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Conserved domains on  [gi|563403458|emb|CDK13391|]
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Peptide chain release factor 1 [Caenorhabditis elegans]

Protein Classification

peptide chain release factor 1( domain architecture ID 1907968)

peptide chain release factor 1 directs the termination of translation in response to the peptide chain termination codons UAG and UAA

CATH:  3.30.160.20|3.30.70.1660|1.10.287.4000
Gene Ontology:  GO:0003747|GO:0016149
SCOP:  4002864|4002570

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PrfA super family cl43066
Protein chain release factor RF1 [Translation, ribosomal structure and biogenesis]; Protein ...
 1-77 4.57e-17

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


The actual alignment was detected with superfamily member COG0216:

Pssm-ID: 439986 [Multi-domain]  Cd Length: 356  Bit Score: 73.50  E-value: 4.57e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 563403458   1 MQKQVDAMLEKIVSKRKLQVGSKARAEKIRTYNFQHDRVTDHRIQMSITGVAEFLsAGEtLQTMIERLQEQHLEDRL 77
Cdd:COG0216  278 YEAEQQKQQAEIAAERKSQVGSGDRSERIRTYNFPQGRVTDHRINLTLYKLDEVM-EGD-LDELIDALIAEDQAEKL 352
 
Name Accession Description Interval E-value
PrfA COG0216
Protein chain release factor RF1 [Translation, ribosomal structure and biogenesis]; Protein ...
 1-77 4.57e-17

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: 73.50  E-value: 4.57e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 563403458   1 MQKQVDAMLEKIVSKRKLQVGSKARAEKIRTYNFQHDRVTDHRIQMSITGVAEFLsAGEtLQTMIERLQEQHLEDRL 77
Cdd:COG0216  278 YEAEQQKQQAEIAAERKSQVGSGDRSERIRTYNFPQGRVTDHRINLTLYKLDEVM-EGD-LDELIDALIAEDQAEKL 352
prfA PRK00591
peptide chain release factor 1; Validated
 10-77 5.31e-15

peptide chain release factor 1; Validated


Pssm-ID: 234801 [Multi-domain]  Cd Length: 359  Bit Score: 67.80  E-value: 5.31e-15
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 563403458  10 EKIVSKRKLQVGSKARAEKIRTYNFQHDRVTDHRIQMSITGVAEFLsAGEtLQTMIERLQEQHLEDRL 77
Cdd:PRK00591 289 AEEAATRKSQVGSGDRSERIRTYNFPQGRVTDHRINLTLYKLDEVM-EGD-LDELIDALIAEDQAEKL 354
prfA TIGR00019
peptide chain release factor 1; This model describes peptide chain release factor 1 (PrfA, ...
 9-82 2.26e-13

peptide chain release factor 1; This model describes peptide chain release factor 1 (PrfA, RF-1), and excludes the related peptide chain release factor 2 (PrfB, RF-2). RF-1 helps recognize and terminate translation at UAA and UAG stop codons. The mitochondrial release factors are prfA-like, although not included above the trusted cutoff for this model. RF-1 does not have a translational frameshift. [Protein synthesis, Translation factors]


Pssm-ID: 129130 [Multi-domain]  Cd Length: 360  Bit Score: 63.17  E-value: 2.26e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 563403458    9 LEKIVSKRKLQVGSKARAEKIRTYNFQHDRVTDHRIQMSITGVAEFLSAGetLQTMIERLQEQHLEDRLDHIIE 82
Cdd:TIGR00019 288 QAAQASTRKSQVGSGDRSERIRTYNFPQNRVTDHRINLTLYKLDEVLEGD--LDELIEALIAEDQAQQLAALSE 359
RF-1 pfam00472
RF-1 domain; This domain is found in peptide chain release factors such as RF-1 and RF-2, and ...
 15-43 7.99e-07

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: 43.18  E-value: 7.99e-07
                          10        20        30
                  ....*....|....*....|....*....|
gi 563403458   15 KRKLQVGSKARAEKIRTYNFQ-HDRVTDHR 43
Cdd:pfam00472  82 RIKSQVGSGDRSEQIRTYNFKpQSRVKDHR 111
 
Name Accession Description Interval E-value
PrfA COG0216
Protein chain release factor RF1 [Translation, ribosomal structure and biogenesis]; Protein ...
 1-77 4.57e-17

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: 73.50  E-value: 4.57e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 563403458   1 MQKQVDAMLEKIVSKRKLQVGSKARAEKIRTYNFQHDRVTDHRIQMSITGVAEFLsAGEtLQTMIERLQEQHLEDRL 77
Cdd:COG0216  278 YEAEQQKQQAEIAAERKSQVGSGDRSERIRTYNFPQGRVTDHRINLTLYKLDEVM-EGD-LDELIDALIAEDQAEKL 352
prfA PRK00591
peptide chain release factor 1; Validated
 10-77 5.31e-15

peptide chain release factor 1; Validated


Pssm-ID: 234801 [Multi-domain]  Cd Length: 359  Bit Score: 67.80  E-value: 5.31e-15
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 563403458  10 EKIVSKRKLQVGSKARAEKIRTYNFQHDRVTDHRIQMSITGVAEFLsAGEtLQTMIERLQEQHLEDRL 77
Cdd:PRK00591 289 AEEAATRKSQVGSGDRSERIRTYNFPQGRVTDHRINLTLYKLDEVM-EGD-LDELIDALIAEDQAEKL 354
prfA TIGR00019
peptide chain release factor 1; This model describes peptide chain release factor 1 (PrfA, ...
 9-82 2.26e-13

peptide chain release factor 1; This model describes peptide chain release factor 1 (PrfA, RF-1), and excludes the related peptide chain release factor 2 (PrfB, RF-2). RF-1 helps recognize and terminate translation at UAA and UAG stop codons. The mitochondrial release factors are prfA-like, although not included above the trusted cutoff for this model. RF-1 does not have a translational frameshift. [Protein synthesis, Translation factors]


Pssm-ID: 129130 [Multi-domain]  Cd Length: 360  Bit Score: 63.17  E-value: 2.26e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 563403458    9 LEKIVSKRKLQVGSKARAEKIRTYNFQHDRVTDHRIQMSITGVAEFLSAGetLQTMIERLQEQHLEDRLDHIIE 82
Cdd:TIGR00019 288 QAAQASTRKSQVGSGDRSERIRTYNFPQNRVTDHRINLTLYKLDEVLEGD--LDELIEALIAEDQAQQLAALSE 359
RF-1 pfam00472
RF-1 domain; This domain is found in peptide chain release factors such as RF-1 and RF-2, and ...
 15-43 7.99e-07

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: 43.18  E-value: 7.99e-07
                          10        20        30
                  ....*....|....*....|....*....|
gi 563403458   15 KRKLQVGSKARAEKIRTYNFQ-HDRVTDHR 43
Cdd:pfam00472  82 RIKSQVGSGDRSEQIRTYNFKpQSRVKDHR 111
 
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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