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Conserved domains on  [gi|1721624163|gb|QEC28856|]
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hypothetical protein BG549_04420 [Mannheimia haemolytica]

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. ...
 6-159 8.73e-72

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: 212.59  E-value: 8.73e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721624163   6 FHQITALLDSHRARYRVVEHPSAGKSEEVAKIRGTEIGQGAKALVCKVKGNGvKQAVLAILPADYQADLTKIAEHLGGLR 85
Cdd:cd04336     1 FERLQELLNTNGARFRVLDHPPEGTSEEVAAIRGTELGQGAKALLCKVKDGS-RRFVLAVLPADKKLDLKAVAAAVGGKK 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1721624163  86 ASLASPAEVAELTDCVFGAIPPFSFHPDLLLVAEPSLFERYAELAFNAGTLERSIILNTEDYQKIVNPVLVQFA 159
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. ...
 6-159 8.73e-72

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: 212.59  E-value: 8.73e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721624163   6 FHQITALLDSHRARYRVVEHPSAGKSEEVAKIRGTEIGQGAKALVCKVKGNGvKQAVLAILPADYQADLTKIAEHLGGLR 85
Cdd:cd04336     1 FERLQELLNTNGARFRVLDHPPEGTSEEVAAIRGTELGQGAKALLCKVKDGS-RRFVLAVLPADKKLDLKAVAAAVGGKK 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1721624163  86 ASLASPAEVAELTDCVFGAIPPFSFHPDLLLVAEPSLFERYAELAFNAGTLERSIILNTEDYQKIVNPVLVQFA 159
Cdd:cd04336    80 ADLASPEEAEELTGCVIGAVPPFSFDPKLKLIADPSLLDRGDEIAFNAGRLDASVVLDTADYLRIARPLVLQFT 153
EbsC COG2606
Cys-tRNA(Pro) deacylase, prolyl-tRNA editing enzyme YbaK/EbsC [Translation, ribosomal ...
 8-160 2.43e-43

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: 140.61  E-value: 2.43e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721624163   8 QITALLDSHRARYRVVEHP-SAGKSEEVAKIRGTEIGQGAKALVCKVKGngvkQAVLAILPADYQADLTKIAEHLGGLRA 86
Cdd:COG2606     2 PVRRALDAAGIPYEVVEHPePAATAEEAAEALGVPPEQIAKTLVFRGDG----GPVLAVVPGDRRLDLKKLAAALGAKKV 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1721624163  87 SLASPAEVAELTDCVFGAIPPFSFHPDLLLVAEPSLFErYAELAFNAGTLERSIILNTEDYQKIVNPVLVQFAK 160
Cdd:COG2606    78 EMADPEEVERLTGYEVGGVSPFGLKKGLPVYVDESLLE-FDEVYVSAGDRGLLVELAPADLARLTGATVADIAR 150
tRNA_edit pfam04073
Aminoacyl-tRNA editing domain; This domain is found either on its own or in association with ...
 25-150 1.50e-26

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: 96.90  E-value: 1.50e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721624163  25 HPSAGKSEEVAKIRGTEIGQGAKALVCKVKGNgvkQAVLAILPADYQADLTKIAEHLGGLRASLASPAEVAELTDCVFGA 104
Cdd:pfam04073   1 HPPAATIEELAAALGVPPGRIAKTLVLKDKKG---KYVLVVVPGDREVDLKKLAKLLGVKRLRLASEEELLELTGVEPGG 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1721624163 105 IPPFSFHP-DLLLVAEPSLFErYAELAFNAGTLERSIILNTEDYQKI 150
Cdd:pfam04073  78 VTPFGLKAkGVPVLVDESLKD-LPDVVVGAGENGATLRLSNADLRKL 123
 
Name Accession Description Interval E-value
YeaK cd04336
YeaK is an uncharacterized Echerichia coli protein with a YbaK-like domain of unknown function. ...
 6-159 8.73e-72

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: 212.59  E-value: 8.73e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721624163   6 FHQITALLDSHRARYRVVEHPSAGKSEEVAKIRGTEIGQGAKALVCKVKGNGvKQAVLAILPADYQADLTKIAEHLGGLR 85
Cdd:cd04336     1 FERLQELLNTNGARFRVLDHPPEGTSEEVAAIRGTELGQGAKALLCKVKDGS-RRFVLAVLPADKKLDLKAVAAAVGGKK 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1721624163  86 ASLASPAEVAELTDCVFGAIPPFSFHPDLLLVAEPSLFERYAELAFNAGTLERSIILNTEDYQKIVNPVLVQFA 159
Cdd:cd04336    80 ADLASPEEAEELTGCVIGAVPPFSFDPKLKLIADPSLLDRGDEIAFNAGRLDASVVLDTADYLRIARPLVLQFT 153
EbsC COG2606
Cys-tRNA(Pro) deacylase, prolyl-tRNA editing enzyme YbaK/EbsC [Translation, ribosomal ...
 8-160 2.43e-43

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: 140.61  E-value: 2.43e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721624163   8 QITALLDSHRARYRVVEHP-SAGKSEEVAKIRGTEIGQGAKALVCKVKGngvkQAVLAILPADYQADLTKIAEHLGGLRA 86
Cdd:COG2606     2 PVRRALDAAGIPYEVVEHPePAATAEEAAEALGVPPEQIAKTLVFRGDG----GPVLAVVPGDRRLDLKKLAAALGAKKV 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1721624163  87 SLASPAEVAELTDCVFGAIPPFSFHPDLLLVAEPSLFErYAELAFNAGTLERSIILNTEDYQKIVNPVLVQFAK 160
Cdd:COG2606    78 EMADPEEVERLTGYEVGGVSPFGLKKGLPVYVDESLLE-FDEVYVSAGDRGLLVELAPADLARLTGATVADIAR 150
YbaK_like cd04332
YbaK-like. The YbaK family of deacylase domains includes the INS amino acid-editing domain of ...
 19-156 2.60e-32

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: 111.87  E-value: 2.60e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721624163  19 RYRVVEHPSAGKS-EEVAKIRGTEIGQGAKALVCKVKGNGVkqaVLAILPADYQADLTKIAEHLGGLRASLASPAEVAEL 97
Cdd:cd04332     1 EYLEYEHTPGAKTiEEAAEALGVPPGQIAKTLVLKDDKGGL---VLVVVPGDHELDLKKLAKALGAKKLRLASEEELEEL 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1721624163  98 TDCVFGAIPPFSFHPDLLLVAEPSLFErYAELAFNAGTLERSIILNTEDYQKIVNPVLV 156
Cdd:cd04332    78 TGCEPGGVGPFGLKKGVPVVVDESLLE-LEDVYVGAGERGADLHLSPADLLRLLGEAEV 135
tRNA_edit pfam04073
Aminoacyl-tRNA editing domain; This domain is found either on its own or in association with ...
 25-150 1.50e-26

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: 96.90  E-value: 1.50e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721624163  25 HPSAGKSEEVAKIRGTEIGQGAKALVCKVKGNgvkQAVLAILPADYQADLTKIAEHLGGLRASLASPAEVAELTDCVFGA 104
Cdd:pfam04073   1 HPPAATIEELAAALGVPPGRIAKTLVLKDKKG---KYVLVVVPGDREVDLKKLAKLLGVKRLRLASEEELLELTGVEPGG 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1721624163 105 IPPFSFHP-DLLLVAEPSLFErYAELAFNAGTLERSIILNTEDYQKI 150
Cdd:pfam04073  78 VTPFGLKAkGVPVLVDESLKD-LPDVVVGAGENGATLRLSNADLRKL 123
YbaK_deacylase cd00002
This CD includes cysteinyl-tRNA(Pro) deacylases from Haemophilus influenzae and Escherichia ...
 10-156 2.00e-12

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: 60.93  E-value: 2.00e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721624163  10 TALLDSHRARYRVVEH---PSAGKSEEVAKIRGTEIGQGAKALVCKVKGNGVkqaVLAILPADYQADLTKIAEHLGGLRA 86
Cdd:cd00002     5 IRLLDKAKIPYELHEYehdEDASDGLEAAEKLGLDPEQVFKTLVVEGDKKGL---VVAVVPVDEELDLKKLAKALGAKKV 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721624163  87 SLASPAEVAELTDCVFGAIPPFSFHPDLLLVAEPSLFErYAELAFNAGTLERSIILNTEDYQKIVNPVLV 156
Cdd:cd00002    82 EMAPPKDAERLTGYIRGGISPLGQKKRLPTVIDESALD-LDTIYVSAGKRGLQIELAPQDLAKLTGAKFA 150
ProX_deacylase cd04333
This CD, composed mainly of bacterial single-domain proteins, includes the Thermus ...
 11-135 2.17e-09

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: 52.89  E-value: 2.17e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721624163  11 ALLDSHRARYRVVEHPSAGKS-EEVAKIRGTEIGQGAKALVCKVKGngvkQAVLAILPADYQADLTKIAEHLGGlRASLA 89
Cdd:cd04333     6 AFLAARGLDLEVIELPESTRTaALAAEALGCEPGQIAKSLVFRVDD----EPVLVVTSGDARVDNKKFKALFGE-KLKMA 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1721624163  90 SPAEVAELTDCVFGAIPPFSFHPDLLLVAEPSLFeRYAELAFNAGT 135
Cdd:cd04333    81 DAEEVRELTGFAIGGVCPFGHPEPLPVYLDESLK-RFDEVWAAAGT 125
ProRS-INS cd04334
INS is an amino acid-editing domain inserted (INS) into the bacterial class II prolyl-tRNA ...
 23-122 7.05e-09

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: 51.74  E-value: 7.05e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721624163  23 VEHPSAGKSEEVAKIRGTEIGQGAKALVckVKGNGVKQAVLAILPADYQADLTKIAEHLGGLRASLASPAEVAELTDCVF 102
Cdd:cd04334    30 VATPGQKTIEELAEFLGVPPSQTVKTLL--VKADGEEELVAVLLRGDHELNEVKLENLLGAAPLELASEEEIEAATGAPP 107

                          90       100
                  ....*....|....*....|
gi 1721624163 103 GAIPPFSFhPDLLLVAEPSL 122
Cdd:cd04334   108 GFIGPVGL-KKIPIIADRSV 126
ProX COG3760
Predicted aminoacyl-tRNA deacylase, YbaK-like aminoacyl-tRNA editing domain [General function ...
 11-109 6.03e-06

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


Pssm-ID: 442974  Cd Length: 162  Bit Score: 43.58  E-value: 6.03e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721624163  11 ALLDSHRARYRVVEHPSAGKSEEVAKIRGTEIGQGAKAL-VCKVKGngvKQAVLAILPADYQADLTKIAEHLGGLRASLA 89
Cdd:COG3760     9 ALLDELGIPYETVEHPPVFTVEEAEALRGDLPGAHTKNLfLRDKKG---TRFYLVVVPEDKRVDLKALSKQLGSGRLSFA 85

                          90       100
                  ....*....|....*....|
gi 1721624163  90 SPAEVAELTDCVFGAIPPFS 109
Cdd:COG3760    86 SPERLEEYLGVTPGSVTPFG 105
PrdX_deacylase cd04335
This CD includes bacterial (Agrobacterium tumefaciens and Caulobacter crescentus ProX, and ...
 6-109 1.88e-05

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: 42.51  E-value: 1.88e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721624163   6 FHQITALLDSHRARYRVVEHPSAGKSEEVAKIRGTEIGQGAKALVCKVKGngvKQAVLAILPADYQADLTKIAEHLGGLR 85
Cdd:cd04335     1 EDELLALLDELGIAYETVEHPPVFTVEEADEVLGELPGAHTKNLFLKDKK---GRLYLVTALHDKKVDLKALSKQLGASR 77

                          90       100
                  ....*....|....*....|....
gi 1721624163  86 ASLASPAEVAELTDCVFGAIPPFS 109
Cdd:cd04335    78 LSFASEERLEEKLGVTPGSVTPFA 101
 
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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