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Conserved domains on  [gi|496082547|ref|WP_008807054|]
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MULTISPECIES: alternative ribosome-rescue factor A [Klebsiella]

Protein Classification

alternative ribosome-rescue factor A( domain architecture ID 10006864)

alternative ribosome-rescue factor A (ArfA) rescues the ribosomes stalled at the 3' end of non-stop mRNAs

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
ArfA COG3036
Stalled ribosome alternative rescue factor ArfA [Translation, ribosomal structure and ...
 1-68 1.40e-34

Stalled ribosome alternative rescue factor ArfA [Translation, ribosomal structure and biogenesis];


:

Pssm-ID: 442270  Cd Length: 65  Bit Score: 112.73  E-value: 1.40e-34
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 496082547  1 MSRYQHTKGQIKDNAIEALLHDPLFRQRVEKNKKGKGSYQRKDKHAGRIDREASGKQanrFFTTGLLL 68
Cdd:COG3036   1 MSKYQHGRGQIKDNALKALVTDPLFRQRVEKNKKGKGSYQRKAKHGKKEGWEASGKQ---FFTLGFLL 65
 
Name Accession Description Interval E-value
ArfA COG3036
Stalled ribosome alternative rescue factor ArfA [Translation, ribosomal structure and ...
 1-68 1.40e-34

Stalled ribosome alternative rescue factor ArfA [Translation, ribosomal structure and biogenesis];


Pssm-ID: 442270  Cd Length: 65  Bit Score: 112.73  E-value: 1.40e-34
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 496082547  1 MSRYQHTKGQIKDNAIEALLHDPLFRQRVEKNKKGKGSYQRKDKHAGRIDREASGKQanrFFTTGLLL 68
Cdd:COG3036   1 MSKYQHGRGQIKDNALKALVTDPLFRQRVEKNKKGKGSYQRKAKHGKKEGWEASGKQ---FFTLGFLL 65
ArfA pfam03889
Alternative ribosome-rescue factor A; During translation of messenger RNAs by ribosomes, ...
 4-46 1.56e-25

Alternative ribosome-rescue factor A; During translation of messenger RNAs by ribosomes, translation sometimes pauses or stalls. Ribosomes stalled on mRNAs need to be rescued for reuse in order to maintain proper translation capacity. Rescue systems such as ArfA-RF2 and ArfB (formerly known as YaeJ) are present in many bacterial species. Family members such as ArfA cooperates with the canonical peptide release factor RF2 to hydrolyse the peptidyl-tRNA in the non-stop complex. Structural and biochemical analysis show that ArfA anchors its positively charged C-terminal in the mRNA entry channel of the ribosome. Whereas its N terminus is sandwiched between the decoding centre and the switch loop of RF2, leading to marked conformational changes in both the decoding centre and RF2 thereby triggering RF2 peptidyl-hydrolysing activity.


Pssm-ID: 427571  Cd Length: 44  Bit Score: 89.13  E-value: 1.56e-25
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 496082547   4 YQHTKGQIKDNAIEALLHDPLFRQRVEKNKKGKGSYQRKDKHA 46
Cdd:pfam03889  2 YEHGRGVIRDNALKALVTSPLFRQRVEKNKKGKGSYQRKAKHK 44
 
Name Accession Description Interval E-value
ArfA COG3036
Stalled ribosome alternative rescue factor ArfA [Translation, ribosomal structure and ...
 1-68 1.40e-34

Stalled ribosome alternative rescue factor ArfA [Translation, ribosomal structure and biogenesis];


Pssm-ID: 442270  Cd Length: 65  Bit Score: 112.73  E-value: 1.40e-34
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 496082547  1 MSRYQHTKGQIKDNAIEALLHDPLFRQRVEKNKKGKGSYQRKDKHAGRIDREASGKQanrFFTTGLLL 68
Cdd:COG3036   1 MSKYQHGRGQIKDNALKALVTDPLFRQRVEKNKKGKGSYQRKAKHGKKEGWEASGKQ---FFTLGFLL 65
ArfA pfam03889
Alternative ribosome-rescue factor A; During translation of messenger RNAs by ribosomes, ...
 4-46 1.56e-25

Alternative ribosome-rescue factor A; During translation of messenger RNAs by ribosomes, translation sometimes pauses or stalls. Ribosomes stalled on mRNAs need to be rescued for reuse in order to maintain proper translation capacity. Rescue systems such as ArfA-RF2 and ArfB (formerly known as YaeJ) are present in many bacterial species. Family members such as ArfA cooperates with the canonical peptide release factor RF2 to hydrolyse the peptidyl-tRNA in the non-stop complex. Structural and biochemical analysis show that ArfA anchors its positively charged C-terminal in the mRNA entry channel of the ribosome. Whereas its N terminus is sandwiched between the decoding centre and the switch loop of RF2, leading to marked conformational changes in both the decoding centre and RF2 thereby triggering RF2 peptidyl-hydrolysing activity.


Pssm-ID: 427571  Cd Length: 44  Bit Score: 89.13  E-value: 1.56e-25
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 496082547   4 YQHTKGQIKDNAIEALLHDPLFRQRVEKNKKGKGSYQRKDKHA 46
Cdd:pfam03889  2 YEHGRGVIRDNALKALVTSPLFRQRVEKNKKGKGSYQRKAKHK 44
 
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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