Rv1856c Family assigned · medium auto-curated
H37Rv Rv1856c · MTBC0 mtbc0_001969 ·
225 aa · 2122184–2122861 (-) ·
RefSeq NP_216372.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | oxidoreductase |
|---|---|
| MTBC0 PGAP re-annotation | SDR family oxidoreductase |
| Revised (this work) | SDR family oxidoreductase. Pfam: adh_short (PF00106.32), adh_short_C2 (PF13561.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGQ1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative oxidoreductase Rv1856c |
| EC (curated) |
EC 1.-.-.-
|
UniProt still lists this protein as Putative oxidoreductase Rv1856c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolismQ Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| eggNOG description | Dehydrogenase |
| Orthologous group | COG1028 |
| Gene Ontology (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, GO:0044464, GO:0071944
|
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 | 0.186 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 2 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 |
|---|---|---|---|---|
adh_short | PF00106.32 | 3.0e-13 | 5–174 | short chain dehydrogenase |
adh_short_C2 | PF13561.13 | 1.6e-17 | 14–219 | Enoyl-(Acyl carrier protein) reductase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1855c (oxidoreductase), high confidence from genomic context alone (score 819 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1855c |
oxidoreductase | 819 | 819 ctx | neighborhood:817 |
Rv2524c fas |
fatty acid synthase | 827 | 801 | coexpression:508 experimental:475 |
Rv2434c |
transmembrane protein | 646 | 632 | database:431 |
Rv3810 pirG |
cell surface protein | 599 | 600 ctx | cooccurence:542 |
Rv1857 modA |
molybdate ABC transporter substrate-binding lipoprotein ModA | 582 | 579 ctx | neighborhood:573 |
Rv1858 modB |
molybdenum ABC transporter permease ModB | 559 | 559 ctx | neighborhood:532 |
Rv0998 |
acetyltransferase Pat | 553 | 552 | database:431 |
Rv1859 modC |
molybdenum ABC transporter ATP-binding protein ModC | 550 | 550 ctx | neighborhood:543 |
Rv3707c hyp |
hypothetical protein | 547 | 547 ctx | cooccurence:546 |
Rv1937 |
oxygenase | 591 | 543 | |
Rv2299c htpG |
chaperone protein HtpG | 539 | 520 | database:450 |
Rv0073 |
glutamine ABC transporter ATP-binding protein | 535 | 514 | database:431 |
Rv2564 glnQ |
glutamine ABC transporter ATP-binding protein | 534 | 513 | database:431 |
Rv3728 |
membrane protein | 536 | 510 | database:431 |
Rv3239c |
transmembrane transport protein | 534 | 508 | database:431 |
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: SDR family oxidoreductase
- Pfam (hmmscan --cut_ga): adh_short PF00106.32 (E=3e-13), adh_short_C2 PF13561.13 (E=2e-17)
- (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_216372.1)
- Domains: Pfam-A via hmmscan --cut_ga — adh_short (PF00106.32), adh_short_C2 (PF13561.13)
- 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
COG1028 - Curated reference: UniProt P9WGQ1 (SwissProt, reviewed; 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 —
92 functional partner(s); context anchor
Rv1855c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001969|Rv1856c| MAVEVLVTGGDTDLGRTMAEGFRNDGHKVTLVGARRGDLEVAAKELDVDAVVCDTTDPTSLTEARGLFPRHLDTIVNVPAPSWDAGDPRAYSVSDTANAWRNALDATVLSVVLTVQSVGDHLRSGGSIVSVVAENPPAGGAESAIKAALSNWIAGQAAVFGTRGITINTVACGRSVQTGYEGLSRTPAPVAAEIARLALFLTTPAARHITGQTLHVSHGALAHFG