peptide chain release factor 1, archaeal and eukaryotic forms; Directs the termination of ...
1-384
4.93e-155
peptide chain release factor 1, archaeal and eukaryotic forms; Directs the termination of nascent peptide synthesis (translation) in response to the termination codons UAA, UAG and UGA. This model identifies both archaeal (aRF1) and eukaryotic (eRF1) of the protein. Also known as translation termination factor 1. [Protein synthesis, Translation factors]
The actual alignment was detected with superfamily member TIGR03676:
Pssm-ID: 456209 [Multi-domain] Cd Length: 403 Bit Score: 443.27 E-value: 4.93e-155
peptide chain release factor 1, archaeal and eukaryotic forms; Directs the termination of ...
1-384
4.93e-155
peptide chain release factor 1, archaeal and eukaryotic forms; Directs the termination of nascent peptide synthesis (translation) in response to the termination codons UAA, UAG and UGA. This model identifies both archaeal (aRF1) and eukaryotic (eRF1) of the protein. Also known as translation termination factor 1. [Protein synthesis, Translation factors]
Pssm-ID: 274719 [Multi-domain] Cd Length: 403 Bit Score: 443.27 E-value: 4.93e-155
Peptide chain release factor 1 (eRF1) [Translation, ribosomal structure and biogenesis]; Peptide chain release factor 1 (eRF1) is part of the Pathway/BioSystem: Translation factors
Pssm-ID: 441112 [Multi-domain] Cd Length: 384 Bit Score: 306.82 E-value: 1.02e-101
eRF1 domain 2; The release factor eRF1 terminates protein biosynthesis by recognising stop ...
112-244
1.33e-58
eRF1 domain 2; The release factor eRF1 terminates protein biosynthesis by recognising stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site. This family also includes other proteins for which the precise molecular function is unknown. Many of them are from Archaebacteria. These proteins may also be involved in translation termination but this awaits experimental verification.
Pssm-ID: 397502 Cd Length: 133 Bit Score: 187.10 E-value: 1.33e-58
peptide chain release factor 1, archaeal and eukaryotic forms; Directs the termination of ...
1-384
4.93e-155
peptide chain release factor 1, archaeal and eukaryotic forms; Directs the termination of nascent peptide synthesis (translation) in response to the termination codons UAA, UAG and UGA. This model identifies both archaeal (aRF1) and eukaryotic (eRF1) of the protein. Also known as translation termination factor 1. [Protein synthesis, Translation factors]
Pssm-ID: 274719 [Multi-domain] Cd Length: 403 Bit Score: 443.27 E-value: 4.93e-155
Peptide chain release factor 1 (eRF1) [Translation, ribosomal structure and biogenesis]; Peptide chain release factor 1 (eRF1) is part of the Pathway/BioSystem: Translation factors
Pssm-ID: 441112 [Multi-domain] Cd Length: 384 Bit Score: 306.82 E-value: 1.02e-101
eRF1 domain 2; The release factor eRF1 terminates protein biosynthesis by recognising stop ...
112-244
1.33e-58
eRF1 domain 2; The release factor eRF1 terminates protein biosynthesis by recognising stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site. This family also includes other proteins for which the precise molecular function is unknown. Many of them are from Archaebacteria. These proteins may also be involved in translation termination but this awaits experimental verification.
Pssm-ID: 397502 Cd Length: 133 Bit Score: 187.10 E-value: 1.33e-58
eRF1 domain 3; The release factor eRF1 terminates protein biosynthesis by recognising stop ...
247-384
8.64e-35
eRF1 domain 3; The release factor eRF1 terminates protein biosynthesis by recognising stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site. This family also includes other proteins for which the precise molecular function is unknown. Many of them are from Archaebacteria. These proteins may also be involved in translation termination but this awaits experimental verification.
Pssm-ID: 397503 [Multi-domain] Cd Length: 100 Bit Score: 124.20 E-value: 8.64e-35
eRF1 domain 1; The release factor eRF1 terminates protein biosynthesis by recognising stop ...
1-103
2.40e-27
eRF1 domain 1; The release factor eRF1 terminates protein biosynthesis by recognising stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site. This family also includes other proteins for which the precise molecular function is unknown. Many of them are from Archaebacteria. These proteins may also be involved in translation termination but this awaits experimental verification.
Pssm-ID: 460930 [Multi-domain] Cd Length: 122 Bit Score: 104.88 E-value: 2.40e-27
Bacterial archaeo-eukaryotic release factor family 10; Bacterial family of the ...
99-217
4.01e-06
Bacterial archaeo-eukaryotic release factor family 10; Bacterial family of the archaeo-eukaryotic release factor superfamily. Likely to play roles in biological conflicts or regulation under stress conditions at the ribosome.
Pssm-ID: 436784 Cd Length: 143 Bit Score: 46.13 E-value: 4.01e-06
Actinobacteria/chloroflexi VLRF1 release factor; Archaeo-eukaryotic release factor domain family belonging to the VLRF1 clade, observed primarily in the actinbacteria and chloroflexi bacterial lineages. Contains a conserved glutamine residue in the release factor catalytic loop, suggesting it functions as an active peptidyl-tRNA hydrolase at the ribosome.
Pssm-ID: 436788 [Multi-domain] Cd Length: 130 Bit Score: 39.46 E-value: 6.37e-04
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.
of the residues that compose this conserved feature have been mapped to the query sequence.
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The table lists conserved domains identified on the query sequence. Click on the plus sign (+) on the left to display full descriptions, alignments, and scores.
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(labeled illustration) Standard Display shows only the best scoring domain model from each source, in each hit category listed below for each region on the query sequence.
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