Rv0044c Resolved · high auto-curated
H37Rv Rv0044c · MTBC0 mtbc0_000049 ·
264 aa · 48332–49126 (-) ·
RefSeq NP_214558.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | oxidoreductase |
|---|---|
| MTBC0 PGAP re-annotation | LLM class F420-dependent oxidoreductase |
| Revised (this work) | LLM class F420-dependent oxidoreductase. Pfam: Bac_luciferase (PF00296.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P71701
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible oxidoreductase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| eggNOG description | COG2141 Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases |
| Orthologous group | COG2141 |
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 | 0.521 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 6 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.14% of strains (203) · 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 |
|---|---|---|---|---|
Bac_luciferase | PF00296.27 | 1.1e-31 | 16–197 | Luciferase-like monooxygenase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0045c (hydrolase), high confidence from genomic context alone (score 819 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0045c |
hydrolase | 819 | 819 ctx | neighborhood:813 |
Rv0407 fgd1 |
F420-dependent glucose-6-phosphate dehydrogenase | 804 | 777 ctx | cooccurence:771 |
Rv0046c ino1 |
inositol-3-phosphate synthase | 781 | 777 ctx | neighborhood:776 |
Rv0043c |
HTH-type transcriptional regulator | 766 | 766 ctx | neighborhood:757 |
Rv0132c fgd2 |
F420-dependent glucose-6-phosphate dehydrogenase | 765 | 765 ctx | cooccurence:763 |
Rv3547 ddn |
deazaflavin-dependent nitroreductase | 775 | 761 ctx | cooccurence:761 |
Rv3178 |
nitroreductase | 774 | 760 ctx | cooccurence:759 |
Rv1558 hyp |
hypothetical protein | 768 | 759 ctx | cooccurence:758 |
Rv1261c hyp |
hypothetical protein | 755 | 755 ctx | cooccurence:754 |
Rv3261 fbiA |
2-phospho-L-lactate transferase | 742 | 729 ctx | cooccurence:718 |
Rv0047c hyp |
hypothetical protein | 726 | 727 ctx | neighborhood:725 |
Rv3262 fbiB |
coenzyme F420:L-glutamate ligase | 734 | 718 ctx | cooccurence:680 |
Rv0042c |
transcriptional regulator | 682 | 683 ctx | neighborhood:678 |
Rv2161c hyp |
hypothetical protein | 658 | 658 ctx | cooccurence:655 |
Rv3079c hyp |
hypothetical protein | 651 | 652 ctx | cooccurence:648 |
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: oxidoreductase
- MTBC0 PGAP product: LLM class F420-dependent oxidoreductase
- Pfam (hmmscan --cut_ga): Bac_luciferase PF00296.27 (E=1e-31)
- (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_214558.1)
- Domains: Pfam-A via hmmscan --cut_ga — Bac_luciferase (PF00296.27)
- 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
COG2141 - Curated reference: UniProt P71701 (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
Rv0045c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000049|Rv0044c| MTSLVRPDLPVRIGVQLQPQHAPHYRAVRDAVRRCEDIGVDIAFTWDHFFPLYGDPDGPHFECWTVLGAWAEQTSHIEIGALVTCNSYRNPELLADMARTVDHISGGRLILGIGSGWKQKDYDEYGYRFGTAGSRLDDLAAALPRIKARLGKLNPPPTRDIPVLIGGGGERKTLRLVAEYADIWHSFTAGDSYLAKSAVLSTHCSTVGRNPATIERSAAVDGGGLIASAEALAGLGVTLLTVGCDGPDYDLSAAAALCRWRDGR