Rv0523c Family assigned · low auto-curated
H37Rv Rv0523c · MTBC0 mtbc0_000551 ·
131 aa · 617783–618178 (-) ·
RefSeq NP_215037.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | nitroreductase family deazaflavin-dependent oxidoreductase |
| Revised (this work) | Nitroreductase family deazaflavin-dependent oxidoreductase. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O06389
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)
| Orthologous group | 2C2H7 |
|---|
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 1 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: hemL (glutamate-1-semialdehyde 2,1-aminomutase), medium confidence from genomic context alone (score 595 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) |
|---|---|---|---|---|
Rv0524 hemL |
glutamate-1-semialdehyde 2,1-aminomutase | 594 | 595 ctx | neighborhood:593 |
Rv0525 hyp |
hypothetical protein | 594 | 594 ctx | neighborhood:593 |
Rv0756c hyp |
hypothetical protein | 592 | 593 ctx | cooccurence:590 |
Rv2560 hyp |
hypothetical protein | 562 | 562 ctx | cooccurence:557 |
Rv0527 ccdA |
cytochrome C-type biogenesis protein CcdA | 531 | 531 ctx | neighborhood:531 |
Rv0526 |
thioredoxin | 531 | 531 ctx | neighborhood:531 |
Rv2923c hyp |
hypothetical protein | 513 | 514 ctx | cooccurence:508 |
Rv0676c mmpL5 |
transmembrane transport protein MmpL5 | 504 | 505 ctx | cooccurence:504 |
Rv0402c mmpL1 |
transmembrane transport protein MmpL1 | 489 | 490 ctx | cooccurence:489 |
Rv0466 hyp |
hypothetical protein | 487 | 488 ctx | cooccurence:486 |
Rv2339 mmpL9 |
transmembrane transport protein MmpL9 | 474 | 474 ctx | cooccurence:471 |
Rv0507 mmpL2 |
transmembrane transport protein MmpL2 | 465 | 466 ctx | cooccurence:464 |
Rv1219c raaS |
transcriptional regulator | 455 | 455 ctx | cooccurence:452 |
Rv0528 |
transmembrane protein | 453 | 453 ctx | neighborhood:451 |
Rv0529 ccsA |
cytochrome C-type biogenesis protein CcsA | 453 | 453 ctx | neighborhood:451 |
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: nitroreductase family deazaflavin-dependent oxidoreductase
- (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_215037.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
2C2H7 - Curated reference: UniProt O06389 (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 —
23 functional partner(s); context anchor
hemL - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000551|Rv0523c| MQLPQWLARFNRYVTNPIQRLWAGWLPAFAILEHVGRRSGKPYRTPLNVFSADVDGRAGVAILLTYGPNRDWLKNITAAGGGRMRRYGKTFGVANPRRLTKAEAAPYVSSRWRPVFARLPFDEAVLLTKAD