Rv2857c Resolved · high auto-curated
H37Rv Rv2857c · MTBC0 mtbc0_003038 ·
258 aa · 3189249–3190025 (-) ·
RefSeq NP_217373.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 3-oxoacyl-ACP reductase |
|---|---|
| MTBC0 PGAP re-annotation | 3-oxoacyl-ACP reductase |
| Revised (this work) | 3-oxoacyl-ACP reductase. 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 |
I6Y1W3
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable short-chain type dehydrogenase/reductase |
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 |
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 | 0.18 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 1 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 | 1.4e-47 | 11–201 | short chain dehydrogenase |
adh_short_C2 | PF13561.13 | 7.6e-63 | 20–250 | Enoyl-(Acyl carrier protein) reductase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: glnA4 (glutamine synthetase), high confidence from genomic context alone (score 967 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2860c glnA4 |
glutamine synthetase | 968 | 967 ctx | neighborhood:881 cooccurence:732 |
Rv2858c aldC |
aldehyde dehydrogenase AldC | 953 | 952 ctx | neighborhood:882 cooccurence:485 |
Rv2859c |
glutamine amidotransferase | 927 | 927 ctx | neighborhood:882 |
Rv2524c fas |
fatty acid synthase | 827 | 801 | coexpression:508 experimental:475 |
Rv2861c mapB |
methionine aminopeptidase | 657 | 644 ctx | neighborhood:511 |
Rv1937 |
oxygenase | 593 | 546 | |
Rv2299c htpG |
chaperone protein HtpG | 546 | 527 | database:450 |
Rv3671c marP |
serine protease | 533 | 522 | |
Rv0073 |
glutamine ABC transporter ATP-binding protein | 539 | 518 | database:431 |
Rv2564 glnQ |
glutamine ABC transporter ATP-binding protein | 538 | 517 | database:431 |
Rv3728 |
membrane protein | 537 | 511 | database:431 |
Rv3239c |
transmembrane transport protein | 584 | 509 | database:431 |
Rv2565 |
NTE family protein | 525 | 506 | database:431 |
Rv2434c |
transmembrane protein | 519 | 500 | database:431 |
Rv3299c atsB |
arylsulfatase AtsB | 506 | 498 | coexpression:425 |
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: 3-oxoacyl-ACP reductase
- MTBC0 PGAP product: 3-oxoacyl-ACP reductase
- Pfam (hmmscan --cut_ga): adh_short PF00106.32 (E=1e-47), adh_short_C2 PF13561.13 (E=8e-63)
- (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_217373.1)
- 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 I6Y1W3 (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 —
89 functional partner(s); context anchor
glnA4 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003038|Rv2857c| MMDLSQRLAGRVAVITGGGSGIGLAAGRRMRAEGATIVVGDVDVEAGGAAADELSGLFVPTDVCDEDAVNGLFDGAAETYGRIDIAFNNAGISPPEDNLIENTELAAWQRVQDVNLKSVYLCCRAALRHMVLAGKGSIVNTASFVAVMGSATSQISYTASKGGVLAMSRELGVQFARQGIRVNALCPGPVNTPLLQELFAKNPERAARRMVHVPLGRFAEPDEIAAAVAFLASDDASFITASTFLVDGGISSAYVTPL