ilvN Family assigned · medium auto-curated
H37Rv Rv3002c · MTBC0 mtbc0_003191 ·
168 aa · 3381933–3382439 (-) ·
RefSeq NP_217518.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | acetolactate synthase small subunit |
|---|---|
| MTBC0 PGAP re-annotation | acetolactate synthase small subunit |
| Revised (this work) | Acetolactate synthase small subunit. Pfam: ACT (PF01842.32), ACT_AHAS_ss (PF22629.3), ACT_5 (PF13710.13), ALS_ss_C (PF10369.16). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WKJ3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative acetolactate synthase small subunit |
| EC (curated) |
EC 2.2.1.6
|
| Curated function | Catalyzes the conversion of 2 pyruvate molecules into acetolactate in the first common step of the biosynthetic pathway of the branched-amino acids such as leucine, isoleucine, and valine. |
UniProt still lists this protein as Putative acetolactate synthase small subunit; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | ilvN |
| eggNOG description | acetolactate synthase, small |
| Orthologous group | COG0440 |
| EC number |
EC 2.2.1.6
|
| KEGG orthology |
K01653
|
| KEGG pathways |
map00290, map00650, map00660, map00770, map01100, map01110, map01130, map01210, map01230
|
| KEGG modules |
M00019, M00570
|
| Gene Ontology (52) |
GO:0003674, GO:0003824, GO:0003984, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0005948, GO:0006082 +40 more
|
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 |
|---|---|---|---|---|
ACT | PF01842.32 | 1.2e-17 | 6–71 | ACT domain |
ACT_AHAS_ss | PF22629.3 | 1.5e-27 | 8–75 | AHAS small subunit-like ACT domain |
ACT_5 | PF13710.13 | 2.1e-14 | 15–76 | ACT domain |
ALS_ss_C | PF10369.16 | 6.5e-28 | 87–160 | Small subunit of acetolactate synthase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ilvB1 (acetolactate synthase large subunit IlvB), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3003c ilvB1 |
acetolactate synthase large subunit IlvB | 999 | 1000 ctx | neighborhood:882 cooccurence:769 coexpression:919 experimental:704 database:900 textmining:907 |
Rv3001c ilvC |
ketol-acid reductoisomerase | 999 | 1000 ctx | neighborhood:823 cooccurence:719 coexpression:951 database:900 textmining:938 |
Rv3470c ilvB2 |
acetolactate synthase large subunit | 997 | 997 ctx | cooccurence:731 coexpression:648 experimental:704 database:900 |
Rv1820 ilvG |
acetolactate synthase large subunit IlvG | 998 | 993 | coexpression:650 experimental:704 database:900 textmining:740 |
Rv3509c ilvX |
acetohydroxyacid synthase large subunit | 995 | 992 | coexpression:648 experimental:704 database:900 textmining:490 |
Rv2995c leuB |
3-isopropylmalate dehydrogenase | 995 | 985 | coexpression:768 database:900 textmining:714 |
Rv1559 ilvA |
threonine dehydratase IlvA | 991 | 972 | coexpression:676 database:900 textmining:707 |
Rv0118c oxcA |
oxalyl-CoA decarboxylase OxcA | 958 | 943 ctx | cooccurence:464 coexpression:650 experimental:704 |
Rv3710 leuA |
2-isopropylmalate synthase | 981 | 938 | coexpression:595 database:800 textmining:709 |
Rv2455c korA |
2-oxoglutarate oxidoreductase subunit KorA | 929 | 921 | database:900 |
Rv2454c korB |
2-oxoglutarate oxidoreductase subunit KorB | 905 | 906 | database:900 |
Rv0189c ilvD |
dihydroxy-acid dehydratase | 960 | 892 ctx | cooccurence:583 coexpression:650 textmining:655 |
Rv2496c bkdB |
3-methyl-2-oxobutanoate dehydrogenase subunit beta | 878 | 872 | database:800 |
Rv2987c leuD |
3-isopropylmalate dehydratase small subunit | 895 | 829 | coexpression:761 textmining:416 |
Rv2988c leuC |
3-isopropylmalate dehydratase large subunit | 867 | 828 | coexpression:777 |
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: acetolactate synthase small subunit
- MTBC0 PGAP product: acetolactate synthase small subunit
- Pfam (hmmscan --cut_ga): ACT PF01842.32 (E=1e-17), ACT_AHAS_ss PF22629.3 (E=2e-27), ACT_5 PF13710.13 (E=2e-14), ALS_ss_C PF10369.16 (E=7e-28)
- (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_217518.1)
- Domains: Pfam-A via hmmscan --cut_ga — ACT (PF01842.32), ACT_AHAS_ss (PF22629.3), ACT_5 (PF13710.13), ALS_ss_C (PF10369.16)
- 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
COG0440 - Curated reference: UniProt P9WKJ3 (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 —
44 functional partner(s); context anchor
ilvB1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003191|Rv3002c|ilvN MSPKTHTLSVLVEDKPGVLARVAALFSRRGFNIESLAVGATECKDRSRMTIVVSAEDTPLEQITKQLNKLINVIKIVEQDDEHSVSRELALIKVQADAGSRSQVIEAVNLFRANVIDVSPESLTVEATGNRGKLEALLRVLEPFGIREIAQSGMVSLSRGPRGIGTAK