rubB Resolved · high auto-curated
H37Rv Rv3250c · MTBC0 mtbc0_003458 ·
60 aa · 3652527–3652709 (-) ·
RefSeq NP_217767.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | rubredoxin RubB |
|---|---|
| MTBC0 PGAP re-annotation | rubredoxin RubB |
| Revised (this work) | Rubredoxin RubB. Pfam: Rubredoxin (PF00301.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6YFL7
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Rubredoxin |
| Curated function | Involved in the hydrocarbon hydroxylating system, which transfers electrons from NADH to rubredoxin reductase and then through rubredoxin to alkane 1 monooxygenase. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | rubB |
| eggNOG description | involved in the hydrocarbon hydroxylating system to convert conversion of dodecane to lauric acid, which transfers electrons from NADH to rubredoxin reductase and then through rubredoxin to alkane 1 monooxygenase |
| Orthologous group | COG1773 |
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 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 |
|---|---|---|---|---|
Rubredoxin | PF00301.26 | 6.5e-22 | 7–52 | Rubredoxin |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rubA (rubredoxin RubA), high confidence from genomic context alone (score 958 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3251c rubA |
rubredoxin RubA | 960 | 958 ctx | neighborhood:816 coexpression:759 |
Rv3252c alkB |
transmembrane alkane 1-monooxygenase AlkB | 969 | 943 ctx | neighborhood:882 coexpression:460 textmining:482 |
Rv3249c |
TetR family transcriptional regulator | 922 | 910 ctx | neighborhood:881 |
Rv3253c |
cationic amino acid transport integral membrane protein | 769 | 769 ctx | neighborhood:768 |
Rv1869c |
reductase | 746 | 731 | coexpression:408 experimental:549 |
Rv0688 |
ferredoxin reductase | 746 | 731 | coexpression:408 experimental:549 |
Rv0252 nirB |
nitrite reductase large subunit NirB | 745 | 729 | coexpression:404 experimental:549 |
Rv3248c sahH |
adenosylhomocysteinase | 647 | 647 ctx | neighborhood:642 |
Rv3247c tmk |
thymidylate kinase | 480 | 479 ctx | neighborhood:479 |
Rv3841 bfrB |
bacterioferritin BfrB | 475 | 449 | coexpression:417 |
Rv2428 ahpC |
alkyl hydroperoxide reductase subunit AhpC | 483 | 414 | |
Rv3246c mtrA |
two component DNA-binding response regulator MtrA | 416 | 394 | |
Rv3254 hyp |
hypothetical protein | 406 | 384 | |
Rv2359 zur |
zinc uptake regulation protein | 410 | 375 | |
Rv1909c furA |
ferric uptake regulation protein FurA | 410 | 375 |
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: rubredoxin RubB
- MTBC0 PGAP product: rubredoxin RubB
- Pfam (hmmscan --cut_ga): Rubredoxin PF00301.26 (E=7e-22)
- (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_217767.1)
- Domains: Pfam-A via hmmscan --cut_ga — Rubredoxin (PF00301.26)
- 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
COG1773 - Curated reference: UniProt I6YFL7 (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 —
21 functional partner(s); context anchor
rubA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003458|Rv3250c|rubB MNDYKLFRCIQCGFEYDEALGWPEDGIAAGTRWDDIPDDWSCPDCGAAKSDFEMVEVARS