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Conserved domains on  [gi|446482673|ref|WP_000560527|]
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MULTISPECIES: alternative ribosome rescue aminoacyl-tRNA hydrolase ArfB [Salmonella]

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 3.16e-72

aminoacyl-tRNA hydrolase;


:

Pssm-ID: 181730 [Multi-domain]  Cd Length: 138  Bit Score: 212.32  E-value: 3.16e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446482673   1 MIAISRTVSIADNELEITAIRAQGAGGQHVNKTSSAIHLRFDIRASGLPEYYKQRLLTASHHLISDDGVIIIKAQEFRSQ 80
Cdd:PRK09256   1 MLRITRRLVIPENELEWRFIRASGPGGQNVNKVSTAVELRFDIAASSLPEFYKERLLALAGHRITKDGVIVIKAQEFRSQ 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 446482673  81 ELNREAAIARLVAVIKELTAEQKSRRATRPTRASKERRLSSKAQKSSVKALRGKVR 136
Cdd:PRK09256  81 ERNREDALERLVALIREALKPPKKRRATKPTRGSKERRLESKKQRGEVKALRGKVR 136
 
Name Accession Description Interval E-value
PRK09256 PRK09256
aminoacyl-tRNA hydrolase;
1-136 3.16e-72

aminoacyl-tRNA hydrolase;


Pssm-ID: 181730 [Multi-domain]  Cd Length: 138  Bit Score: 212.32  E-value: 3.16e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446482673   1 MIAISRTVSIADNELEITAIRAQGAGGQHVNKTSSAIHLRFDIRASGLPEYYKQRLLTASHHLISDDGVIIIKAQEFRSQ 80
Cdd:PRK09256   1 MLRITRRLVIPENELEWRFIRASGPGGQNVNKVSTAVELRFDIAASSLPEFYKERLLALAGHRITKDGVIVIKAQEFRSQ 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 446482673  81 ELNREAAIARLVAVIKELTAEQKSRRATRPTRASKERRLSSKAQKSSVKALRGKVR 136
Cdd:PRK09256  81 ERNREDALERLVALIREALKPPKKRRATKPTRGSKERRLESKKQRGEVKALRGKVR 136
PrfB COG1186
Protein chain release factor PrfB [Translation, ribosomal structure and biogenesis]; Protein ...
 1-136 1.75e-53

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: 164.92  E-value: 1.75e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446482673   1 MIAISRTVSIADNELEITAIRAQGAGGQHVNKTSSAIHLRFDIRASGLPeyyKQRLltashhlisDDGVIIIKAQEFRSQ 80
Cdd:COG1186   14 LRMISPEIEIPESDLRIDTYRASGAGGQNVNKVSSAVRLTHDIASSSLP---DSRL---------TPGGIVVKAQEERSQ 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 446482673  81 ELNREAAIARLVAVIKELTAEQKSRRATRPTRASKERRLSSKAQKSSVKALRGKVR 136
Cdd:COG1186   82 HQNREDALKRLKALLYEAELEPKERRATKPTRGSKKRRLWGKQIRSMVKDLRGNVD 137
RF-1 pfam00472
RF-1 domain; This domain is found in peptide chain release factors such as RF-1 and RF-2, and ...
 7-132 9.08e-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: 93.64  E-value: 9.08e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446482673    7 TVSIADNELEITAIRAQGAGGQHVNKTSSAIHLrfdirasglpeyykqrlltasHHLISDdgvIIIKAQEFRSQELNREA 86
Cdd:pfam00472   4 EIEIDPKDLRIDTFRSSGAGGQHVNKTDSAVRL---------------------THIPTG---IVVKCQDERSQHQNREK 59

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 446482673   87 AIARLVAVIKELTAEQKSRRATRPTRA------SKERRLSSKAQKSSVKALR 132
Cdd:pfam00472  60 ALKRLRARLYELEEEKEEEKKRRIKSQvgsgdrSEQIRTYNFKPQSRVKDHR 111
release_prfH TIGR03072
putative peptide chain release factor H; Members of this protein family are bacterial proteins ...
 10-109 1.72e-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: 1.72e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446482673   10 IADNELEITAIRAQGAGGQHVNKTSSAihlrfdIRASglpeyykqrlltashHLISDdgvIIIKAQEFRSQELNREAAIA 89
Cdd:TIGR03072 103 ATEDEIRFETLRSSGPGGQHVNKTESA------VRAT---------------HLASG---ISVKVQSERSQHANKRLATL 158

                          90       100
                  ....*....|....*....|.
gi 446482673   90 RLVAVIKELTAEQKSR-RATR 109
Cdd:TIGR03072 159 LLAVRLADLQQEQAAAlRAER 179
 
Name Accession Description Interval E-value
PRK09256 PRK09256
aminoacyl-tRNA hydrolase;
1-136 3.16e-72

aminoacyl-tRNA hydrolase;


Pssm-ID: 181730 [Multi-domain]  Cd Length: 138  Bit Score: 212.32  E-value: 3.16e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446482673   1 MIAISRTVSIADNELEITAIRAQGAGGQHVNKTSSAIHLRFDIRASGLPEYYKQRLLTASHHLISDDGVIIIKAQEFRSQ 80
Cdd:PRK09256   1 MLRITRRLVIPENELEWRFIRASGPGGQNVNKVSTAVELRFDIAASSLPEFYKERLLALAGHRITKDGVIVIKAQEFRSQ 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 446482673  81 ELNREAAIARLVAVIKELTAEQKSRRATRPTRASKERRLSSKAQKSSVKALRGKVR 136
Cdd:PRK09256  81 ERNREDALERLVALIREALKPPKKRRATKPTRGSKERRLESKKQRGEVKALRGKVR 136
PrfB COG1186
Protein chain release factor PrfB [Translation, ribosomal structure and biogenesis]; Protein ...
 1-136 1.75e-53

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: 164.92  E-value: 1.75e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446482673   1 MIAISRTVSIADNELEITAIRAQGAGGQHVNKTSSAIHLRFDIRASGLPeyyKQRLltashhlisDDGVIIIKAQEFRSQ 80
Cdd:COG1186   14 LRMISPEIEIPESDLRIDTYRASGAGGQNVNKVSSAVRLTHDIASSSLP---DSRL---------TPGGIVVKAQEERSQ 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 446482673  81 ELNREAAIARLVAVIKELTAEQKSRRATRPTRASKERRLSSKAQKSSVKALRGKVR 136
Cdd:COG1186   82 HQNREDALKRLKALLYEAELEPKERRATKPTRGSKKRRLWGKQIRSMVKDLRGNVD 137
RF-1 pfam00472
RF-1 domain; This domain is found in peptide chain release factors such as RF-1 and RF-2, and ...
 7-132 9.08e-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: 93.64  E-value: 9.08e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446482673    7 TVSIADNELEITAIRAQGAGGQHVNKTSSAIHLrfdirasglpeyykqrlltasHHLISDdgvIIIKAQEFRSQELNREA 86
Cdd:pfam00472   4 EIEIDPKDLRIDTFRSSGAGGQHVNKTDSAVRL---------------------THIPTG---IVVKCQDERSQHQNREK 59

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 446482673   87 AIARLVAVIKELTAEQKSRRATRPTRA------SKERRLSSKAQKSSVKALR 132
Cdd:pfam00472  60 ALKRLRARLYELEEEKEEEKKRRIKSQvgsgdrSEQIRTYNFKPQSRVKDHR 111
PrfA COG0216
Protein chain release factor RF1 [Translation, ribosomal structure and biogenesis]; Protein ...
 8-109 2.91e-10

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: 56.55  E-value: 2.91e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446482673   8 VSIADNELEITAIRAQGAGGQHVNKTSSAIHLRfdirasglpeyykqrlltashHLISddGvIIIKAQEFRSQELNREAA 87
Cdd:COG0216  214 VEINPKDLRIDTFRSSGAGGQHVNTTDSAVRIT---------------------HLPT--G-IVVECQDERSQHKNKAKA 269

                         90       100
                 ....*....|....*....|....
gi 446482673  88 IARLVAVI--KELTAEQKSRRATR 109
Cdd:COG0216  270 MKVLRARLyeAEQQKQQAEIAAER 293
prfA PRK00591
peptide chain release factor 1; Validated
 8-109 4.68e-10

peptide chain release factor 1; Validated


Pssm-ID: 234801 [Multi-domain]  Cd Length: 359  Bit Score: 55.85  E-value: 4.68e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446482673   8 VSIADNELEITAIRAQGAGGQHVNKTSSAIHLRfdirasglpeyykqrlltashHLISddGvIIIKAQEFRSQELNREAA 87
Cdd:PRK00591 216 VEINPKDLRIDTFRSSGAGGQHVNTTDSAVRIT---------------------HLPT--G-IVVECQDERSQHKNKAKA 271

                         90       100
                 ....*....|....*....|....
gi 446482673  88 IARLVAVI--KELTAEQKSRRATR 109
Cdd:PRK00591 272 MKVLRARLydAERQKAQAEEAATR 295
release_prfH TIGR03072
putative peptide chain release factor H; Members of this protein family are bacterial proteins ...
 10-109 1.72e-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: 1.72e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446482673   10 IADNELEITAIRAQGAGGQHVNKTSSAihlrfdIRASglpeyykqrlltashHLISDdgvIIIKAQEFRSQELNREAAIA 89
Cdd:TIGR03072 103 ATEDEIRFETLRSSGPGGQHVNKTESA------VRAT---------------HLASG---ISVKVQSERSQHANKRLATL 158

                          90       100
                  ....*....|....*....|.
gi 446482673   90 RLVAVIKELTAEQKSR-RATR 109
Cdd:TIGR03072 159 LLAVRLADLQQEQAAAlRAER 179
PRK05589 PRK05589
peptide chain release factor 2; Provisional
 8-98 2.50e-07

peptide chain release factor 2; Provisional


Pssm-ID: 235520 [Multi-domain]  Cd Length: 325  Bit Score: 48.26  E-value: 2.50e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446482673   8 VSIADNELEITAIRAQGAGGQHVNKTSSAihlrfdIRASGLPEYykqrlltashhlisddgvIIIKAQEFRSQELNREAA 87
Cdd:PRK05589 191 IEIRSEDLKIDTYRAGGAGGQHVNKTESA------VRITHIPTG------------------IVVQCQNERSQHSNKETA 246

                         90
                 ....*....|.
gi 446482673  88 IARLVAVIKEL 98
Cdd:PRK05589 247 MKMLKSKLVEL 257
PRK08787 PRK08787
peptide chain release factor 2; Provisional
 8-137 1.38e-06

peptide chain release factor 2; Provisional


Pssm-ID: 136970 [Multi-domain]  Cd Length: 313  Bit Score: 46.19  E-value: 1.38e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446482673   8 VSIADNELEITAIRAQGAGGQHVNKTSSAIHLRfdirasglpeyykqrlltashHLISDdgvIIIKAQEFRSQELNREAA 87
Cdd:PRK08787 171 IDINPADLRTDVYRSSGAGGQHVNKTESAVRIT---------------------HIPTN---TVVACQTGRSQHQNRDNA 226

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 446482673  88 IARLVAVIKELtaEQKSRRATRPTRASKERRLSSKAQ-------KSSVKALRGKVRR 137
Cdd:PRK08787 227 MKMLAAKLYEL--EVQKRNAEKDALEATKSDIGWGSQirnyvldQSRIKDLRTGIER 281
PRK07342 PRK07342
peptide chain release factor 2; Provisional
 8-115 1.76e-05

peptide chain release factor 2; Provisional


Pssm-ID: 235997 [Multi-domain]  Cd Length: 339  Bit Score: 42.94  E-value: 1.76e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446482673   8 VSIADNELEITAIRAQGAGGQHVNKTSSAIhlRFDIRASGlpeyykqrlltashhlisddgvIIIKAQEFRSQELNREAA 87
Cdd:PRK07342 194 VDVNESDVRIDTYRSSGAGGQHVNTTDSAV--RITHIPTG----------------------IVVQCQQERSQHKNRAKA 249

                         90       100
                 ....*....|....*....|....*....
gi 446482673  88 IARLVAVIKEltAEQKSRR-ATRPTRASK 115
Cdd:PRK07342 250 WSMLRARLYE--EELKKREeATNAAAASK 276
prfB TIGR00020
peptide chain release factor 2; In many but not all taxa, there is a conserved real ...
 8-109 1.91e-05

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: 42.84  E-value: 1.91e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446482673    8 VSIADNELEITAIRAQGAGGQHVNKTSSAihlrfdIRASGLPeyykqrllTAshhlisddgvIIIKAQEFRSQELNREAA 87
Cdd:TIGR00020 230 IEIKPEDLRIDTYRASGAGGQHVNKTDSA------VRITHIP--------TG----------IVVQCQNDRSQHKNKDSA 285

                          90       100
                  ....*....|....*....|....*..
gi 446482673   88 IARLVA-----VIKELTAEQKSRRATR 109
Cdd:TIGR00020 286 MKVLKAklyelEMEKEQAEKDAKEGEK 312
PRK06746 PRK06746
peptide chain release factor 2; Provisional
 8-103 3.55e-03

peptide chain release factor 2; Provisional


Pssm-ID: 75726 [Multi-domain]  Cd Length: 326  Bit Score: 36.25  E-value: 3.55e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446482673   8 VSIADNELEITAIRAQGAGGQHVNKTSSAIhlrfdiRASGLPEYykqrlltashhlisddgvIIIKAQEFRSQELNREAA 87
Cdd:PRK06746 192 IEVRTEDLKIDTYRASGAGGQHVNTTDSAV------RITHTPTN------------------TVVTCQSERSQIKNREHA 247

                         90
                 ....*....|....*.
gi 446482673  88 IARLVAVIKELTAEQK 103
Cdd:PRK06746 248 MKMLKAKLYQKKLEEQ 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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