Rv3035 Family assigned · medium auto-curated
H37Rv Rv3035 · MTBC0 - ·
360 aa · 3395379–3396461 (+) ·
RefSeq NP_217551.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Contains PQQ_2 (PF13360.14) domain(s); putative function inferred from the domain architecture. |
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 |
I6XFZ8
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Protein Rv3035 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Pyrrolo-quinoline quinone |
| Orthologous group | COG1520 |
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 | 0.228 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 8 synonymous, 5 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 |
|---|---|---|---|---|
PQQ_2 | PF13360.14 | 9.4e-07 | 189–333 | Outer membrane protein assembly factor BamB |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lprC (lipoprotein LprC), high confidence from genomic context alone (score 774 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) |
|---|---|---|---|---|
Rv1275 lprC |
lipoprotein LprC | 774 | 774 ctx | cooccurence:770 |
Rv1274 lprB |
lipoprotein LprB | 773 | 774 ctx | cooccurence:771 |
Rv1476 |
membrane protein | 772 | 772 ctx | cooccurence:771 |
Rv3802c |
membrane protein | 770 | 771 ctx | cooccurence:767 |
Rv3792 aftA |
arabinofuranosyltransferase | 769 | 769 ctx | cooccurence:766 |
Rv1125 hyp |
hypothetical protein | 767 | 767 ctx | cooccurence:766 |
Rv3668c |
protease | 763 | 763 ctx | cooccurence:761 |
Rv0383c ttfA hyp |
hypothetical protein | 770 | 761 ctx | cooccurence:761 |
Rv0466 hyp |
hypothetical protein | 761 | 761 ctx | cooccurence:760 |
Rv2876 |
transmembrane protein | 759 | 759 ctx | cooccurence:757 |
Rv3244c lpqB |
lipoprotein LpqB | 757 | 757 ctx | cooccurence:752 |
Rv2672 |
protease | 756 | 757 ctx | cooccurence:745 |
Rv3805c aftB |
terminal beta-(1->2)-arabinofuranosyltransferase | 764 | 756 ctx | cooccurence:753 |
Rv3346c |
transmembrane protein | 755 | 755 ctx | cooccurence:754 |
Rv2673 aftC |
alpha-(1->3)-arabinofuranosyltransferase | 752 | 753 ctx | cooccurence:751 |
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): hypothetical protein
- Pfam (hmmscan --cut_ga): PQQ_2 PF13360.14 (E=9e-07)
- (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_217551.1)
- Domains: Pfam-A via hmmscan --cut_ga — PQQ_2 (PF13360.14)
- 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
COG1520 - Curated reference: UniProt I6XFZ8 (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 —
134 functional partner(s); context anchor
lprC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3035| MAAGPALSARGYLALNGQTPAGCSLMEWQNDNNGRQRWCVRLVQGGGFAGPLFDGFDNLYVGQPGAIISFPPTQWTRWRQPVIGMPSTPRFLGHGRLLVSTHLGQLLVFDTRRGMVVGSPVDLVDGIDPTDATRGLADCAPARPGCPVAAAPAFSSVNGTVVVSVWQPGEPAAKLVGLKYHAEQLVREWTSDAVSAGVLASPVLSADGSTVYVNGRDHRLWALNAADGKAKWSAPLGFLAQTPPALTPHGLIVSGGGPDTALAAFRDAGDHAEGAWRRDDVTALSTASLAGTGVGYTVISGPNHDGTPGLSLLVFDPANGHTVNSYPLPGATGYPVGVSVGNDRRVVTATSDGQVYSFAP