Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | macrolide ABC transporter ATP-binding protein |
|---|
| MTBC0 PGAP re-annotation | energy-dependent translational throttle protein EttA |
|---|
| Revised (this work) | Energy-dependent translational throttle protein EttA. Pfam: ABC_tran (PF00005.34), ABC_tran_Xtn (PF12848.14). |
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Auto-curated: this verdict and function were generated by rules from
PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WQK3
SwissProt · reviewed
· Evidence at protein level
|
|---|
| UniProt name | Energy-dependent translational throttle protein EttA |
|---|
| EC (curated) |
EC 3.6.1.-
|
|---|
| Curated function | A translation factor that gates the progression of the 70S ribosomal initiation complex (IC, containing tRNA(fMet) in the P-site) into the translation elongation cycle by using a mechanism sensitive to the ATP/ADP ratio. Binds to the 70S ribosome E-site where it modulates the state of the translating ribosome during subunit translocation. ATP hydrolysis probably frees it from the ribosome, which can enter the elongation phase..; FUNCTION: Binding to the E-site in the pre-ATP hydrolysis state reduces movement of the 30S subunit relative to the whole 70S ribosome; EttA has different conformation. |
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Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|
| Preferred name | yjjK |
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| eggNOG description | ABC transporter |
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| Orthologous group | COG0488 |
|---|
| Gene Ontology (15) |
GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0008150, GO:0016020, GO:0030312, GO:0040007, GO:0044424 +3 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 |
0.418 · purifying
|
|---|
| Polymorphic sites (≥ 0.1% of strains) |
3 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 |
|---|
ABC_tran | PF00005.34 |
2.7e-26 | 21–188 |
ABC transporter |
ABC_tran_Xtn | PF12848.14 |
3.1e-14 | 227–306 |
ABC transporter |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|
Rv2442c rplU |
50S ribosomal protein L21 |
920 |
921 |
experimental:898 |
Rv3443c rplM |
50S ribosomal protein L13 |
918 |
919 |
experimental:898 |
Rv2785c rpsO |
30S ribosomal protein S15 |
920 |
918 |
experimental:898 |
Rv0707 rpsC |
30S ribosomal protein S3 |
917 |
917 |
experimental:898 |
Rv0702 rplD |
50S ribosomal protein L4 |
919 |
915 |
experimental:898 |
Rv0720 rplR |
50S ribosomal protein L18 |
911 |
911 |
experimental:898 |
Rv0701 rplC |
50S ribosomal protein L3 |
914 |
910 |
experimental:898 |
Rv2909c rpsP |
30S ribosomal protein S16 |
910 |
910 |
experimental:898 |
Rv0979A rpmF |
50S ribosomal protein L32 |
908 |
909 |
experimental:898 |
Rv0683 rpsG |
30S ribosomal protein S7 |
913 |
908 |
experimental:898 |
Rv0708 rplP |
50S ribosomal protein L16 |
912 |
908 |
experimental:898 |
Rv3458c rpsD |
30S ribosomal protein S4 |
912 |
908 |
experimental:898 |
Rv0703 rplW |
50S ribosomal protein L23 |
911 |
908 |
experimental:898 |
Rv0722 rpmD |
50S ribosomal protein L30 |
908 |
908 |
experimental:898 |
Rv0705 rpsS |
30S ribosomal protein S19 |
907 |
908 |
experimental:898 |
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: macrolide ABC transporter ATP-binding protein
- MTBC0 PGAP product: energy-dependent translational throttle protein EttA
- Pfam (hmmscan --cut_ga): ABC_tran PF00005.34 (E=3e-26), ABC_tran_Xtn PF12848.14 (E=3e-14)
- (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_216993.1)
- Domains: Pfam-A via hmmscan --cut_ga — ABC_tran (PF00005.34), ABC_tran_Xtn (PF12848.14)
- 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
COG0488
- Curated reference: UniProt
P9WQK3
(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 —
92 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002639|Rv2477c|ettA
MAEFIYTMKKVRKAHGDKVILDDVTLSFYPGAKIGVVGPNGAGKSSVLRIMAGLDKPNNGDAFLATGATVGILQQEPPLNEDKTVRGNVEEGMGDIKIKLDRFNEVAELMATDYTDELMEEMGRLQEELDHADAWDLDAQLEQAMDALRCPPADEPVTNLSGGERRRVALCKLLLSKPDLLLLDEPTNHLDAESVQWLEQHLASYPGAILAVTHDRYFLDNVAEWILELDRGRAYPYEGNYSTYLEKKAERLAVQGRKDAKLQKRLTEELAWVRSGAKARQAKSKARLQRYEEMAAEAEKTRKLDFEEIQIPVGPRLGNVVVEVDHLDKGYDGRALIKDLSFSLPRNGIVGVIGPNGVGKTTLFKTIVGLETPDSGSVKVGETVKLSYVDQARAGIDPRKTVWEVVSDGLDYIQVGQTEVPSRAYVSAFGFKGPDQQKPAGVLSGGERNRLNLALTLKQGGNLILLDEPTNDLDVETLGSLENALLNFPGCAVVISHDRWFLDRTCTHILAWEGDDDNEAKWFWFEGNFGAYEENKVERLGVDAARPHRVTHRKLTRG
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