Rv1855c Resolved · high auto-curated
H37Rv Rv1855c · MTBC0 mtbc0_001968 ·
307 aa · 2121222–2122145 (-) ·
RefSeq NP_216371.1
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 |
P95159
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 | Oxidoreductase |
| 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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
Bac_luciferase | PF00296.27 | 6.9e-42 | 22–242 | Luciferase-like monooxygenase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1856c (oxidoreductase), high confidence from genomic context alone (score 819 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1856c |
oxidoreductase | 819 | 819 ctx | neighborhood:817 |
Rv3178 |
nitroreductase | 749 | 734 ctx | cooccurence:732 |
Rv3520c |
coenzyme F420-dependent oxidoreductase | 728 | 729 ctx | cooccurence:716 |
Rv3261 fbiA |
2-phospho-L-lactate transferase | 742 | 728 ctx | cooccurence:716 |
Rv3547 ddn |
deazaflavin-dependent nitroreductase | 730 | 713 ctx | cooccurence:713 |
Rv3093c |
oxidoreductase | 700 | 701 ctx | cooccurence:700 |
Rv1261c hyp |
hypothetical protein | 695 | 696 ctx | cooccurence:691 |
Rv3072c hyp |
hypothetical protein | 690 | 690 ctx | cooccurence:690 |
Rv1558 hyp |
hypothetical protein | 696 | 685 ctx | cooccurence:682 |
Rv3262 fbiB |
coenzyme F420:L-glutamate ligase | 679 | 659 ctx | cooccurence:611 |
Rv2983 cofC |
2-phospho-L-lactate guanylyltransferase | 650 | 614 ctx | cooccurence:600 |
Rv1854c ndh |
NADH dehydrogenase | 596 | 597 ctx | neighborhood:584 |
Rv1360 |
oxidoreductase | 579 | 579 ctx | cooccurence:577 |
Rv1857 modA |
molybdate ABC transporter substrate-binding lipoprotein ModA | 507 | 508 ctx | neighborhood:507 |
Rv1859 modC |
molybdenum ABC transporter ATP-binding protein ModC | 464 | 463 ctx | neighborhood:450 |
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=7e-42)
- (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_216371.1)
- 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 P95159 (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 —
25 functional partner(s); context anchor
Rv1856c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001968|Rv1855c| MTIRLGLQIPNFSYGTGVEKLFPSVIAQAREAEAAGYDSLFVMDHFYQLPMLGTPDQPMLEAYTALGALATATERLQLGALVTGNTYRSPTLLAKIITTLDVVSAGRAILGIGAGWFELEHRQLGFEFGTFSDRFNRLEEALQILEPMVKGERPTFFGDWYTTESAMAEPRYRDRIPILIGGGGEKKTFAIAARFADHLNIVAAVDELPRKMRALAARCDEAGRDRSTLQTSLLLTVMIDETLSPDAIPAEMSGRVVVGSPAQIADQIQAKVLDAGVDGLIINLAPHGYLPGVITTAAEALRPLLGV