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Conserved domains on  [gi|446558204|ref|WP_000635550|]
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MULTISPECIES: alternative ribosome rescue aminoacyl-tRNA hydrolase ArfB [Enterobacteriaceae]

Protein Classification

aminoacyl-tRNA hydrolase( domain architecture ID 10013157)

aminoacyl-tRNA hydrolase similar to Escherichia coli ArfB, alternative ribosome rescue factor B, a peptide chain release factor which functions as a stalled-ribosome rescue factor

EC:  3.1.1.29
Gene Ontology:  GO:0004045|GO:0072344|GO:0006415|GO:0003747
PubMed:  18247350

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK09256 PRK09256
aminoacyl-tRNA hydrolase;
1-136 2.62e-74

aminoacyl-tRNA hydrolase;


:

Pssm-ID: 181730 [Multi-domain]  Cd Length: 138  Bit Score: 217.71  E-value: 2.62e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446558204   1 MIVISRHVAIPDGELEITAIRAQGAGGQHVNKTSTAIHLRFDIRASSLPEYYKERLLAASHHLISSDGVIVIKAQEYRSQ 80
Cdd:PRK09256   1 MLRITRRLVIPENELEWRFIRASGPGGQNVNKVSTAVELRFDIAASSLPEFYKERLLALAGHRITKDGVIVIKAQEFRSQ 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 446558204  81 ELNREAALARLVAVIKELTTEQKARRPTRPTRASKERRLASKAQKSSVKAMRGKVR 136
Cdd:PRK09256  81 ERNREDALERLVALIREALKPPKKRRATKPTRGSKERRLESKKQRGEVKALRGKVR 136
 
Name Accession Description Interval E-value
PRK09256 PRK09256
aminoacyl-tRNA hydrolase;
1-136 2.62e-74

aminoacyl-tRNA hydrolase;


Pssm-ID: 181730 [Multi-domain]  Cd Length: 138  Bit Score: 217.71  E-value: 2.62e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446558204   1 MIVISRHVAIPDGELEITAIRAQGAGGQHVNKTSTAIHLRFDIRASSLPEYYKERLLAASHHLISSDGVIVIKAQEYRSQ 80
Cdd:PRK09256   1 MLRITRRLVIPENELEWRFIRASGPGGQNVNKVSTAVELRFDIAASSLPEFYKERLLALAGHRITKDGVIVIKAQEFRSQ 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 446558204  81 ELNREAALARLVAVIKELTTEQKARRPTRPTRASKERRLASKAQKSSVKAMRGKVR 136
Cdd:PRK09256  81 ERNREDALERLVALIREALKPPKKRRATKPTRGSKERRLESKKQRGEVKALRGKVR 136
PrfB COG1186
Protein chain release factor PrfB [Translation, ribosomal structure and biogenesis]; Protein ...
 1-138 2.59e-56

Protein chain release factor PrfB [Translation, ribosomal structure and biogenesis]; Protein chain release factor PrfB is part of the Pathway/BioSystem: Translation factors


Pssm-ID: 440799 [Multi-domain]  Cd Length: 140  Bit Score: 172.24  E-value: 2.59e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446558204   1 MIVISRHVAIPDGELEITAIRAQGAGGQHVNKTSTAIHLRFDIRASSLPeyyKERLlaashhlisSDGVIVIKAQEYRSQ 80
Cdd:COG1186   14 LRMISPEIEIPESDLRIDTYRASGAGGQNVNKVSSAVRLTHDIASSSLP---DSRL---------TPGGIVVKAQEERSQ 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 446558204  81 ELNREAALARLVAVIKELTTEQKARRPTRPTRASKERRLASKAQKSSVKAMRGKVRSG 138
Cdd:COG1186   82 HQNREDALKRLKALLYEAELEPKERRATKPTRGSKKRRLWGKQIRSMVKDLRGNVDDG 139
RF-1 pfam00472
RF-1 domain; This domain is found in peptide chain release factors such as RF-1 and RF-2, and ...
 8-132 3.27e-26

RF-1 domain; This domain is found in peptide chain release factors such as RF-1 and RF-2, and a number of smaller proteins of unknown function. This domain contains the peptidyl-tRNA hydrolase activity. The domain contains a highly conserved motif GGQ, where the glutamine is thought to coordinate the water that mediates the hydrolysis.


Pssm-ID: 459823 [Multi-domain]  Cd Length: 111  Bit Score: 94.80  E-value: 3.27e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446558204    8 VAIPDGELEITAIRAQGAGGQHVNKTSTAIHLrfdirasslpeyykerllaasHHLISSdgvIVIKAQEYRSQELNREAA 87
Cdd:pfam00472   5 IEIDPKDLRIDTFRSSGAGGQHVNKTDSAVRL---------------------THIPTG---IVVKCQDERSQHQNREKA 60

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 446558204   88 LARLVAVIKELTTEQKARRPTRPTRA------SKERRLASKAQKSSVKAMR 132
Cdd:pfam00472  61 LKRLRARLYELEEEKEEEKKRRIKSQvgsgdrSEQIRTYNFKPQSRVKDHR 111
prfB TIGR00020
peptide chain release factor 2; In many but not all taxa, there is a conserved real ...
 7-103 8.05e-08

peptide chain release factor 2; In many but not all taxa, there is a conserved real translational frameshift at a TGA codon. RF-2 helps terminate translation at TGA codons and can therefore regulate its own production by readthrough when RF-2 is insufficient. There is a Pfam model called "RF-1" for the superfamily of RF-1, RF-2, mitochondrial, RF-H, etc. [Protein synthesis, Translation factors]


Pssm-ID: 272858 [Multi-domain]  Cd Length: 364  Bit Score: 49.77  E-value: 8.05e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446558204    7 HVAIPDGELEITAIRAQGAGGQHVNKTSTAihlrfdIRASSLPEYykerllaashhlissdgvIVIKAQEYRSQELNREA 86
Cdd:TIGR00020 229 DIEIKPEDLRIDTYRASGAGGQHVNKTDSA------VRITHIPTG------------------IVVQCQNDRSQHKNKDS 284

                          90
                  ....*....|....*..
gi 446558204   87 ALARLVAVIKELTTEQK 103
Cdd:TIGR00020 285 AMKVLKAKLYELEMEKE 301
 
Name Accession Description Interval E-value
PRK09256 PRK09256
aminoacyl-tRNA hydrolase;
1-136 2.62e-74

aminoacyl-tRNA hydrolase;


Pssm-ID: 181730 [Multi-domain]  Cd Length: 138  Bit Score: 217.71  E-value: 2.62e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446558204   1 MIVISRHVAIPDGELEITAIRAQGAGGQHVNKTSTAIHLRFDIRASSLPEYYKERLLAASHHLISSDGVIVIKAQEYRSQ 80
Cdd:PRK09256   1 MLRITRRLVIPENELEWRFIRASGPGGQNVNKVSTAVELRFDIAASSLPEFYKERLLALAGHRITKDGVIVIKAQEFRSQ 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 446558204  81 ELNREAALARLVAVIKELTTEQKARRPTRPTRASKERRLASKAQKSSVKAMRGKVR 136
Cdd:PRK09256  81 ERNREDALERLVALIREALKPPKKRRATKPTRGSKERRLESKKQRGEVKALRGKVR 136
PrfB COG1186
Protein chain release factor PrfB [Translation, ribosomal structure and biogenesis]; Protein ...
 1-138 2.59e-56

Protein chain release factor PrfB [Translation, ribosomal structure and biogenesis]; Protein chain release factor PrfB is part of the Pathway/BioSystem: Translation factors


Pssm-ID: 440799 [Multi-domain]  Cd Length: 140  Bit Score: 172.24  E-value: 2.59e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446558204   1 MIVISRHVAIPDGELEITAIRAQGAGGQHVNKTSTAIHLRFDIRASSLPeyyKERLlaashhlisSDGVIVIKAQEYRSQ 80
Cdd:COG1186   14 LRMISPEIEIPESDLRIDTYRASGAGGQNVNKVSSAVRLTHDIASSSLP---DSRL---------TPGGIVVKAQEERSQ 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 446558204  81 ELNREAALARLVAVIKELTTEQKARRPTRPTRASKERRLASKAQKSSVKAMRGKVRSG 138
Cdd:COG1186   82 HQNREDALKRLKALLYEAELEPKERRATKPTRGSKKRRLWGKQIRSMVKDLRGNVDDG 139
RF-1 pfam00472
RF-1 domain; This domain is found in peptide chain release factors such as RF-1 and RF-2, and ...
 8-132 3.27e-26

RF-1 domain; This domain is found in peptide chain release factors such as RF-1 and RF-2, and a number of smaller proteins of unknown function. This domain contains the peptidyl-tRNA hydrolase activity. The domain contains a highly conserved motif GGQ, where the glutamine is thought to coordinate the water that mediates the hydrolysis.


Pssm-ID: 459823 [Multi-domain]  Cd Length: 111  Bit Score: 94.80  E-value: 3.27e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446558204    8 VAIPDGELEITAIRAQGAGGQHVNKTSTAIHLrfdirasslpeyykerllaasHHLISSdgvIVIKAQEYRSQELNREAA 87
Cdd:pfam00472   5 IEIDPKDLRIDTFRSSGAGGQHVNKTDSAVRL---------------------THIPTG---IVVKCQDERSQHQNREKA 60

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 446558204   88 LARLVAVIKELTTEQKARRPTRPTRA------SKERRLASKAQKSSVKAMR 132
Cdd:pfam00472  61 LKRLRARLYELEEEKEEEKKRRIKSQvgsgdrSEQIRTYNFKPQSRVKDHR 111
prfA PRK00591
peptide chain release factor 1; Validated
 8-118 8.53e-10

peptide chain release factor 1; Validated


Pssm-ID: 234801 [Multi-domain]  Cd Length: 359  Bit Score: 55.08  E-value: 8.53e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446558204   8 VAIPDGELEITAIRAQGAGGQHVNKTSTAIHLRfdirasslpeyykerllaashHLISSdgvIVIKAQEYRSQELNREAA 87
Cdd:PRK00591 216 VEINPKDLRIDTFRSSGAGGQHVNTTDSAVRIT---------------------HLPTG---IVVECQDERSQHKNKAKA 271

                         90       100       110
                 ....*....|....*....|....*....|.
gi 446558204  88 LARLVAVIKELTTEQKARrptrptRASKERR 118
Cdd:PRK00591 272 MKVLRARLYDAERQKAQA------EEAATRK 296
PrfA COG0216
Protein chain release factor RF1 [Translation, ribosomal structure and biogenesis]; Protein ...
 8-106 3.04e-09

Protein chain release factor RF1 [Translation, ribosomal structure and biogenesis]; Protein chain release factor RF1 is part of the Pathway/BioSystem: Translation factors


Pssm-ID: 439986 [Multi-domain]  Cd Length: 356  Bit Score: 53.47  E-value: 3.04e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446558204   8 VAIPDGELEITAIRAQGAGGQHVNKTSTAIHLRfdirasslpeyykerllaashHLISsdGvIVIKAQEYRSQELNREAA 87
Cdd:COG0216  214 VEINPKDLRIDTFRSSGAGGQHVNTTDSAVRIT---------------------HLPT--G-IVVECQDERSQHKNKAKA 269

                         90
                 ....*....|....*....
gi 446558204  88 LARLVAVIKELttEQKARR 106
Cdd:COG0216  270 MKVLRARLYEA--EQQKQQ 286
prfB TIGR00020
peptide chain release factor 2; In many but not all taxa, there is a conserved real ...
 7-103 8.05e-08

peptide chain release factor 2; In many but not all taxa, there is a conserved real translational frameshift at a TGA codon. RF-2 helps terminate translation at TGA codons and can therefore regulate its own production by readthrough when RF-2 is insufficient. There is a Pfam model called "RF-1" for the superfamily of RF-1, RF-2, mitochondrial, RF-H, etc. [Protein synthesis, Translation factors]


Pssm-ID: 272858 [Multi-domain]  Cd Length: 364  Bit Score: 49.77  E-value: 8.05e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446558204    7 HVAIPDGELEITAIRAQGAGGQHVNKTSTAihlrfdIRASSLPEYykerllaashhlissdgvIVIKAQEYRSQELNREA 86
Cdd:TIGR00020 229 DIEIKPEDLRIDTYRASGAGGQHVNKTDSA------VRITHIPTG------------------IVVQCQNDRSQHKNKDS 284

                          90
                  ....*....|....*..
gi 446558204   87 ALARLVAVIKELTTEQK 103
Cdd:TIGR00020 285 AMKVLKAKLYELEMEKE 301
release_prfH TIGR03072
putative peptide chain release factor H; Members of this protein family are bacterial proteins ...
 9-105 1.90e-07

putative peptide chain release factor H; Members of this protein family are bacterial proteins homologous to peptide chain release factors 1 (RF-1, product of the prfA gene), and 2 (RF-2, product of the prfB gene). The member from Escherichia coli K-12, designated prfH, appears to be a pseudogene. This class I release factor is always found as the downstream gene of a two-gene operon. [Protein synthesis, Translation factors]


Pssm-ID: 213768  Cd Length: 200  Bit Score: 47.84  E-value: 1.90e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446558204    9 AIPDGELEITAIRAQGAGGQHVNKTSTAihlrfdIRASslpeyykerllaashHLISSdgvIVIKAQEYRSQELNREAAL 88
Cdd:TIGR03072 102 EATEDEIRFETLRSSGPGGQHVNKTESA------VRAT---------------HLASG---ISVKVQSERSQHANKRLAT 157

                          90
                  ....*....|....*..
gi 446558204   89 ARLVAVIKELTTEQKAR 105
Cdd:TIGR03072 158 LLLAVRLADLQQEQAAA 174
PRK05589 PRK05589
peptide chain release factor 2; Provisional
 8-98 2.84e-07

peptide chain release factor 2; Provisional


Pssm-ID: 235520 [Multi-domain]  Cd Length: 325  Bit Score: 47.88  E-value: 2.84e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446558204   8 VAIPDGELEITAIRAQGAGGQHVNKTSTAihlrfdIRASSLPEYykerllaashhlissdgvIVIKAQEYRSQELNREAA 87
Cdd:PRK05589 191 IEIRSEDLKIDTYRAGGAGGQHVNKTESA------VRITHIPTG------------------IVVQCQNERSQHSNKETA 246

                         90
                 ....*....|.
gi 446558204  88 LARLVAVIKEL 98
Cdd:PRK05589 247 MKMLKSKLVEL 257
PRK08787 PRK08787
peptide chain release factor 2; Provisional
 8-103 2.56e-06

peptide chain release factor 2; Provisional


Pssm-ID: 136970 [Multi-domain]  Cd Length: 313  Bit Score: 45.42  E-value: 2.56e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446558204   8 VAIPDGELEITAIRAQGAGGQHVNKTSTAihlrfdIRASSLPEYykerllaashhlissdgvIVIKAQEYRSQELNREAA 87
Cdd:PRK08787 171 IDINPADLRTDVYRSSGAGGQHVNKTESA------VRITHIPTN------------------TVVACQTGRSQHQNRDNA 226

                         90
                 ....*....|....*.
gi 446558204  88 LARLVAVIKELTTEQK 103
Cdd:PRK08787 227 MKMLAAKLYELEVQKR 242
PRK07342 PRK07342
peptide chain release factor 2; Provisional
 8-115 4.37e-05

peptide chain release factor 2; Provisional


Pssm-ID: 235997 [Multi-domain]  Cd Length: 339  Bit Score: 41.79  E-value: 4.37e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446558204   8 VAIPDGELEITAIRAQGAGGQHVNKTSTAIHLRfdirasslpeyykerllaashHLISSdgvIVIKAQEYRSQELNREAA 87
Cdd:PRK07342 194 VDVNESDVRIDTYRSSGAGGQHVNTTDSAVRIT---------------------HIPTG---IVVQCQQERSQHKNRAKA 249

                         90       100
                 ....*....|....*....|....*...
gi 446558204  88 LARLVAVIKELTTeQKARRPTRPTRASK 115
Cdd:PRK07342 250 WSMLRARLYEEEL-KKREEATNAAAASK 276
PRK06746 PRK06746
peptide chain release factor 2; Provisional
 14-103 4.72e-03

peptide chain release factor 2; Provisional


Pssm-ID: 75726 [Multi-domain]  Cd Length: 326  Bit Score: 35.86  E-value: 4.72e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446558204  14 ELEITAIRAQGAGGQHVNKTSTAihlrfdIRASSLPEYykerllaashhlissdgvIVIKAQEYRSQELNREAALARLVA 93
Cdd:PRK06746 198 DLKIDTYRASGAGGQHVNTTDSA------VRITHTPTN------------------TVVTCQSERSQIKNREHAMKMLKA 253

                         90
                 ....*....|
gi 446558204  94 VIKELTTEQK 103
Cdd:PRK06746 254 KLYQKKLEEQ 263
 
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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