Rv3369 Family assigned · medium auto-curated
H37Rv Rv3369 · MTBC0 - ·
144 aa · 3780978–3781412 (+) ·
RefSeq NP_217886.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Contains PNPOx_N (PF01243.28) 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 |
O50398
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Pyridoxamine 5'-phosphate oxidase |
| Orthologous group | COG3871 |
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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 0 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.24% of strains (355) · 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 |
|---|---|---|---|---|
PNPOx_N | PF01243.28 | 1.8e-18 | 13–140 | Pyridoxamine 5'-phosphate oxidase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3368c (oxidoreductase), medium confidence from genomic context alone (score 578 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) |
|---|---|---|---|---|
Rv3368c |
oxidoreductase | 578 | 578 ctx | neighborhood:573 |
Rv2216 |
epimerase family protein | 515 | 516 | coexpression:512 |
Rv1001 arcA |
arginine deiminase | 443 | 443 | coexpression:443 |
Rv1770 hyp |
hypothetical protein | 434 | 435 ctx | cooccurence:431 |
Rv2946c pks1 |
polyketide synthase | 426 | 427 | |
Rv3072c hyp |
hypothetical protein | 426 | 426 ctx | cooccurence:423 |
Rv2323c hyp |
hypothetical protein | 418 | 418 | coexpression:416 |
Rv1043c hyp |
hypothetical protein | 408 | 409 | |
Rv2043c pncA |
pyrazinamidase/nicotinamidase PncA | 408 | 408 | coexpression:408 |
Rv1015c rplY |
50S ribosomal protein L25/general stress protein Ctc | 407 | 408 | coexpression:408 |
Rv1364c |
sigma factor regulatory protein | 401 | 402 | coexpression:402 |
Rv1155 |
pyridoxine/pyridoxamine 5'-phosphate oxidase | 846 | 251 | textmining:804 |
Rv1636 TB15.3 |
iron-regulated universal stress protein | 757 | 249 | textmining:690 |
Rv1875 hyp |
hypothetical protein | 839 | 217 | textmining:803 |
Rv0121c hyp |
hypothetical protein | 893 | 215 | textmining:870 |
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): PNPOx_N PF01243.28 (E=2e-18)
- (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_217886.1)
- Domains: Pfam-A via hmmscan --cut_ga — PNPOx_N (PF01243.28)
- 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
COG3871 - Curated reference: UniProt O50398 (TrEMBL, unreviewed; 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 —
29 functional partner(s); context anchor
Rv3368c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3369| MWAGYRWAMSVELTQEVSARLTSDLYGWLTTVARSGQPVPRLVWFYFDGTDLTVYSMPQAAKVAHITAHPQVSLNLDSDGNGAGIIVVGGTAAVVATDVDCRDDAPYWAKYREDAAKFGLTEAIAAYSTRLKITPTRVWTTPTG