Rv1138c Resolved · high auto-curated
H37Rv Rv1138c · MTBC0 mtbc0_001223 ·
338 aa · 1273912–1274928 (-) ·
RefSeq NP_215654.1
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), FAD_binding_2 (PF00890.31). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O06538
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible oxidoreductase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | srsC |
| eggNOG description | FAD dependent oxidoreductase |
| Orthologous group | COG0644 |
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 | 1.138 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 3 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.81% of strains (1176) · 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 | 1.8e-11 | 5–169 | FAD binding domain |
FAD_binding_2 | PF00890.31 | 9.5e-05 | 7–38 | FAD binding domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1137c (Hypothetical protein; Rv1137c, (MTCI65.04c), len: 122 aa. Hypothetical unknown protein.), high confidence from genomic context alone (score 945 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1139c hyp |
hypothetical protein | 988 | 979 ctx | neighborhood:881 cooccurence:767 textmining:489 |
Rv1137c |
Hypothetical protein; Rv1137c, (MTCI65.04c), len: 122 aa. Hypothetical unknown protein. | 945 | 945 ctx | neighborhood:737 coexpression:801 |
Rv1660 pks10 |
chalcone synthase | 905 | 867 ctx | cooccurence:764 |
Rv1665 pks11 |
chalcone synthase | 847 | 786 ctx | cooccurence:762 |
Rv0736 rslA |
anti-sigma-L factor RslA | 791 | 767 | coexpression:767 |
Rv3029c fixA |
electron transfer flavoprotein subunit beta | 781 | 752 | experimental:652 |
Rv1372 pks18 |
alpha-pyrone synthesis polyketide synthase-like protein | 753 | 654 ctx | cooccurence:613 |
Rv3028c fixB |
electron transfer flavoprotein subunit alpha | 634 | 586 | experimental:446 |
Rv0735 sigL |
ECF RNA polymerase sigma factor SigL | 514 | 514 | coexpression:514 |
Rv2062c cobN |
cobalamin biosynthesis protein CobN | 517 | 454 | coexpression:436 |
Rv2850c |
magnesium chelatase | 589 | 434 | coexpression:416 |
Rv2638 hyp |
hypothetical protein | 404 | 404 | |
Rv1140 |
integral membrane protein | 401 | 401 | |
Rv3806c ubiA |
decaprenyl-phosphate phosphoribosyltransferase | 438 | 363 | |
Rv0958 |
magnesium chelatase | 409 | 353 |
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=2e-11), FAD_binding_2 PF00890.31 (E=1e-04)
- (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_215654.1)
- Domains: Pfam-A via hmmscan --cut_ga — FAD_binding_3 (PF01494.26), FAD_binding_2 (PF00890.31)
- 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
COG0644 - Curated reference: UniProt O06538 (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 —
17 functional partner(s); context anchor
Rv1137c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001223|Rv1138c| MTSYDTDLLVVGGGPGGLATALHARARGLSVIVAEPRENPIDKACGEGLMPGGLAELTSLGVDPVGLPFHGIAYVGEHRRVQARFRTGPGRGVRRTTLHAALAARAKEQDTEWIRSRVATIQQDAHGVTAAGVRAKWLVAADGLHSAVRRAVGIKATAGTPRRYGVRWHYRLPVWSDFVEVHWSRWGEAYVTPVEPDLVGVAILSRQRPELAWFPSLAHHLQDASRGHARGCGPLRQVVSRRVAGRVLLVGDAAGYEDALTGEGISLAVKQAAAAVSAIVDDTPASYEAAWHRITRDYRLVTRGLVLASTPRAARRAIVPLCALLPTAFRYGVNILAY