Rv1204c Still unknown · low auto-curated
H37Rv Rv1204c · MTBC0 - ·
562 aa · 1346936–1348624 (-) ·
RefSeq NP_215720.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Conserved hypothetical protein; no recognised domain. Function unknown. |
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 |
O05305
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | AAA+ ATPase domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | luxR family |
| Orthologous group | COG2909 |
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 | 1.538 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 8 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: lprB (lipoprotein LprB), medium confidence from genomic context alone (score 646 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) |
|---|---|---|---|---|
Rv1203c hyp |
hypothetical protein | 990 | 990 ctx | neighborhood:686 fusion:871 cooccurence:770 |
Rv1274 lprB |
lipoprotein LprB | 645 | 646 ctx | cooccurence:634 |
Rv1125 hyp |
hypothetical protein | 554 | 553 ctx | cooccurence:546 |
Rv1205 log hyp |
hypothetical protein | 549 | 549 ctx | neighborhood:547 |
Rv2405 hyp |
hypothetical protein | 538 | 539 ctx | cooccurence:536 |
Rv1275 lprC |
lipoprotein LprC | 538 | 538 ctx | cooccurence:522 |
Rv0010c |
membrane protein | 530 | 530 ctx | cooccurence:530 |
Rv2876 |
transmembrane protein | 502 | 502 ctx | cooccurence:499 |
Rv2171 lppM |
lipoprotein LppM | 498 | 499 ctx | cooccurence:494 |
Rv0207c hyp |
hypothetical protein | 495 | 495 ctx | cooccurence:495 |
Rv3668c |
protease | 482 | 482 ctx | cooccurence:480 |
Rv3035 hyp |
hypothetical protein | 472 | 473 ctx | cooccurence:465 |
Rv1206 fadD6 |
fatty-acid--CoA ligase FadD6 | 472 | 452 ctx | neighborhood:445 |
Rv1208 gpgS |
glucosyl-3-phosphoglycerate synthase | 430 | 430 | |
Rv3839 hyp |
hypothetical protein | 429 | 429 ctx | cooccurence:429 |
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
- (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_215720.1)
- 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
COG2909 - Curated reference: UniProt O05305 (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 —
21 functional partner(s); context anchor
lprB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1204c| MRVWKHVEAAVDSPDRCGVVLVGPHGVGKTLLAQLAAEQVMSEDGRSGRARWVVGTAPGRAIPFGAFRHLISLPASGADIGRPAALLRAARSSLTGDAGDLLLVVDDAHNLDPLSATLVYQLARAGAARLVVTVASEAEPPDAIAALWSDDLLTRVAIEPLDRAQTAAFVESALDATLDVADADELFRRSLGNPLYLRHLIDGGGLEHVDGRWRCRDEDRRPLSGVIDEYLCALPEPARAVVDYLAIAEPLARTDLVALVGGEQLDTLGQAEAAGAVRVGPDSDTSEIFVGHPLYADRARAVLTAEHAHALRVSLVAQLAKHPSDHVSDQLRLSSLAIDVPASATPAAVTDAATAAGQALRLGDVRLAERLARAALDRSDALAARLPLAYALGWQGRGREADAVLAAVNPAELTETELMAWAIPRAANRFWMLNEPERATAFLQTTRSRVTEPTARSTLDALAATFAMNSGNLPRAITLATEVLSGPAADDMAVAWAASAAALSSARMGRFGDVDRLAERASAAEHPGLLRFTVGLAQITSLLLAGDVAPAQELAKRFTDFA