Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | acetyl-CoA carboxylase biotin carboxyl carrier protein subunit |
|---|
| MTBC0 PGAP re-annotation | biotin/lipoyl-binding carrier protein |
|---|
| Revised (this work) | Biotin/lipoyl-binding carrier protein. Pfam: BSH_RND (PF25917.1), Biotin_lipoyl (PF00364.29). |
|---|
Auto-curated: this verdict and function were generated by rules from
PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WPQ1
SwissProt · reviewed
· Evidence at protein level
|
|---|
| UniProt name | Biotinylated protein TB7.3 |
|---|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|
| eggNOG description | Biotin-lipoyl like |
|---|
| Orthologous group | COG1038 |
|---|
| KEGG orthology |
K02160
|
|---|
| KEGG pathways |
map00061, map00620, map00640, map00720, map01100, map01110, map01120, map01130, map01200, map01212
|
|---|
| KEGG modules |
M00082, M00376
|
|---|
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 |
0.967 · relaxed/neutral
|
|---|
| Polymorphic sites (≥ 0.1% of strains) |
1 synonymous, 3 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 |
|---|
BSH_RND | PF25917.1 |
1.1e-06 | 4–67 |
RND MFP, barrel-sandwich hybrid domain |
Biotin_lipoyl | PF00364.29 |
6.9e-17 | 10–70 |
Biotin-requiring enzyme |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|
Rv2247 accD6 |
acetyl-/propionyl-CoA carboxylase subunit beta |
972 |
971 |
database:956 |
Rv2501c accA1 |
acetyl/propionyl-CoA carboxylase subuit alpha |
982 |
964 |
database:958 textmining:524 |
Rv3285 accA3 |
bifunctional protein acetyl-/propionyl-CoA carboxylase subunit alpha AccA |
964 |
964 |
database:958 |
Rv1837c glcB |
malate synthase |
924 |
915 |
database:900 |
Rv3667 acs |
acetyl-CoAsynthetase |
923 |
914 |
database:900 |
Rv3710 leuA |
2-isopropylmalate synthase |
923 |
913 |
database:900 |
Rv0408 pta |
phosphate acetyltransferase |
937 |
912 |
database:900 |
Rv2495c bkdC |
branched-chain keto acid dehydrogenase E2 component |
912 |
907 |
database:900 |
Rv2524c fas |
fatty acid synthase |
916 |
904 |
database:900 |
Rv0753c mmsA |
methylmalonate-semialdehyde dehydrogenase |
906 |
902 |
database:900 |
Rv2455c korA |
2-oxoglutarate oxidoreductase subunit KorA |
939 |
901 |
database:900 textmining:414 |
Rv2243 fabD |
malonyl CoA-acyl carrier protein transacylase |
905 |
901 |
database:900 |
Rv0649 fabD2 |
malonyl CoA-acyl carrier protein transacylase |
900 |
901 |
database:900 |
Rv2454c korB |
2-oxoglutarate oxidoreductase subunit KorB |
911 |
900 |
database:900 |
Rv3535c hsaG |
acetaldehyde dehydrogenase |
900 |
900 |
database:900 |
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: acetyl-CoA carboxylase biotin carboxyl carrier protein subunit
- MTBC0 PGAP product: biotin/lipoyl-binding carrier protein
- Pfam (hmmscan --cut_ga): BSH_RND PF25917.1 (E=1e-06), Biotin_lipoyl PF00364.29 (E=7e-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_217737.1)
- Domains: Pfam-A via hmmscan --cut_ga — BSH_RND (PF25917.1), Biotin_lipoyl (PF00364.29)
- 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
COG1038
- Curated reference: UniProt
P9WPQ1
(SwissProt, reviewed; 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 —
59 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003427|Rv3221c|TB7.3
MAEDVRAEIVASVLEVVVNEGDQIDKGDVVVLLESMKMEIPVLAEAAGTVSKVAVSVGDVIQAGDLIAVIS
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