Rv0897c Resolved · high auto-curated
H37Rv Rv0897c · MTBC0 mtbc0_000951 ·
535 aa · 1004022–1005629 (-) ·
RefSeq NP_215412.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | oxidoreductase |
|---|---|
| MTBC0 PGAP re-annotation | NAD(P)/FAD-dependent oxidoreductase |
| Revised (this work) | NAD(P)/FAD-dependent oxidoreductase. Pfam: FAD_binding_3 (PF01494.26), Thi4 (PF01946.24), FAD_oxidored (PF12831.14), GIDA (PF01134.29), FAD_binding_2 (PF00890.31), NAD_binding_8 (PF13450.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WKP7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv0897c |
UniProt still lists this protein as Uncharacterized protein Rv0897c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
Q Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| eggNOG description | NAD(P)-binding Rossmann-like domain |
| Orthologous group | COG1233 |
| Gene Ontology (8) |
GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0044424, GO:0044444, GO:0044464
|
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 | 0.678 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 11 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.62% of strains (899) · 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 |
|---|---|---|---|---|
FAD_binding_3 | PF01494.26 | 6.6e-06 | 8–42 | FAD binding domain |
Thi4 | PF01946.24 | 3.3e-06 | 8–52 | Thi4 family |
FAD_oxidored | PF12831.14 | 5.8e-07 | 9–48 | FAD dependent oxidoreductase |
GIDA | PF01134.29 | 8.9e-06 | 9–54 | Glucose inhibited division protein A |
FAD_binding_2 | PF00890.31 | 4.8e-05 | 9–47 | FAD binding domain |
NAD_binding_8 | PF13450.13 | 1.1e-09 | 12–57 | NAD(P)-binding Rossmann-like domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: arfA (peptidoglycan-binding protein ArfA), high confidence from genomic context alone (score 759 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0898c hyp |
hypothetical protein | 851 | 851 ctx | neighborhood:847 |
Rv0899 arfA |
peptidoglycan-binding protein ArfA | 759 | 759 ctx | neighborhood:758 |
Rv3397c phyA |
phytoene synthase | 759 | 666 | coexpression:654 |
Rv0901 arfC |
membrane protein | 519 | 519 ctx | neighborhood:514 |
Rv2850c |
magnesium chelatase | 561 | 496 | coexpression:433 |
Rv0900 arfB |
membrane protein | 488 | 488 ctx | neighborhood:485 |
Rv0958 |
magnesium chelatase | 403 | 367 | |
Rv2062c cobN |
cobalamin biosynthesis protein CobN | 414 | 359 |
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: NAD(P)/FAD-dependent oxidoreductase
- Pfam (hmmscan --cut_ga): FAD_binding_3 PF01494.26 (E=7e-06), Thi4 PF01946.24 (E=3e-06), FAD_oxidored PF12831.14 (E=6e-07), GIDA PF01134.29 (E=9e-06), FAD_binding_2 PF00890.31 (E=5e-05), NAD_binding_8 PF13450.13 (E=1e-09)
- (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_215412.1)
- Domains: Pfam-A via hmmscan --cut_ga — FAD_binding_3 (PF01494.26), Thi4 (PF01946.24), FAD_oxidored (PF12831.14), GIDA (PF01134.29), FAD_binding_2 (PF00890.31), NAD_binding_8 (PF13450.13)
- 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
COG1233 - Curated reference: UniProt P9WKP7 (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 —
8 functional partner(s); context anchor
arfA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000951|Rv0897c| MSDHDRDFDVVVVGGGHNGLVAAAYLARAGLRVRLLERLAQTGGAAVSIQAFDGVEVALSRYSYLVSLLPSRIVADLGAPVRLARRPFSSYTPAPATAGRSGLLIGPTGEPRAAHLAAIGAAPDAHGFAAFYRRCRLVTARLWPTLIEPLRTREQARRDIVEYGGHEAAAAWQAMVDEPIGHAIAGAVANDLLRGVIATDALIGTFARMHEPSLMQNICFLYHLVGGGTGVWHVPIGGMGSVTSALATAAARHGAEIVTGADVFALDPDGTVRYHSDGSDGAEHLVRGRFVLVGVTPAVLASLLGEPVAALAPGAQVKVNMVVRRLPRLRDDSVTPQQAFAGTFHVNETWSQLDAAYSQAASGRLPDPLPCEAYCHSLTDPSILSARLRDAGAQTLTVFGLHTPHSVFGDTEGLAERLTAAVLASLNSVLAEPIQDVLWTDAQSKPCIETTTTLDLQRTLGMTGGNIFHGALSWPFADNDDPLDTPARQWGVATDHERIMLCGSGARRGGAVSGIGGHNAAMAVLACLASRRKSP