Rv1894c Family assigned · medium auto-curated
H37Rv Rv1894c · MTBC0 mtbc0_002008 ·
376 aa · 2158803–2159933 (-) ·
RefSeq NP_216410.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | nitronate monooxygenase family protein |
| Revised (this work) | Nitronate monooxygenase family protein. Pfam: NMO (PF03060.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O07738
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein |
UniProt still lists this protein as Uncharacterized 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 | 2-nitropropane dioxygenase |
| Orthologous group | COG2070 |
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 | 0.546 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 7 missense, 0 nonsense, 5 frameshift |
| Disruption | 5 distinct premature-stop/frameshift site(s); most common in 1.32% of strains (1914) · convergent |
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 |
|---|---|---|---|---|
NMO | PF03060.22 | 3.9e-43 | 22–313 | Nitronate monooxygenase |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2524c fas |
fatty acid synthase | 780 | 746 | coexpression:710 |
Rv2940c mas |
multifunctional mycocerosic acid synthase | 574 | 502 | |
Rv2933 ppsC |
phthiocerol synthesis polyketide synthase type I PpsC | 574 | 501 | |
Rv1527c pks5 |
polyketide synthase | 574 | 501 | |
Rv3825c pks2 |
phthioceranic/hydroxyphthioceranic acid synthase | 573 | 500 | |
Rv2048c pks12 |
polyketide synthase | 572 | 500 | |
Rv2246 kasB |
3-oxoacyl-ACP synthase 2 | 462 | 434 | coexpression:416 |
Rv2245 kasA |
3-oxoacyl-ACP synthase 1 | 462 | 434 | coexpression:416 |
Rv3800c pks13 |
polyketide synthase | 562 | 429 | |
Rv2243 fabD |
malonyl CoA-acyl carrier protein transacylase | 458 | 427 | coexpression:408 |
Rv2946c pks1 |
polyketide synthase | 499 | 424 | |
Rv3522 ltp4 |
lipid transfer protein | 419 | 420 | |
Rv1661 pks7 |
polyketide synthase | 477 | 417 | |
Rv2932 ppsB |
phthiocerol synthesis polyketide synthase type I PpsB | 470 | 415 | |
Rv1181 pks4 |
polyketide beta-ketoacyl synthase | 473 | 413 |
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: nitronate monooxygenase family protein
- Pfam (hmmscan --cut_ga): NMO PF03060.22 (E=4e-43)
- (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_216410.1)
- Domains: Pfam-A via hmmscan --cut_ga — NMO (PF03060.22)
- 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
COG2070 - Curated reference: UniProt O07738 (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 — 18 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002008|Rv1894c| MHTAICDELGIEFPIFAFTHCRDVVVAVSKAGGFGVLGAVGFTPEQLEIELNWIDEHIGDHPYGVDIVIPNKYEGMDSQLSADELAKTLRSMVPQEHLDFARKILADHGVPVEDADEDSLQLLGWTEATATPQVDAALKHPKMTMVANALGTPPADMIKHIHDSGRKVAALCGSPSQARKHADAGVDIIIAQGGEAGGHCGEVGSIVLWPQVVKEVAPVPVLAAGGIGSGQQIAAALALGTQGAWTGSQWLMVEEAANTAVQQAAYVKATSRDTVRSRSFTGKPARMLRNDWTEAWEQPESPKPLGMPLQYMVSGMAVKATHKYPNETVDVAFNPVGQVVGQFTKVEKTATVIERWVQEYLEATARLDALNAAASV