rubA Resolved · high auto-curated
H37Rv Rv3251c · MTBC0 mtbc0_003459 ·
55 aa · 3652714–3652881 (-) ·
RefSeq NP_217768.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | rubredoxin RubA |
|---|---|
| MTBC0 PGAP re-annotation | rubredoxin |
| Revised (this work) | Rubredoxin. 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 |
O05894
TrEMBL · unreviewed
· Inferred from homology
|
|---|---|
| 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 | rubA |
| eggNOG description | Belongs to the rubredoxin family |
| 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.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
Rubredoxin | PF00301.26 | 3.8e-20 | 4–50 | Rubredoxin |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: alkB (transmembrane alkane 1-monooxygenase AlkB), high confidence from genomic context alone (score 989 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3252c alkB |
transmembrane alkane 1-monooxygenase AlkB | 990 | 989 ctx | neighborhood:881 coexpression:856 |
Rv3250c rubB |
rubredoxin RubB | 960 | 958 ctx | neighborhood:816 coexpression:759 |
Rv3249c |
TetR family transcriptional regulator | 864 | 865 ctx | neighborhood:830 |
Rv1869c |
reductase | 747 | 732 | coexpression:410 experimental:549 |
Rv0688 |
ferredoxin reductase | 746 | 730 | coexpression:407 experimental:549 |
Rv0252 nirB |
nitrite reductase large subunit NirB | 745 | 729 | coexpression:404 experimental:549 |
Rv3248c sahH |
adenosylhomocysteinase | 583 | 584 ctx | neighborhood:581 |
Rv3253c |
cationic amino acid transport integral membrane protein | 576 | 576 ctx | neighborhood:575 |
Rv3841 bfrB |
bacterioferritin BfrB | 473 | 447 | coexpression:415 |
Rv2428 ahpC |
alkyl hydroperoxide reductase subunit AhpC | 483 | 414 | |
Rv3247c tmk |
thymidylate kinase | 409 | 409 ctx | neighborhood:409 |
Rv3254 hyp |
hypothetical protein | 408 | 386 | |
Rv2359 zur |
zinc uptake regulation protein | 409 | 374 | |
Rv1909c furA |
ferric uptake regulation protein FurA | 408 | 373 | |
Rv3554 fdxB |
electron transfer protein FdxB | 454 | 134 |
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 RubA
- MTBC0 PGAP product: rubredoxin
- Pfam (hmmscan --cut_ga): Rubredoxin PF00301.26 (E=4e-20)
- (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_217768.1)
- 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 O05894 (TrEMBL, unreviewed; Inferred from homology)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
22 functional partner(s); context anchor
alkB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003459|Rv3251c|rubA MAAYRCPVCDYVYDEANGDAREGFPAGTGWDQIPDDWCCPDCAVREKVDFEKIGG