efp Resolved · high auto-curated
H37Rv Rv2534c · MTBC0 - ·
187 aa · 2858727–2859290 (-) ·
RefSeq NP_217050.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | elongation factor P |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Elongation factor P. Pfam: EFP_N (PF08207.19), EFP (PF01132.28), Elong-fact-P_C (PF09285.18). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WNM3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Elongation factor P |
| Curated function | Involved in peptide bond synthesis. Stimulates efficient translation and peptide-bond synthesis on native or reconstituted 70S ribosomes in vitro. Probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase (By similarity). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | efp |
| eggNOG description | Involved in peptide bond synthesis. Stimulates efficient translation and peptide-bond synthesis on native or reconstituted 70S ribosomes in vitro. Probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase |
| Orthologous group | COG0231 |
| KEGG orthology |
K02356
|
| Gene Ontology (42) |
GO:0003674, GO:0003676, GO:0003723, GO:0003746, GO:0005488, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0006412, GO:0006414, GO:0006518 +30 more
|
Orthology-based transfer (eggNOG 5.0.2, diamond). EC/KO/GO/CAZy are computed annotations, not manual curation; cross-check against the primary literature before treating a specific reaction as established.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | 0.111 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 1 missense, 0 nonsense, 0 frameshift |
pN/pS from segregating SNPs (singletons removed) normalised by possible sites. Low pN/pS = purifying selection (a strong signal that a "hypothetical" is a real, constrained gene). A high pN/pS is ambiguous: relaxed constraint or positive selection (drug resistance, antigenic variation) inflate it; e.g. rpoB/katG/pncA score high here for resistance, not loss of function. A clonal disruption (one allele over a clade) suggests lineage pseudogenisation; a convergent one (many independent alleles) is typical of resistance loss-of-function.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
EFP_N | PF08207.19 | 3.6e-26 | 3–60 | Elongation factor P (EF-P) KOW-like domain |
EFP | PF01132.28 | 6.2e-24 | 65–123 | Elongation factor P (EF-P) OB domain |
Elong-fact-P_C | PF09285.18 | 1.6e-25 | 129–184 | Elongation factor P, C-terminal |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rpsQ (30S ribosomal protein S17), high confidence from genomic context alone (score 993 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0710 rpsQ |
30S ribosomal protein S17 | 994 | 993 ctx | cooccurence:435 coexpression:844 experimental:928 |
Rv0720 rplR |
50S ribosomal protein L18 | 993 | 991 | coexpression:819 experimental:928 |
Rv0706 rplV |
50S ribosomal protein L22 | 992 | 991 | coexpression:812 experimental:928 |
Rv3443c rplM |
50S ribosomal protein L13 | 991 | 991 | coexpression:847 experimental:928 |
Rv3458c rpsD |
30S ribosomal protein S4 | 991 | 991 | coexpression:845 experimental:928 |
Rv0700 rpsJ |
30S ribosomal protein S10 | 993 | 990 | coexpression:861 experimental:928 |
Rv0682 rpsL |
30S ribosomal protein S12 | 992 | 990 | coexpression:840 experimental:928 |
Rv0683 rpsG |
30S ribosomal protein S7 | 991 | 990 | coexpression:839 experimental:928 |
Rv0714 rplN |
50S ribosomal protein L14 | 991 | 990 | coexpression:845 experimental:928 |
Rv2890c rpsB |
30S ribosomal protein S2 | 991 | 989 | coexpression:822 experimental:928 |
Rv0707 rpsC |
30S ribosomal protein S3 | 990 | 989 | coexpression:847 experimental:928 |
Rv2785c rpsO |
30S ribosomal protein S15 | 990 | 989 | coexpression:810 experimental:928 |
Rv0701 rplC |
50S ribosomal protein L3 | 989 | 988 | coexpression:836 experimental:928 |
Rv0641 rplA |
50S ribosomal protein L1 | 990 | 987 | coexpression:767 experimental:928 |
Rv0705 rpsS |
30S ribosomal protein S19 | 989 | 987 | coexpression:824 experimental:928 |
STRING combines evidence channels (neighborhood, fusion, cooccurrence, coexpression, experimental, database, text-mining) into a 0–1000 score. The ctx badge marks edges carried by the genomic-context channels (conserved neighborhood, fusion, phylogenetic co-occurrence), which are independent of orthology and structure and the strongest signal for an unknown gene. The no text-mining column recomputes the score from data alone, so a link that does not depend on the literature is visible. Association is a function hypothesis, not proof: corroborate with the operon context and the primary literature before assigning a function.
Evidence
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): elongation factor P
- Pfam (hmmscan --cut_ga): EFP_N PF08207.19 (E=4e-26), EFP PF01132.28 (E=6e-24), Elong-fact-P_C PF09285.18 (E=2e-25)
- (auto-curated by rules from PGAP + Pfam + Foldseek; not hand-reviewed)
Sources
- Ancestral sequence & coordinates: Harrison LB et al. (2024), An imputed ancestral reference genome for the MTBC, doi:10.1101/2023.09.07.556366
- Product annotation: NCBI PGAP on MTBC0; legacy from H37Rv NC_000962.3 (RefSeq NP_217050.1)
- Domains: Pfam-A via hmmscan --cut_ga — EFP_N (PF08207.19), EFP (PF01132.28), Elong-fact-P_C (PF09285.18)
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Controlled vocabulary: eggNOG-mapper 2.1.12 (Cantalapiedra et al. 2021,
doi:10.1093/molbev/msab293), eggNOG 5.0 DB
(Huerta-Cepas et al. 2019) — OG
COG0231 - Curated reference: UniProt P9WNM3 (SwissProt, reviewed; Evidence at protein level)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
225 functional partner(s); context anchor
rpsQ - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2534c|efp MATTADFKNGLVLVIDGQLWTITEFQHVKPGKGPAFVRTKLKNVLSGKVVDKTFNAGVKVDTATVDRRDTTYLYRDGSDFVFMDSQDYEQHPLPEALVGDAARFLLEGMPVQVAFHNGVPLYIELPVTVELEVTHTEPGLQGDRSSAGTKPATLQTGAQINVPLFINTGDKLKVDSRDGSYLGRVNA