Rv2989 Family assigned · medium auto-curated
H37Rv Rv2989 · MTBC0 mtbc0_003174 ·
233 aa · 3367456–3368157 (+) ·
RefSeq NP_217505.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | IclR family transcriptional regulator |
| Revised (this work) | IclR family transcriptional regulator. Pfam: HTH_IclR (PF09339.17), IclR_C (PF01614.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53238
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable transcriptional regulatory protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | ltbR |
| eggNOG description | Transcriptional regulator |
| Orthologous group | COG1414 |
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 | 0.397 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 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 |
|---|---|---|---|---|
HTH_IclR | PF09339.17 | 1.7e-10 | 9–54 | IclR helix-turn-helix domain |
IclR_C | PF01614.25 | 3.4e-21 | 83–229 | Bacterial transcriptional regulator IclR C-terminal |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: leuC (3-isopropylmalate dehydratase large subunit), high confidence from genomic context alone (score 969 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2988c leuC |
3-isopropylmalate dehydratase large subunit | 983 | 969 ctx | neighborhood:785 coexpression:860 textmining:499 |
Rv2987c leuD |
3-isopropylmalate dehydratase small subunit | 964 | 952 ctx | neighborhood:764 coexpression:804 |
Rv0264c hyp |
hypothetical protein | 667 | 668 | coexpression:656 |
Rv0263c hyp |
hypothetical protein | 657 | 657 | coexpression:645 |
Rv2239c hyp |
hypothetical protein | 614 | 615 ctx | cooccurence:613 |
Rv2986c hupB |
DNA-binding protein HU | 464 | 444 ctx | neighborhood:440 |
Rv1249c |
membrane protein | 439 | 439 | coexpression:420 |
Rv2631 rtcB |
RNA-splicing ligase RtcB | 458 | 52 | textmining:453 |
Rv3600c coaX |
type III pantothenate kinase | 577 | 51 | textmining:573 |
Rv3742c |
oxidoreductase | 440 | 47 | textmining:437 |
Rv2003c hyp |
hypothetical protein | 530 | 44 | textmining:529 |
Rv2037c |
transmembrane protein | 651 | 41 | textmining:651 |
Rv3603c hyp |
hypothetical protein | 539 | 41 | textmining:539 |
Rv1291c hyp |
hypothetical protein | 431 | 41 | textmining:431 |
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: transcriptional regulator
- MTBC0 PGAP product: IclR family transcriptional regulator
- Pfam (hmmscan --cut_ga): HTH_IclR PF09339.17 (E=2e-10), IclR_C PF01614.25 (E=3e-21)
- (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_217505.1)
- Domains: Pfam-A via hmmscan --cut_ga — HTH_IclR (PF09339.17), IclR_C (PF01614.25)
- 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
COG1414 - Curated reference: UniProt O53238 (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 —
14 functional partner(s); context anchor
leuC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003174|Rv2989| MRQHSGIGVLDKAVGVLHAVAESPCGLAELCDRTDLPRATAYRLAAALEVHRLLGRGQDGHWRLGPAITELATHVDDPLLVACAAVLPQLRDATGESVQVYRREGTSRVCVAALEPAAGLRDTVPVGARLPMTAGSGAKVLLAHTDAATQAAVLPKAVFSARALAEVCRRGWAQSVAEREPGVASVSAPVRDGRGVVIAAISVSGPIDRMGRRPGVRWAADLLSAADALTRRL