Rv3254 Resolved · medium auto-curated
H37Rv Rv3254 · MTBC0 mtbc0_003462 ·
462 aa · 3655818–3657206 (+) ·
RefSeq NP_217771.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | oxidoreductase |
| Revised (this work) | 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 |
O05897
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Protein Rv3254 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversionH Coenzyme transport and metabolism
|
|---|---|
| eggNOG description | COG0654 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases |
| Orthologous group | COG0654 |
| Gene Ontology (58) |
GO:0003674, GO:0005488, GO:0005506, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0006725, GO:0006766 +46 more
|
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 | 0.413 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 6 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: Rv0538 (membrane protein), medium confidence from genomic context alone (score 643 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) |
|---|---|---|---|---|
Rv0538 |
membrane protein | 642 | 643 ctx | cooccurence:638 |
Rv0339c iniR |
transcriptional regulator | 635 | 634 ctx | cooccurence:623 |
Rv2164c hyp |
hypothetical protein | 622 | 622 ctx | cooccurence:620 |
Rv1814 erg3 |
membrane-bound C-5 sterol desaturase | 641 | 613 | coexpression:405 |
Rv1853 ureD |
urease accessory protein UreD | 607 | 608 ctx | cooccurence:600 |
Rv3732 hyp |
hypothetical protein | 598 | 599 ctx | cooccurence:595 |
Rv3253c |
cationic amino acid transport integral membrane protein | 856 | 598 ctx | neighborhood:553 textmining:658 |
Rv2264c hyp |
hypothetical protein | 586 | 568 ctx | cooccurence:504 |
Rv1963c mce3R |
transcriptional repressor Mce3R | 535 | 534 ctx | cooccurence:522 |
Rv2709 |
transmembrane protein | 523 | 523 ctx | cooccurence:520 |
Rv1666c cyp139 |
cytochrome P450 Cyp139 | 510 | 492 | |
Rv3788 hyp |
hypothetical protein | 492 | 492 ctx | cooccurence:489 |
Rv0343 iniC |
iIsoniazid inductible protein IniC | 471 | 471 ctx | cooccurence:450 |
Rv0134 ephF |
epoxide hydrolase EphF | 471 | 462 ctx | fusion:446 |
Rv3835 hyp |
hypothetical protein | 479 | 460 ctx | cooccurence:441 |
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: 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_217771.1)
- 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
COG0654 - Curated reference: UniProt O05897 (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 —
50 functional partner(s); context anchor
Rv0538 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003462|Rv3254| MVIGASIAGLCAARVLSDFYSTVTVFERDELPEAPANRATVPQDRHLHMLMARGAQEFDSLFPGLLHDMVAAGVPMLENRPDCIYLGAAGHVLGTGHTLRKEFTAYVPSRPHLEWQLRRRVLQLSNVQIVRRLVTEPQFERRQQRVVGVLLDSPGSGQDREREEFIAADLVVDAAGRGTRLPVWLTQWGYRRPAEDTVDIGISYASHQFRIPDGLIAEKVVVAGASHDQSLGLGMLCYEDGTWVLTTFGVADAKPPPTFDEMRALADKLLPARFTAALAQAQPIGCPAFHAFPASRWRRYDKLERFPRGIVPFGDAVASFNPTFGQGMTMTSLQAGHLRRALKARNSAMKGDLAAELNRATAKTTYPVWMMNAIGDISFHHATAEPLPRWWRPAGSLFDQFLGAAETDPVLAEWFLRRFSLLDSLYMVPSVPIIGRAIAHNLRLWLKEQRERRQPVTTRRSP