alkB Resolved · high auto-curated
H37Rv Rv3252c · MTBC0 mtbc0_003460 ·
416 aa · 3652881–3654131 (-) ·
RefSeq NP_217769.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane alkane 1-monooxygenase AlkB |
|---|---|
| MTBC0 PGAP re-annotation | alkane 1-monooxygenase |
| Revised (this work) | Alkane 1-monooxygenase. Pfam: FA_desaturase (PF00487.31). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O05895
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable transmembrane alkane 1-monooxygenase AlkB |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | alkB |
| eggNOG description | PFAM Fatty acid desaturase |
| Orthologous group | COG3239 |
| EC number |
EC 1.14.15.3
|
| KEGG orthology |
K00496
|
| KEGG pathways |
map00071, map00930
|
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 | 0.542 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 5 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.66% of strains (960) · 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 |
|---|---|---|---|---|
FA_desaturase | PF00487.31 | 9.7e-38 | 138–371 | Fatty acid desaturase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rubA (rubredoxin RubA), high confidence from genomic context alone (score 989 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3251c rubA |
rubredoxin RubA | 990 | 989 ctx | neighborhood:881 coexpression:856 |
Rv3249c |
TetR family transcriptional regulator | 947 | 947 ctx | neighborhood:881 cooccurence:488 |
Rv3250c rubB |
rubredoxin RubB | 969 | 943 ctx | neighborhood:882 coexpression:460 textmining:482 |
Rv0761c adhB |
alcohol dehydrogenase B | 905 | 901 | database:900 |
Rv0162c adhE1 |
zinc-type alcohol dehydrogenase subunit E | 905 | 901 | database:900 |
Rv0768 aldA |
aldehyde dehydrogenase AldA | 904 | 901 | database:900 |
Rv1530 adh |
alcohol dehydrogenase | 904 | 901 | database:900 |
Rv0147 |
aldehyde dehydrogenase | 904 | 901 | database:900 |
Rv1862 adhA |
alcohol dehydrogenase A | 924 | 900 | database:900 |
Rv0223c |
aldehyde dehydrogenase | 903 | 900 | database:900 |
Rv3293 pcd |
piperideine-6-carboxylic acid dehydrogenase | 903 | 900 | database:900 |
Rv3248c sahH |
adenosylhomocysteinase | 632 | 617 ctx | neighborhood:615 |
Rv3253c |
cationic amino acid transport integral membrane protein | 586 | 585 ctx | neighborhood:577 |
Rv1814 erg3 |
membrane-bound C-5 sterol desaturase | 528 | 484 | |
Rv3247c tmk |
thymidylate kinase | 575 | 455 ctx | neighborhood:455 |
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: transmembrane alkane 1-monooxygenase AlkB
- MTBC0 PGAP product: alkane 1-monooxygenase
- Pfam (hmmscan --cut_ga): FA_desaturase PF00487.31 (E=1e-37)
- (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_217769.1)
- Domains: Pfam-A via hmmscan --cut_ga — FA_desaturase (PF00487.31)
- 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
COG3239 - Curated reference: UniProt O05895 (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 —
29 functional partner(s); context anchor
rubA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003460|Rv3252c|alkB MTTQIGSGGPEAPRPPEVEEWRDKKRYLWLMGLIAPTALVVMLPLIWGMNQLGWHAAAQVPLWIGPILLYVLLPLLDLRFGPDGQNPPDEVTDRLENDKYYRYCTYIYIPFQYLSVVLGAYLFTAANLSWLGFDGALSWAGKLGVALSVGVLGGVGINTAHEMGHKKDSLERWLSKITLAQTCYGHFYIEHNRGHHVRVSTPEDPASARFGETLWEFLPRSVIGGLRSAVHLEAQRLRRLGVSPWNPMTYLRNDVLNAWLMSVVLWGGLIAVFGPALIPFVIIQAVFGFSLLEAVNYLEHYGLLRQKSANGRYERCAPVHSWNSDHIVTNLFLYHLQRHSDHHANPTRRYQTLRSMAGAPNLPSGYASMISLTYFPPLWRKVMDHRVLEHYGGDITRVNLHPRVREKALARYGASA