Rv1895 Resolved · high auto-curated
H37Rv Rv1895 · MTBC0 - ·
384 aa · 2142521–2143675 (+) ·
RefSeq NP_216411.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | zinc-binding alcohol dehydrogenase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Zinc-binding alcohol dehydrogenase. Pfam: ADH_N (PF08240.18), ADH_zinc_N (PF00107.33), ADH_zinc_N_2 (PF13602.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
O07737
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable zinc-binding alcohol dehydrogenase Rv1895 |
| EC (curated) |
EC 1.1.1.1
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| eggNOG description | Dehydrogenase |
| Orthologous group | COG1063 |
| EC number |
EC 1.1.1.1
|
| KEGG orthology |
K00001
|
| KEGG pathways |
map00010, map00071, map00350, map00625, map00626, map00830, map00980, map00982, map01100, map01110, map01120, map01130, map01220
|
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) pseudogene candidate
| pN/pS | 0.616 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 5 missense, 0 nonsense, 3 frameshift |
| Disruption | 3 distinct premature-stop/frameshift site(s); most common in 29.85% of strains (43352) · 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 |
|---|---|---|---|---|
ADH_N | PF08240.18 | 3.7e-23 | 24–136 | Alcohol dehydrogenase GroES-like domain |
ADH_zinc_N | PF00107.33 | 1.1e-24 | 176–301 | Zinc-binding dehydrogenase |
ADH_zinc_N_2 | PF13602.13 | 4.1e-06 | 220–324 | Zinc-binding dehydrogenase |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1562c treZ |
malto-oligosyltrehalose trehalohydrolase | 530 | 503 | coexpression:405 |
Rv0032 bioF2 |
8-amino-7-oxononanoate synthase | 488 | 456 | coexpression:425 |
Rv1569 bioF1 |
8-amino-7-oxononanoate synthase | 481 | 449 | coexpression:417 |
Rv3846 sodA |
superoxide dismutase | 450 | 424 | coexpression:423 |
Rv3045 adhC |
NADP-dependent alcohol dehydrogenase | 451 | 423 | |
Rv1862 adhA |
alcohol dehydrogenase A | 443 | 415 | |
Rv1326c glgB |
1,4-alpha-glucan branching protein | 442 | 410 | coexpression:403 |
Rv0162c adhE1 |
zinc-type alcohol dehydrogenase subunit E | 413 | 388 | |
Rv0761c adhB |
alcohol dehydrogenase B | 409 | 383 | |
Rv3086 adhD |
alcohol dehydrogenase D | 401 | 376 | |
Rv0777 purB |
adenylosuccinate lyase PurB | 400 | 373 | |
Rv1832 gcvB |
glycine dehydrogenase | 509 | 253 | |
Rv1937 |
oxygenase | 418 | 239 | |
Rv0126 treS |
trehalose synthase/amylase TreS | 618 | 209 | textmining:538 |
Rv3322c |
methyltransferase | 765 | 139 | textmining:739 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): zinc-binding alcohol dehydrogenase
- Pfam (hmmscan --cut_ga): ADH_N PF08240.18 (E=4e-23), ADH_zinc_N PF00107.33 (E=1e-24), ADH_zinc_N_2 PF13602.13 (E=4e-06)
- (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_216411.1)
- Domains: Pfam-A via hmmscan --cut_ga — ADH_N (PF08240.18), ADH_zinc_N (PF00107.33), ADH_zinc_N_2 (PF13602.13)
- 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
COG1063 - Curated reference: UniProt O07737 (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 — 18 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1895| MRAVVIDGAGSVRVNTQPDPALPGPDGVVVAVTAAGICGSDLHFYEGEYPFTEPVALGHEAVGTIVEAGPQVRTVGVGDLVMVSSVAGCGVCPGCETHDPVMCFSGPMIFGAGVLGGAQADLLAVPAADFQVLKIPEGITTEQALLLTDNLATGWAAAQRADISFGSAVAVIGLGAVGLCALRSAFIHGAATVFAVDRVKGRLQRAATWGATPIPSPAAETILAATRGRGADSVIDAVGTDASMSDALNAVRPGGTVSVVGVHDLQPFPVPALTCLLRSITLRMTMAPVQRTWPELIPLLQSGRLDVDGIFTTTLPLDEAAKGYATARARSGEELRFCLRPDSRDVLGAHETVDLYVHVRRCQSVADLQLEGAADGVDGPSMLN