iniR Family assigned · medium auto-curated
H37Rv Rv0339c · MTBC0 mtbc0_000359 ·
832 aa · 409273–411771 (-) ·
RefSeq NP_214853.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | isoniazid response ATPase/transcriptional regulator IniR |
| Revised (this work) | Isoniazid response ATPase/transcriptional regulator IniR. Pfam: GerE (PF00196.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O33269
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible transcriptional regulatory protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | gerE |
| eggNOG description | Transcriptional regulator |
| Orthologous group | COG2771 |
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 | 0.559 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 13 synonymous, 18 missense, 1 nonsense, 2 frameshift |
| Disruption | 3 distinct premature-stop/frameshift site(s); most common in 0.27% of strains (390) · 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 |
|---|---|---|---|---|
GerE | PF00196.26 | 8.6e-14 | 762–816 | Bacterial regulatory proteins, luxR family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: embR (transcriptional regulator EmbR), high confidence from genomic context alone (score 897 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1267c embR |
transcriptional regulator EmbR | 899 | 897 ctx | cooccurence:506 coexpression:800 |
Rv1963c mce3R |
transcriptional repressor Mce3R | 891 | 891 ctx | cooccurence:608 coexpression:734 |
Rv3263 |
DNA methylase | 889 | 889 | coexpression:859 |
Rv1776c |
transcriptional regulator | 867 | 868 ctx | cooccurence:500 coexpression:746 |
Rv3124 moaR1 |
transcriptional regulator MoaR | 860 | 856 | coexpression:785 |
Rv3736 |
AraC/XylS family transcriptional regulator | 859 | 854 | coexpression:802 |
Rv1675c cmr |
HTH-type transcriptional regulator Cmr | 847 | 842 | coexpression:818 |
Rv0342 iniA |
isoniazid inductible protein IniA | 837 | 837 ctx | cooccurence:774 |
Rv3183 higA3 |
transcriptional regulator | 840 | 835 | coexpression:812 |
Rv0343 iniC |
iIsoniazid inductible protein IniC | 852 | 834 ctx | cooccurence:774 |
Rv1359 |
transcriptional regulator | 834 | 834 | coexpression:813 |
Rv0691c mftR |
mycofactocin biosynthesis transcriptional regulator MftR | 833 | 833 | coexpression:833 |
Rv2488c |
LuxR family transcriptional regulator | 835 | 828 | coexpression:806 |
Rv3840 |
transcriptional regulator | 824 | 822 | coexpression:822 |
Rv1027c kdpE |
transcriptional regulator KdpE | 823 | 817 | coexpression:795 |
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: isoniazid response ATPase/transcriptional regulator IniR
- Pfam (hmmscan --cut_ga): GerE PF00196.26 (E=9e-14)
- (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_214853.1)
- Domains: Pfam-A via hmmscan --cut_ga — GerE (PF00196.26)
- 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
COG2771 - Curated reference: UniProt O33269 (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 —
116 functional partner(s); context anchor
embR - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000359|Rv0339c|iniR MQHRGCKNRGQAYDASVTDSLTEVPPAARRALLELANAPTVPVKVLITGGIGTGKTTVLAAARDTLRRSGLTVLACPPPDGEPPETALVIDDAQLLTDTELLRLTERVADSRLTVVAAAEAREHHRALRALTMALERDRPRISLGPLPVAEHLRDCTAGLPFLIHAVSARAQAPAQAAKVALIERLRRLDEPTLDTLLMMSLTHELGVSDVAAALGISVTDARGLVDRAHASGLIESSHTAAFLQSVHDAIAQIVGNAHHHEVETSLLRSQLDISPVSAELALRLAEHGLRDERLADILTRYAADTRDASVRCARLYRAAVHAGAKGLTVRLADALARTGDCTAAATLADDLLSSPDATERAAAVRVAASVAVHDGNTGHAAELFGWLGPHPDTMVSSAATIVFAANGDLATARATLRLKDAGPPTMAARCARNLAEGLLLTMDQPYPVAMAKLGQAIATEQSLSQVIPDSPAALVTLAAIHAGDPVRARSVIGRAVRAGADPLFQRRHLLLSGWIKMQEGQLPSASADVAAASAGTHLHRRDALWAAALQTAISRRTGDIGALQQHWYAAMEALAEYSLDLFALLPLGELWVAAARMRQVDQLQHTLDQALTLLDSLGNPALWSNSLHWAGVHAGILANSPESVAPHGQALGAMVAHSTLAQALSDAGRTWLRVLAENVDADEVTAAARSLSHVGLTSDATRLAGQAALQTSDARVSGAMLQLARDLKLGNDFGEPPSGAGDTEPASGTPPAPRQPPAGSPLSDREREVAELLLLGMPYRDIGARLFISAKTVEHHVARIRQRLGAGSRSEMLSMLRAMLAPESLTADERR