fadB5 Family assigned · medium auto-curated
H37Rv Rv1912c · MTBC0 mtbc0_002027 ·
334 aa · 2176197–2177201 (-) ·
RefSeq NP_216428.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | oxidoreductase FadB |
|---|---|
| MTBC0 PGAP re-annotation | medium chain dehydrogenase/reductase family protein |
| Revised (this work) | Medium chain dehydrogenase/reductase family protein. Pfam: ADH_N (PF08240.18), ADH_zinc_N (PF00107.33), ADH_zinc_N_2 (PF13602.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O07721
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible oxidoreductase FadB5 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | fadB5 |
| eggNOG description | Thought to be involved in fatty acid degradation. FadB and FadA are the alpha and beta subunits of the multifunctional enzyme complex of the fatty acid degradation cycle |
| Orthologous group | COG0604 |
| EC number |
EC 1.6.5.5
|
| KEGG orthology |
K00344
|
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 | 0.455 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 4 missense, 1 nonsense, 3 frameshift |
| Disruption | 4 distinct premature-stop/frameshift site(s); most common in 17.63% of strains (25606) · convergent |
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 |
|---|---|---|---|---|
ADH_N | PF08240.18 | 2.3e-13 | 27–107 | Alcohol dehydrogenase GroES-like domain |
ADH_zinc_N | PF00107.33 | 5.3e-18 | 152–262 | Zinc-binding dehydrogenase |
ADH_zinc_N_2 | PF13602.13 | 1.7e-17 | 184–332 | Zinc-binding dehydrogenase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mbtC (polyketide synthetase), high confidence from genomic context alone (score 913 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2382c mbtC |
polyketide synthetase | 914 | 913 ctx | fusion:897 |
Rv1663 pks17 |
polyketide synthase | 911 | 907 ctx | fusion:888 |
Rv1180 pks3 |
polyketide beta-ketoacyl synthase | 906 | 906 ctx | fusion:888 |
Rv2947c pks15 |
polyketide synthase | 905 | 905 ctx | fusion:887 |
Rv1664 pks9 |
polyketide synthase | 891 | 890 ctx | fusion:869 |
Rv0405 pks6 |
membrane bound polyketide synthase | 756 | 744 ctx | fusion:686 |
Rv1913 hyp |
hypothetical protein | 659 | 659 ctx | neighborhood:654 |
Rv1911c lppC |
lipoprotein LppC | 860 | 595 ctx | neighborhood:584 textmining:669 |
Rv2932 ppsB |
phthiocerol synthesis polyketide synthase type I PpsB | 597 | 571 ctx | fusion:461 |
Rv1910c hyp |
hypothetical protein | 893 | 478 ctx | neighborhood:464 textmining:804 |
Rv2935 ppsE |
phthiocerol synthesis polyketide synthase type I PpsE | 444 | 441 | |
Rv2931 ppsA |
phthiocerol synthesis polyketide synthase type I PpsA | 461 | 434 | |
Rv3800c pks13 |
polyketide synthase | 421 | 343 | |
Rv1909c furA |
ferric uptake regulation protein FurA | 425 | 308 | |
Rv3141 fadB4 |
NADPH quinone oxidoreductase FadB | 497 | 298 |
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 FadB
- MTBC0 PGAP product: medium chain dehydrogenase/reductase family protein
- Pfam (hmmscan --cut_ga): ADH_N PF08240.18 (E=2e-13), ADH_zinc_N PF00107.33 (E=5e-18), ADH_zinc_N_2 PF13602.13 (E=2e-17)
- (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_216428.1)
- Domains: Pfam-A via hmmscan --cut_ga — ADH_N (PF08240.18), ADH_zinc_N (PF00107.33), ADH_zinc_N_2 (PF13602.13)
- 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
COG0604 - Curated reference: UniProt O07721 (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 —
23 functional partner(s); context anchor
mbtC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002027|Rv1912c|fadB5 MRAVVITKHGDPSVLQVRQRPDPPPPGPGQLRVAVRAAGVNFADHLARVGLYPDAPKLPAVVGYEVAGTVEAVGDGVDPNRVGERVLAGTRFGGYCEIVNVAATDSVVLPDALSFEQGAAVPVNYATAWAALHGYGSLRAGERVLIHAAAGGVGIAAVQFAKAAKAEVHGTASPQKHQKLAEFGVDRAIDYRRDGWWQGLGPYDVVLDALGGTSLRRSYTLLRPGGRLVGYGISNMQHGEKRSMRRVAPHALSMLRGFNLMKQLEESKTVIGLNMLRLWDDRRTLEPWIAPLTKALNDGTILPIVHAIVPFAEAPEAHRILAARENVGKVVLVP