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Conserved domains on  [gi|488990318|ref|WP_002901088|]
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MULTISPECIES: YbaK/prolyl-tRNA synthetase associated domain-containing protein [Klebsiella]

Protein Classification

YbaK/prolyl-tRNA synthetase associated domain-containing protein( domain architecture ID 10137858)

uncharaterized YbaK/prolyl-tRNA synthetase associated domain-containing protein may function as an aminoacyl-tRNA deacylase involved in tRNA editing; similar to Escherichia coli YeaK

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YeaK cd04336
YeaK is an uncharacterized Echerichia coli protein with a YbaK-like domain of unknown function. ...
 10-163 3.03e-75

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: 221.83  E-value: 3.03e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488990318  10 HQRLCALLDEHRARYRVMAHEAVGQCEAVSAIRGTALGQGAKALVCKVKGNGvNQHVLAILAADRQADLASLARHIGGSK 89
Cdd:cd04336    1 FERLQELLNTNGARFRVLDHPPEGTSEEVAAIRGTELGQGAKALLCKVKDGS-RRFVLAVLPADKKLDLKAVAAAVGGKK 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488990318  90 ASLASPAEVEALTACVFGAIPPFSFHPALRLVADPLLFERFPQIAFNAGRLDRSIILDTEDYLHIARPEIATFR 163
Cdd:cd04336   80 ADLASPEEAEELTGCVIGAVPPFSFDPKLKLIADPSLLDRGDEIAFNAGRLDASVVLDTADYLRIARPLVLQFT 153
 
Name Accession Description Interval E-value
YeaK cd04336
YeaK is an uncharacterized Echerichia coli protein with a YbaK-like domain of unknown function. ...
 10-163 3.03e-75

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: 221.83  E-value: 3.03e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488990318  10 HQRLCALLDEHRARYRVMAHEAVGQCEAVSAIRGTALGQGAKALVCKVKGNGvNQHVLAILAADRQADLASLARHIGGSK 89
Cdd:cd04336    1 FERLQELLNTNGARFRVLDHPPEGTSEEVAAIRGTELGQGAKALLCKVKDGS-RRFVLAVLPADKKLDLKAVAAAVGGKK 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488990318  90 ASLASPAEVEALTACVFGAIPPFSFHPALRLVADPLLFERFPQIAFNAGRLDRSIILDTEDYLHIARPEIATFR 163
Cdd:cd04336   80 ADLASPEEAEELTGCVIGAVPPFSFDPKLKLIADPSLLDRGDEIAFNAGRLDASVVLDTADYLRIARPLVLQFT 153
EbsC COG2606
Cys-tRNA(Pro) deacylase, prolyl-tRNA editing enzyme YbaK/EbsC [Translation, ribosomal ...
 11-164 8.54e-38

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: 126.74  E-value: 8.54e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488990318  11 QRLCALLDEHRARYRVMAHE-AVGQCEAVSAIRGTALGQGAKALVCKVKGngvnQHVLAILAADRQADLASLARHIGGSK 89
Cdd:COG2606    1 TPVRRALDAAGIPYEVVEHPePAATAEEAAEALGVPPEQIAKTLVFRGDG----GPVLAVVPGDRRLDLKKLAAALGAKK 76

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488990318  90 ASLASPAEVEALTACVFGAIPPFSFHPALRLVADPLLFErFPQIAFNAGRLDRSIILDTEDYLHIARPEIATFRR 164
Cdd:COG2606   77 VEMADPEEVERLTGYEVGGVSPFGLKKGLPVYVDESLLE-FDEVYVSAGDRGLLVELAPADLARLTGATVADIAR 150
tRNA_edit pfam04073
Aminoacyl-tRNA editing domain; This domain is found either on its own or in association with ...
 29-152 3.65e-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: 93.44  E-value: 3.65e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488990318   29 HEAVGQCEAVSAIRGTALGQGAKALVCKVKGNgvnQHVLAILAADRQADLASLARHIGGSKASLASPAEVEALTACVFGA 108
Cdd:pfam04073   1 HPPAATIEELAAALGVPPGRIAKTLVLKDKKG---KYVLVVVPGDREVDLKKLAKLLGVKRLRLASEEELLELTGVEPGG 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 488990318  109 IPPFSFHPA-LRLVADPLLFErFPQIAFNAGRLDRSIILDTEDYL 152
Cdd:pfam04073  78 VTPFGLKAKgVPVLVDESLKD-LPDVVVGAGENGATLRLSNADLR 121
 
Name Accession Description Interval E-value
YeaK cd04336
YeaK is an uncharacterized Echerichia coli protein with a YbaK-like domain of unknown function. ...
 10-163 3.03e-75

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: 221.83  E-value: 3.03e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488990318  10 HQRLCALLDEHRARYRVMAHEAVGQCEAVSAIRGTALGQGAKALVCKVKGNGvNQHVLAILAADRQADLASLARHIGGSK 89
Cdd:cd04336    1 FERLQELLNTNGARFRVLDHPPEGTSEEVAAIRGTELGQGAKALLCKVKDGS-RRFVLAVLPADKKLDLKAVAAAVGGKK 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488990318  90 ASLASPAEVEALTACVFGAIPPFSFHPALRLVADPLLFERFPQIAFNAGRLDRSIILDTEDYLHIARPEIATFR 163
Cdd:cd04336   80 ADLASPEEAEELTGCVIGAVPPFSFDPKLKLIADPSLLDRGDEIAFNAGRLDASVVLDTADYLRIARPLVLQFT 153
EbsC COG2606
Cys-tRNA(Pro) deacylase, prolyl-tRNA editing enzyme YbaK/EbsC [Translation, ribosomal ...
 11-164 8.54e-38

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: 126.74  E-value: 8.54e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488990318  11 QRLCALLDEHRARYRVMAHE-AVGQCEAVSAIRGTALGQGAKALVCKVKGngvnQHVLAILAADRQADLASLARHIGGSK 89
Cdd:COG2606    1 TPVRRALDAAGIPYEVVEHPePAATAEEAAEALGVPPEQIAKTLVFRGDG----GPVLAVVPGDRRLDLKKLAAALGAKK 76

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488990318  90 ASLASPAEVEALTACVFGAIPPFSFHPALRLVADPLLFErFPQIAFNAGRLDRSIILDTEDYLHIARPEIATFRR 164
Cdd:COG2606   77 VEMADPEEVERLTGYEVGGVSPFGLKKGLPVYVDESLLE-FDEVYVSAGDRGLLVELAPADLARLTGATVADIAR 150
YbaK_like cd04332
YbaK-like. The YbaK family of deacylase domains includes the INS amino acid-editing domain of ...
 23-157 3.67e-26

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: 96.46  E-value: 3.67e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488990318  23 RYRVMAHEAVGQ-CEAVSAIRGTALGQGAKALVCKVKGNGvnqHVLAILAADRQADLASLARHIGGSKASLASPAEVEAL 101
Cdd:cd04332    1 EYLEYEHTPGAKtIEEAAEALGVPPGQIAKTLVLKDDKGG---LVLVVVPGDHELDLKKLAKALGAKKLRLASEEELEEL 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 488990318 102 TACVFGAIPPFSFHPALRLVADPLLFErFPQIAFNAGRLDRSIILDTEDYLHIARP 157
Cdd:cd04332   78 TGCEPGGVGPFGLKKGVPVVVDESLLE-LEDVYVGAGERGADLHLSPADLLRLLGE 132
tRNA_edit pfam04073
Aminoacyl-tRNA editing domain; This domain is found either on its own or in association with ...
 29-152 3.65e-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: 93.44  E-value: 3.65e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488990318   29 HEAVGQCEAVSAIRGTALGQGAKALVCKVKGNgvnQHVLAILAADRQADLASLARHIGGSKASLASPAEVEALTACVFGA 108
Cdd:pfam04073   1 HPPAATIEELAAALGVPPGRIAKTLVLKDKKG---KYVLVVVPGDREVDLKKLAKLLGVKRLRLASEEELLELTGVEPGG 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 488990318  109 IPPFSFHPA-LRLVADPLLFErFPQIAFNAGRLDRSIILDTEDYL 152
Cdd:pfam04073  78 VTPFGLKAKgVPVLVDESLKD-LPDVVVGAGENGATLRLSNADLR 121
YbaK_deacylase cd00002
This CD includes cysteinyl-tRNA(Pro) deacylases from Haemophilus influenzae and Escherichia ...
 16-160 7.94e-15

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: 67.48  E-value: 7.94e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488990318  16 LLDEHRARYRVMAHEAVGQCE-AVSAIRgtALGQGA----KALVCKVKGNGvnqHVLAILAADRQADLASLARHIGGSKA 90
Cdd:cd00002    7 LLDKAKIPYELHEYEHDEDASdGLEAAE--KLGLDPeqvfKTLVVEGDKKG---LVVAVVPVDEELDLKKLAKALGAKKV 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488990318  91 SLASPAEVEALTACVFGAIPPFSFHPALRLVADPLLFErFPQIAFNAGRLDRSIILDTEDYLHIARPEIA 160
Cdd:cd00002   82 EMAPPKDAERLTGYIRGGISPLGQKKRLPTVIDESALD-LDTIYVSAGKRGLQIELAPQDLAKLTGAKFA 150
ProX COG3760
Predicted aminoacyl-tRNA deacylase, YbaK-like aminoacyl-tRNA editing domain [General function ...
 11-150 1.47e-09

Predicted aminoacyl-tRNA deacylase, YbaK-like aminoacyl-tRNA editing domain [General function prediction only];


Pssm-ID: 442974  Cd Length: 162  Bit Score: 53.59  E-value: 1.47e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488990318  11 QRLCALLDEHRARYRVMAHEAVGQCEAVSAIRGTALGQGAKAL-VCKVKGNgvnQHVLAILAADRQADLASLARHIGGSK 89
Cdd:COG3760    5 QELYALLDELGIPYETVEHPPVFTVEEAEALRGDLPGAHTKNLfLRDKKGT---RFYLVVVPEDKRVDLKALSKQLGSGR 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488990318  90 ASLASPAEVEALTACVFGAIPPFSfhpalrLVADP-----LLFER----FPQIAFNAGRLDRSIILDTED 150
Cdd:COG3760   82 LSFASPERLEEYLGVTPGSVTPFG------LINDTenrvtVVLDAdlleAELINCHPLVNTATLKISTDD 145
PrdX_deacylase cd04335
This CD includes bacterial (Agrobacterium tumefaciens and Caulobacter crescentus ProX, and ...
 11-163 4.52e-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: 52.14  E-value: 4.52e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488990318  11 QRLCALLDEHRARYRVMAHEAVGQCEAVSAIRGTALGQGAKALVCKVKGNgvnQHVLAILAADRQADLASLARHIGGSKA 90
Cdd:cd04335    2 DELLALLDELGIAYETVEHPPVFTVEEADEVLGELPGAHTKNLFLKDKKG---RLYLVTALHDKKVDLKALSKQLGASRL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488990318  91 SLASPAEVEALTACVFGAIPPFsfhpAL--------RLVADPLLFERfPQIAFNAGRLDRSIILDTEDYLHIARPEIATF 162
Cdd:cd04335   79 SFASEERLEEKLGVTPGSVTPF----ALindkendvQVVLDKDLLEE-ERVGFHPLTNTATVGISTEDLLKFLEATGHEP 153


                 .
gi 488990318 163 R 163
Cdd:cd04335  154 T 154
ProX_deacylase cd04333
This CD, composed mainly of bacterial single-domain proteins, includes the Thermus ...
 43-133 1.56e-07

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: 47.88  E-value: 1.56e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488990318  43 GTALGQGAKALVCKVKGngvnQHVLAILAADRQADLASLARHIGGsKASLASPAEVEALTACVFGAIPPFSFHPALRLVA 122
Cdd:cd04333   35 GCEPGQIAKSLVFRVDD----EPVLVVTSGDARVDNKKFKALFGE-KLKMADAEEVRELTGFAIGGVCPFGHPEPLPVYL 109

                         90
                 ....*....|.
gi 488990318 123 DPLLFeRFPQI 133
Cdd:cd04333  110 DESLK-RFDEV 119
ProRS-INS cd04334
INS is an amino acid-editing domain inserted (INS) into the bacterial class II prolyl-tRNA ...
 35-124 2.22e-06

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: 45.20  E-value: 2.22e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488990318  35 CEAVSAIRGTALGQGAKALVckVKGNGVNQHVLAILAADRQADLASLARHIGGSKASLASPAEVEALTACVFGAIPPFSF 114
Cdd:cd04334   38 IEELAEFLGVPPSQTVKTLL--VKADGEEELVAVLLRGDHELNEVKLENLLGAAPLELASEEEIEAATGAPPGFIGPVGL 115

                         90
                 ....*....|
gi 488990318 115 hPALRLVADP 124
Cdd:cd04334  116 -KKIPIIADR 124
 
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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