDEVWAAAGTPNAAFRLTPDELERLTGAE 144
 
Name Accession Description Interval E-value
ProX_deacylase cd04333
This CD, composed mainly of bacterial single-domain proteins, includes the Thermus ...
 5-150 5.10e-50

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: 157.28  E-value: 5.10e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499656893   5 LARVRSALEAAGVAAEIREMPAETRTAEQAAAAAGCALDQIVKSILFLGAesGQLHLFLTAGGNQVSVEKAGALAGEALG 84
Cdd:cd04333    1 VERVRAFLAARGLDLEVIELPESTRTAALAAEALGCEPGQIAKSLVFRVD--DEPVLVVTSGDARVDNKKFKALFGEKLK 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 499656893  85 RADAATVRAQSGFAIGGVAPVGHLVPLPVWLDPRLMEFREVWAAGGTPRHIFAVAPDILQRLTGAQ 150
Cdd:cd04333   79 MADAEEVRELTGFAIGGVCPFGHPEPLPVYLDESLKRFDEVWAAAGTPNAAFRLTPDELERLTGAE 144
EbsC COG2606
Cys-tRNA(Pro) deacylase, prolyl-tRNA editing enzyme YbaK/EbsC [Translation, ribosomal ...
 7-155 2.46e-36

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: 122.51  E-value: 2.46e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499656893   7 RVRSALEAAGVAAEIREMPAETRTAEQAAAAAGCALDQIVKSILFLGaeSGQLHLFLTAGGNQVSVEKAGALAGEA-LGR 85
Cdd:COG2606    2 PVRRALDAAGIPYEVVEHPEPAATAEEAAEALGVPPEQIAKTLVFRG--DGGPVLAVVPGDRRLDLKKLAAALGAKkVEM 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499656893  86 ADAATVRAQSGFAIGGVAPVGHLVPLPVWLDPRLMEFREVWAAGGTPRHIFAVAPDILQRLTGAQIGQFT 155
Cdd:COG2606   80 ADPEEVERLTGYEVGGVSPFGLKKGLPVYVDESLLEFDEVYVSAGDRGLLVELAPADLARLTGATVADIA 149
tRNA_edit pfam04073
Aminoacyl-tRNA editing domain; This domain is found either on its own or in association with ...
 27-146 3.55e-11

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: 56.84  E-value: 3.55e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499656893   27 ETRTAEQAAAAAGCALDQIVKSILFLGAEsGQLHLFLTAGGNQVSVEKAGALAGEA-LGRADAATVRAQSGFAIGGVAPV 105
Cdd:pfam04073   3 PAATIEELAAALGVPPGRIAKTLVLKDKK-GKYVLVVVPGDREVDLKKLAKLLGVKrLRLASEEELLELTGVEPGGVTPF 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 499656893  106 GHLVP-LPVWLDPRLMEFREVWAAGGTPRHIFAVAPDILQRL 146
Cdd:pfam04073  82 GLKAKgVPVLVDESLKDLPDVVVGAGENGATLRLSNADLRKL 123
PRK10670 PRK10670
Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase YbaK;
43-150 1.36e-03

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


Pssm-ID: 182634  Cd Length: 159  Bit Score: 37.03  E-value: 1.36e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499656893  43 DQIVKSILF-LGAESGQLHLFLTAGGNQVSVEK-AGALAGEALGRADAATVRAQSGFAIGGVAPVGHLVPLPVWLDPRLM 120
Cdd:PRK10670  42 DQVYKTLLVaVNGDMKHLAVAVTPVAGQLDLKKvAKALGAKKVEMADPMVAQRSTGYLVGGISPLGQKKRLPTVIDAPAQ 121

                         90       100       110
                 ....*....|....*....|....*....|
gi 499656893 121 EFREVWAAGGTPRHIFAVAPDILQRLTGAQ 150
Cdd:PRK10670 122 EFATIYVSGGKRGLDIELAAGDLAKLLDAK 151
 
Name Accession Description Interval E-value
ProX_deacylase cd04333
This CD, composed mainly of bacterial single-domain proteins, includes the Thermus ...
 5-150 5.10e-50

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: 157.28  E-value: 5.10e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499656893   5 LARVRSALEAAGVAAEIREMPAETRTAEQAAAAAGCALDQIVKSILFLGAesGQLHLFLTAGGNQVSVEKAGALAGEALG 84
Cdd:cd04333    1 VERVRAFLAARGLDLEVIELPESTRTAALAAEALGCEPGQIAKSLVFRVD--DEPVLVVTSGDARVDNKKFKALFGEKLK 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 499656893  85 RADAATVRAQSGFAIGGVAPVGHLVPLPVWLDPRLMEFREVWAAGGTPRHIFAVAPDILQRLTGAQ 150
Cdd:cd04333   79 MADAEEVRELTGFAIGGVCPFGHPEPLPVYLDESLKRFDEVWAAAGTPNAAFRLTPDELERLTGAE 144
EbsC COG2606
Cys-tRNA(Pro) deacylase, prolyl-tRNA editing enzyme YbaK/EbsC [Translation, ribosomal ...
 7-155 2.46e-36

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: 122.51  E-value: 2.46e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499656893   7 RVRSALEAAGVAAEIREMPAETRTAEQAAAAAGCALDQIVKSILFLGaeSGQLHLFLTAGGNQVSVEKAGALAGEA-LGR 85
Cdd:COG2606    2 PVRRALDAAGIPYEVVEHPEPAATAEEAAEALGVPPEQIAKTLVFRG--DGGPVLAVVPGDRRLDLKKLAAALGAKkVEM 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499656893  86 ADAATVRAQSGFAIGGVAPVGHLVPLPVWLDPRLMEFREVWAAGGTPRHIFAVAPDILQRLTGAQIGQFT 155
Cdd:COG2606   80 ADPEEVERLTGYEVGGVSPFGLKKGLPVYVDESLLEFDEVYVSAGDRGLLVELAPADLARLTGATVADIA 149
YbaK_like cd04332
YbaK-like. The YbaK family of deacylase domains includes the INS amino acid-editing domain of ...
 18-149 3.85e-20

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: 80.66  E-value: 3.85e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499656893  18 AAEIREMPAETRTAEQAAAAAGCALDQIVKSILFLgAESGQLHLFLTAGGNQVSVEKAGALAGEA-LGRADAATVRAQSG 96
Cdd:cd04332    1 EYLEYEHTPGAKTIEEAAEALGVPPGQIAKTLVLK-DDKGGLVLVVVPGDHELDLKKLAKALGAKkLRLASEEELEELTG 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 499656893  97 FAIGGVAPVGHLVPLPVWLDPRLMEFREVWAAGGTPRHIFAVAPDILQRLTGA 149
Cdd:cd04332   80 CEPGGVGPFGLKKGVPVVVDESLLELEDVYVGAGERGADLHLSPADLLRLLGE 132
tRNA_edit pfam04073
Aminoacyl-tRNA editing domain; This domain is found either on its own or in association with ...
 27-146 3.55e-11

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: 56.84  E-value: 3.55e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499656893   27 ETRTAEQAAAAAGCALDQIVKSILFLGAEsGQLHLFLTAGGNQVSVEKAGALAGEA-LGRADAATVRAQSGFAIGGVAPV 105
Cdd:pfam04073   3 PAATIEELAAALGVPPGRIAKTLVLKDKK-GKYVLVVVPGDREVDLKKLAKLLGVKrLRLASEEELLELTGVEPGGVTPF 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 499656893  106 GHLVP-LPVWLDPRLMEFREVWAAGGTPRHIFAVAPDILQRL 146
Cdd:pfam04073  82 GLKAKgVPVLVDESLKDLPDVVVGAGENGATLRLSNADLRKL 123
YbaK_deacylase cd00002
This CD includes cysteinyl-tRNA(Pro) deacylases from Haemophilus influenzae and Escherichia ...
 11-152 2.21e-05

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: 42.05  E-value: 2.21e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499656893  11 ALEAAGVAAEIREMPAETRTAEQAAAAAGCALD--QIVKSILFLGaESGQLHLFLTAGGNQVSVEKAGALAGE-ALGRAD 87
Cdd:cd00002    7 LLDKAKIPYELHEYEHDEDASDGLEAAEKLGLDpeQVFKTLVVEG-DKKGLVVAVVPVDEELDLKKLAKALGAkKVEMAP 85

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 499656893  88 AATVRAQSGFAIGGVAPVGHLVPLPVWLDPRLMEFREVWAAGGTPRHIFAVAPDILQRLTGAQIG 152
Cdd:cd00002   86 PKDAERLTGYIRGGISPLGQKKRLPTVIDESALDLDTIYVSAGKRGLQIELAPQDLAKLTGAKFA 150
PRK10670 PRK10670
Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase YbaK;
43-150 1.36e-03

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


Pssm-ID: 182634  Cd Length: 159  Bit Score: 37.03  E-value: 1.36e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499656893  43 DQIVKSILF-LGAESGQLHLFLTAGGNQVSVEK-AGALAGEALGRADAATVRAQSGFAIGGVAPVGHLVPLPVWLDPRLM 120
Cdd:PRK10670  42 DQVYKTLLVaVNGDMKHLAVAVTPVAGQLDLKKvAKALGAKKVEMADPMVAQRSTGYLVGGISPLGQKKRLPTVIDAPAQ 121

                         90       100       110
                 ....*....|....*....|....*....|
gi 499656893 121 EFREVWAAGGTPRHIFAVAPDILQRLTGAQ 150
Cdd:PRK10670 122 EFATIYVSGGKRGLDIELAAGDLAKLLDAK 151
ProRS-INS cd04334
INS is an amino acid-editing domain inserted (INS) into the bacterial class II prolyl-tRNA ...
 43-121 9.03e-03

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: 34.80  E-value: 9.03e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499656893  43 DQIVKSILFLGAESGQLHLFLTAGGNQVSVEKAGALAGEA-LGRADAATVRAQSGFAIGGVAPVGhLVPLPVWLDPRLME 121
Cdd:cd04334   50 SQTVKTLLVKADGEEELVAVLLRGDHELNEVKLENLLGAApLELASEEEIEAATGAPPGFIGPVG-LKKIPIIADRSVAD 128
 
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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