Rv0976c Family assigned · medium auto-curated
H37Rv Rv0976c · MTBC0 mtbc0_001042 ·
560 aa · 1095708–1097390 (-) ·
RefSeq NP_215491.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | acyclic terpene utilization AtuA family protein |
| Revised (this work) | Acyclic terpene utilization AtuA family protein. Pfam: AtuA (PF07287.18), AtuA_ferredoxin (PF23544.2). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O86320
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Exopolyphosphatase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| eggNOG description | Acyclic terpene utilisation family protein AtuA |
| Orthologous group | COG3185 |
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 | 0.98 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 8 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.26% of strains (373) · clonal |
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 |
|---|---|---|---|---|
AtuA | PF07287.18 | 2.8e-155 | 1–415 | Acyclic terpene utilisation family protein AtuA |
AtuA_ferredoxin | PF23544.2 | 2.7e-16 | 456–553 | AtuA ferredoxin-like domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: accD2 (acetyl-/propionyl-CoA carboxylase subunit beta), high confidence from genomic context alone (score 992 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0974c accD2 |
acetyl-/propionyl-CoA carboxylase subunit beta | 992 | 992 ctx | neighborhood:881 coexpression:907 |
Rv0975c fadE13 |
acyl-CoA dehydrogenase FadE13 | 986 | 986 ctx | neighborhood:881 coexpression:859 |
Rv0973c accA2 |
acetyl/propionyl-CoA carboxylase subuit alpha | 984 | 983 ctx | neighborhood:881 coexpression:832 |
Rv0972c fadE12 |
acyl-CoA dehydrogenase fadE12 | 961 | 960 ctx | neighborhood:881 cooccurence:487 |
Rv0971c echA7 |
enoyl-CoA hydratase EchA7 | 912 | 908 ctx | neighborhood:881 |
Rv0036c hyp |
hypothetical protein | 700 | 701 ctx | cooccurence:628 |
Rv0981 mprA |
two-component response regulator MrpA | 548 | 548 ctx | neighborhood:544 |
Rv0979A rpmF |
50S ribosomal protein L32 | 544 | 544 ctx | neighborhood:544 |
Rv2502c accD1 |
acetyl-/propionyl-CoA carboxylase subunit beta | 544 | 516 | coexpression:454 |
Rv0977 PE_PGRS16 |
PE-PGRS family protein PE_PGRS16 | 502 | 502 ctx | neighborhood:502 |
Rv2247 accD6 |
acetyl-/propionyl-CoA carboxylase subunit beta | 506 | 476 | coexpression:446 |
Rv3280 accD5 |
propionyl-CoA carboxylase subunit beta | 506 | 476 | coexpression:446 |
Rv3799c accD4 |
propionyl-CoA carboxylase subunit beta AccD | 506 | 476 | coexpression:446 |
Rv0939 |
bifunctional 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase/cyclase/dehydrase | 593 | 454 | |
Rv2912c |
TetR family HTH-type transcriptional regulator | 455 | 446 |
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: hypothetical protein
- MTBC0 PGAP product: acyclic terpene utilization AtuA family protein
- Pfam (hmmscan --cut_ga): AtuA PF07287.18 (E=3e-155), AtuA_ferredoxin PF23544.2 (E=3e-16)
- (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_215491.1)
- Domains: Pfam-A via hmmscan --cut_ga — AtuA (PF07287.18), AtuA_ferredoxin (PF23544.2)
- 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
COG3185 - Curated reference: UniProt O86320 (TrEMBL, unreviewed; Predicted)
- 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 —
34 functional partner(s); context anchor
accD2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001042|Rv0976c| MRIGNCSGFYGDRLSAMREMLTGGELDYLTGDYLAELTMLILGRDRMKNPDRGYAKTFLAQLEDCLGLAHDRGVRIVTNAGGLNPAGLANAVRALAARLGIPAQVAHVEGDDLQPRAAELGLGTPLTANAYLGAWGIVDCFERGADVVVTGRVTDASVVVGAAAAHFGWGRTDYHRLAGAVVAGHVIECGVQATGGNYAFFTEIGDLTHAGFPLAEIAADGSSVITKHHGTGGLVSVDTITAQLLYEITGARYANPDVTARMDSVELSPDGPDRVRISGVIGEPPPPTYKVSLNSIGGFRNAMTFVLTGLDIDAKADLVRRQLEAALTVKPAELQWTLARTDHPDADTEETASALLTCVARDPDPANVGRQFSSAAVELALASYPGFTATAPPGDGQVYGVFTPGYVDAGKVAHIAVHADGTRTEIPCATETLELAPAHPPALPDPLPAGPTRRVPLGLIAGARSGDKGGSANVGVWVRTDEQWRWLAHTLTVELLKELLPETAGLVVTRHVLPNLRALNFVIEAILGQGVAYQARFDPQAKGLGEWLRSRHVEIPETLL