Rv1303 Family assigned · medium auto-curated
H37Rv Rv1303 · MTBC0 mtbc0_001395 ·
161 aa · 1468805–1469290 (+) ·
RefSeq NP_215819.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | ATP synthase subunit I |
| Revised (this work) | ATP synthase subunit I. Pfam: ATP-synt_I (PF03899.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WM31
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv1303 |
UniProt still lists this protein as Uncharacterized protein Rv1303; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | ATP synthase I chain |
| Orthologous group | 29217 |
| Gene Ontology (2) |
GO:0008150, GO:0040007
|
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 | 0.775 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 2 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 |
|---|---|---|---|---|
ATP-synt_I | PF03899.22 | 2.7e-13 | 21–114 | ATP synthase I chain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: atpB (ATP synthase subunit A), high confidence from genomic context alone (score 977 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) |
|---|---|---|---|---|
Rv1304 atpB |
ATP synthase subunit A | 981 | 977 ctx | neighborhood:882 cooccurence:684 coexpression:423 |
Rv1305 atpE |
ATP synthase subunit C | 965 | 958 ctx | neighborhood:813 cooccurence:667 |
Rv1306 atpF |
ATP synthase subunit B | 955 | 955 ctx | neighborhood:778 coexpression:731 |
Rv1307 atpH |
ATP synthase subunit b/delta | 958 | 943 ctx | neighborhood:778 cooccurence:610 |
Rv1309 atpG |
ATP synthase subunit gamma | 777 | 777 ctx | neighborhood:738 |
Rv1308 atpA |
ATP synthase subunit alpha | 805 | 771 ctx | neighborhood:738 |
Rv1310 atpD |
ATP synthase subunit beta | 721 | 722 ctx | neighborhood:707 |
Rv0309 hyp |
hypothetical protein | 717 | 718 ctx | cooccurence:717 |
Rv3035 hyp |
hypothetical protein | 710 | 711 ctx | cooccurence:710 |
Rv0185 hyp |
hypothetical protein | 700 | 700 ctx | cooccurence:700 |
Rv1125 hyp |
hypothetical protein | 686 | 686 ctx | cooccurence:685 |
Rv1598c hyp |
hypothetical protein | 684 | 684 ctx | cooccurence:684 |
Rv1301 |
threonylcarbamoyl-AMP synthase | 678 | 678 ctx | neighborhood:676 |
Rv1300 hemK |
release factor glutamine methyltransferase | 672 | 672 ctx | neighborhood:670 |
Rv1299 prfA |
peptide chain release factor PrfA | 672 | 672 ctx | neighborhood:670 |
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: ATP synthase subunit I
- Pfam (hmmscan --cut_ga): ATP-synt_I PF03899.22 (E=3e-13)
- (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_215819.1)
- Domains: Pfam-A via hmmscan --cut_ga — ATP-synt_I (PF03899.22)
- 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
29217 - Curated reference: UniProt P9WM31 (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 —
72 functional partner(s); context anchor
atpB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001395|Rv1303| MTTPAQDAPLVFPSVAFRPVRLFFINVGLAAVAMLVAGVFGHLTVGMFLGLGLLLGLLNALLVRRSAESITAKEHPLKRSMALNSASRLAIITILGLIIAYIFRPAGLGVVFGLAFFQVLLVATTALPVLKKLRTATEEPVATYSSNGQTGGSEGRSASDD