Rv1985c Family assigned · medium auto-curated
H37Rv Rv1985c · MTBC0 mtbc0_002109 ·
303 aa · 2252604–2253515 (-) ·
RefSeq NP_216501.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | HTH-type transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | ArgP/LysG family DNA-binding transcriptional regulator |
| Revised (this work) | ArgP/LysG family DNA-binding transcriptional regulator. Pfam: HTH_1 (PF00126.34), LysR_substrate (PF03466.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMF5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | HTH-type transcriptional regulator LysG |
| Curated function | Positively regulates the expression of the exporter LysE and represses its own expression. Activity requires the presence of a coinducer, lysine or histidine. Acts by binding to lysG-lysE promoter region. Also up-regulates the expression of ppsB, ppsC and ppsD, by binding to the upstream region of ppsB. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | iciA |
| eggNOG description | Transcriptional regulator |
| Orthologous group | COG0583 |
| KEGG orthology |
K05596
|
| Gene Ontology (47) |
GO:0001130, GO:0003674, GO:0003676, GO:0003677, GO:0003688, GO:0003690, GO:0003700, GO:0005488, GO:0006275, GO:0006355, GO:0008150, GO:0008156 +35 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 | 0.356 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.44% of strains (639) · 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 |
|---|---|---|---|---|
HTH_1 | PF00126.34 | 8.1e-18 | 10–65 | Bacterial regulatory helix-turn-helix protein, lysR family |
LysR_substrate | PF03466.26 | 4.5e-10 | 95–263 | LysR substrate binding domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lysE (amino acid transporter), high confidence from genomic context alone (score 905 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1986 lysE |
amino acid transporter | 973 | 905 ctx | neighborhood:595 cooccurence:774 textmining:727 |
Rv3736 |
AraC/XylS family transcriptional regulator | 872 | 865 | coexpression:840 |
Rv3167c |
TetR family transcriptional regulator | 853 | 851 | coexpression:833 |
Rv0691c mftR |
mycofactocin biosynthesis transcriptional regulator MftR | 847 | 845 | coexpression:826 |
Rv3183 higA3 |
transcriptional regulator | 850 | 844 | coexpression:844 |
Rv3263 |
DNA methylase | 836 | 836 | coexpression:836 |
Rv1776c |
transcriptional regulator | 863 | 833 | coexpression:812 |
Rv1674c |
transcriptional regulator | 841 | 831 | coexpression:828 |
Rv3855 ethR |
HTH-type transcriptional repressor EthR | 833 | 831 | coexpression:810 |
Rv3830c |
TetR family transcriptional regulator | 829 | 827 | coexpression:805 |
Rv3840 |
transcriptional regulator | 833 | 826 | coexpression:826 |
Rv1725c hyp |
hypothetical protein | 831 | 825 | coexpression:824 |
Rv1931c |
transcriptional regulator | 828 | 822 | coexpression:822 |
Rv0653c |
transcriptional regulator | 825 | 822 | coexpression:800 |
Rv3055 |
TetR family transcriptional regulator | 825 | 822 | coexpression:800 |
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: HTH-type transcriptional regulator
- MTBC0 PGAP product: ArgP/LysG family DNA-binding transcriptional regulator
- Pfam (hmmscan --cut_ga): HTH_1 PF00126.34 (E=8e-18), LysR_substrate PF03466.26 (E=4e-10)
- (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_216501.1)
- Domains: Pfam-A via hmmscan --cut_ga — HTH_1 (PF00126.34), LysR_substrate (PF03466.26)
- 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
COG0583 - Curated reference: UniProt P9WMF5 (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 —
81 functional partner(s); context anchor
lysE - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002109|Rv1985c| MVDPQLDGPQLAALAAVVELGSFDAAAERLHVTPSAVSQRIKSLEQQVGQVLVVREKPCRATTAGIPLLRLAAQTALLESEALAEMGGNASLKRTRITIAVNADSMATWFSAVFDGLGDVLLDVRIEDQDHSARLLREGVAMGAVTTERNPVPGCRVHPLGEMRYLPVASRPFVQRHLSDGFTAAAAAKAPSLAWNRDDGLQDMLVRKAFRRAITRPTHFVPTTEGFTAAARAGLGWGMFPEKLAASPLADGSFVRVCDIHLDVPLYWQCWKLDSPIIARITDTVRAAASGLYRGQQRRRRPG