Rv2161c Family assigned · medium auto-curated
H37Rv Rv2161c · MTBC0 mtbc0_002297 ·
288 aa · 2449654–2450520 (-) ·
RefSeq NP_216677.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | TIGR03619 family F420-dependent LLM class oxidoreductase |
| Revised (this work) | TIGR03619 family F420-dependent LLM class 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 |
O06216
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)
| 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 | 3.987 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 11 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
Bac_luciferase | PF00296.27 | 2.9e-38 | 20–232 | Luciferase-like monooxygenase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2160c (Rv2160c, (MTCY270.08), len: 113 aa. Conserved hypothetical protein, possibly a TetR-family transcriptional regulator, similar to C-terminal ), high confidence from genomic context alone (score 859 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) |
|---|---|---|---|---|
Rv2160A |
Rv2160A, len: 211 aa. Conserved hypothetical protein, possibly a TetR-family transcriptional regulator,similar to N-terminal half of AL51266 | 876 | 876 | coexpression:860 |
Rv2160c |
Rv2160c, (MTCY270.08), len: 113 aa. Conserved hypothetical protein, possibly a TetR-family transcriptional regulator, similar to C-terminal | 980 | 859 ctx | neighborhood:484 coexpression:738 textmining:870 |
Rv2159c hyp |
hypothetical protein | 978 | 842 | coexpression:819 textmining:870 |
Rv3093c |
oxidoreductase | 730 | 730 ctx | cooccurence:730 |
Rv3520c |
coenzyme F420-dependent oxidoreductase | 719 | 720 ctx | cooccurence:709 |
Rv2951c |
phthiodiolone/phenolphthiodiolone dimycocerosates ketoreductase | 718 | 718 ctx | cooccurence:717 |
Rv3262 fbiB |
coenzyme F420:L-glutamate ligase | 727 | 710 ctx | cooccurence:669 |
Rv1936 |
monooxygenase | 676 | 677 ctx | cooccurence:673 |
Rv0044c |
oxidoreductase | 658 | 658 ctx | cooccurence:655 |
Rv3178 |
nitroreductase | 676 | 656 ctx | cooccurence:653 |
Rv3261 fbiA |
2-phospho-L-lactate transferase | 675 | 655 ctx | cooccurence:637 |
Rv0407 fgd1 |
F420-dependent glucose-6-phosphate dehydrogenase | 645 | 645 ctx | cooccurence:641 |
Rv3547 ddn |
deazaflavin-dependent nitroreductase | 628 | 605 ctx | cooccurence:605 |
Rv1261c hyp |
hypothetical protein | 597 | 598 ctx | cooccurence:595 |
Rv2162c PE_PGRS38 |
PE-PGRS family protein PE_PGRS38 | 905 | 540 ctx | neighborhood:540 textmining:803 |
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: TIGR03619 family F420-dependent LLM class oxidoreductase
- Pfam (hmmscan --cut_ga): Bac_luciferase PF00296.27 (E=3e-38)
- (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_216677.1)
- 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 O06216 (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
Rv2160c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002297|Rv2161c| MLVSLMQFVTDLTPPPQLVAVWAEERGFAGLYVPEKTHVPISRSTPWPGGELPDWYRRCYDPVVALAAAAAVTTRLRVGTGACLVAVHDPILLAKQIASLCAMSGERFVLGVGFGWNVEELADHGVPFADRIAVTVDKLAAMRALWAAEPVHYEGTHASVPPSWAWPKPAVAPPVLFGCRPSARAFEVIARHGDGWQPIEGYGELLGALPMLHAAFERAGRDPATAQVCVYSSAGDPATLHEYRRAGVAEVALALPSAGRDQVLAALDRSAPLVDAFAGDDREVKSHA