tsf Resolved · high auto-curated
H37Rv Rv2889c · MTBC0 mtbc0_003071 ·
271 aa · 3219121–3219936 (-) ·
RefSeq NP_217405.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | elongation factor EF-Ts |
|---|---|
| MTBC0 PGAP re-annotation | translation elongation factor Ts |
| Revised (this work) | Translation elongation factor Ts. Pfam: EF_TS (PF00889.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WNM1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Elongation factor Ts |
| Curated function | Associates with the EF-Tu.GDP complex and induces the exchange of GDP to GTP. It remains bound to the aminoacyl-tRNA.EF-Tu.GTP complex up to the GTP hydrolysis stage on the ribosome (By similarity). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | tsf |
| eggNOG description | Associates with the EF-Tu.GDP complex and induces the exchange of GDP to GTP. It remains bound to the aminoacyl-tRNA.EF- Tu.GTP complex up to the GTP hydrolysis stage on the ribosome |
| Orthologous group | COG0264 |
| KEGG orthology |
K02357
|
| Gene Ontology (49) |
GO:0003674, GO:0003676, GO:0003723, GO:0003746, GO:0005488, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886 +37 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 | 0.347 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 4 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 |
|---|---|---|---|---|
EF_TS | PF00889.26 | 1.5e-61 | 75–270 | Elongation factor TS |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rpsB (30S ribosomal protein S2), high confidence from genomic context alone (score 998 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0685 tuf |
elongation factor Tu | 999 | 1000 | coexpression:861 experimental:999 database:664 textmining:771 |
Rv2890c rpsB |
30S ribosomal protein S2 | 999 | 998 ctx | neighborhood:876 coexpression:964 textmining:622 |
Rv1307 atpH |
ATP synthase subunit b/delta | 997 | 995 | coexpression:994 textmining:453 |
Rv3442c rpsI |
30S ribosomal protein S9 | 989 | 975 | coexpression:957 database:404 textmining:587 |
Rv2882c frr |
ribosome recycling factor | 984 | 960 ctx | cooccurence:491 coexpression:860 textmining:618 |
Rv3443c rplM |
50S ribosomal protein L13 | 977 | 948 | coexpression:915 textmining:591 |
Rv1643 rplT |
50S ribosomal protein L20 | 975 | 944 | coexpression:858 database:404 textmining:583 |
Rv0652 rplL |
50S ribosomal protein L7/L12 | 978 | 939 | coexpression:885 database:404 textmining:670 |
Rv0056 rplI |
50S ribosomal protein L9 | 953 | 939 | coexpression:882 database:404 |
Rv0702 rplD |
50S ribosomal protein L4 | 973 | 938 | coexpression:883 textmining:583 |
Rv0641 rplA |
50S ribosomal protein L1 | 969 | 933 | coexpression:863 textmining:562 |
Rv1630 rpsA |
30S ribosomal protein S1 | 955 | 930 | coexpression:862 experimental:474 |
Rv2909c rpsP |
30S ribosomal protein S16 | 946 | 930 | coexpression:881 database:404 |
Rv2888c amiC |
amidase AmiC | 930 | 930 ctx | neighborhood:882 |
Rv0715 rplX |
50S ribosomal protein L24 | 937 | 928 | coexpression:860 |
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
- Legacy H37Rv annotation: elongation factor EF-Ts
- MTBC0 PGAP product: translation elongation factor Ts
- Pfam (hmmscan --cut_ga): EF_TS PF00889.26 (E=2e-61)
- (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_217405.1)
- Domains: Pfam-A via hmmscan --cut_ga — EF_TS (PF00889.26)
- 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
COG0264 - Curated reference: UniProt P9WNM1 (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 —
221 functional partner(s); context anchor
rpsB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003071|Rv2889c|tsf MANFTAADVKRLRELTGAGMLACKNALAETDGDFDKAVEALRIKGAKDVGKRAERATAEGLVAAKDGALIELNCETDFVAKNAEFQTLADQVVAAAAAAKPADVDALKGASIGDKTVEQAIAELSAKIGEKLELRRVAIFDGTVEAYLHRRSADLPPAVGVLVEYRGDDAAAAHAVALQIAALRARYLSRDDVPEDIVASERRIAEETARAEGKPEQALPKIVEGRLNGFFKDAVLLEQASVSDNKKTVKALLDVAGVTVTRFVRFEVGQA