ideR Family assigned · medium auto-curated
H37Rv Rv2711 · MTBC0 mtbc0_002885 ·
230 aa · 3045980–3046672 (+) ·
RefSeq NP_217227.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | iron-dependent repressor and activator IdeR |
|---|---|
| MTBC0 PGAP re-annotation | iron-dependent transcriptional regulator IdeR |
| Revised (this work) | Iron-dependent transcriptional regulator IdeR. Pfam: Fe_dep_repress (PF01325.26), Fe_dep_repr_C (PF02742.22), DtxR (PF18357.8), FeoA (PF04023.21). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMH1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Iron-dependent repressor IdeR |
| Curated function | Metal-dependent DNA-binding protein that controls transcription of many genes involved in iron metabolism. Acts as a repressor of siderophore biosynthesis and as a positive modulator of iron storage. Also regulates expression of transporters, proteins involved in siderophore synthesis, iron storage and transcriptional regulators. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | ideR |
| eggNOG description | repressor |
| Orthologous group | COG1321 |
| KEGG orthology |
K03709
|
| Gene Ontology (96) |
GO:0003674, GO:0003676, GO:0003677, GO:0005488, GO:0005506, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005886, GO:0006355 +84 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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 0 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 |
|---|---|---|---|---|
Fe_dep_repress | PF01325.26 | 4.4e-21 | 3–62 | Iron dependent repressor, N-terminal DNA binding domain |
Fe_dep_repr_C | PF02742.22 | 1.6e-30 | 65–133 | Iron dependent repressor, metal binding and dimerisation domain |
DtxR | PF18357.8 | 9.5e-10 | 152–229 | Diphteria toxin repressor SH3 domain |
FeoA | PF04023.21 | 2.5e-08 | 152–229 | FeoA domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: sigB (RNA polymerase sigma factor SigB), high confidence from genomic context alone (score 928 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2710 sigB |
RNA polymerase sigma factor SigB | 943 | 928 ctx | neighborhood:756 coexpression:716 |
Rv0983 pepD |
serine protease PepD | 761 | 762 | coexpression:757 |
Rv2744c 35kd_ag hyp |
hypothetical protein | 740 | 731 | coexpression:731 |
Rv2917 hyp |
hypothetical protein | 580 | 580 ctx | cooccurence:478 |
Rv2709 |
transmembrane protein | 559 | 559 ctx | neighborhood:486 |
Rv3859c gltB |
glutamate synthase large subunit | 547 | 548 ctx | neighborhood:544 |
Rv0082 |
oxidoreductase | 468 | 468 | experimental:468 |
Rv3258c hyp |
hypothetical protein | 466 | 466 ctx | cooccurence:461 |
Rv1932 tpx |
2-Cys peroxiredoxin | 476 | 448 | coexpression:416 |
Rv2256c hyp |
hypothetical protein | 446 | 446 ctx | cooccurence:429 |
Rv2359 zur |
zinc uptake regulation protein | 877 | 440 | coexpression:421 textmining:789 |
Rv1909c furA |
ferric uptake regulation protein FurA | 672 | 439 | coexpression:420 textmining:439 |
Rv2216 |
epimerase family protein | 437 | 438 | coexpression:438 |
Rv2215 dlaT |
pyruvate dehydrogenase E2 component dihydrolipoamide acyltransferase | 425 | 426 ctx | cooccurence:417 |
Rv2903c lepB |
signal peptidase | 423 | 424 | coexpression:424 |
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: iron-dependent repressor and activator IdeR
- MTBC0 PGAP product: iron-dependent transcriptional regulator IdeR
- Pfam (hmmscan --cut_ga): Fe_dep_repress PF01325.26 (E=4e-21), Fe_dep_repr_C PF02742.22 (E=2e-30), DtxR PF18357.8 (E=1e-09), FeoA PF04023.21 (E=2e-08)
- (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_217227.1)
- Domains: Pfam-A via hmmscan --cut_ga — Fe_dep_repress (PF01325.26), Fe_dep_repr_C (PF02742.22), DtxR (PF18357.8), FeoA (PF04023.21)
- 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
COG1321 - Curated reference: UniProt P9WMH1 (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 —
61 functional partner(s); context anchor
sigB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002885|Rv2711|ideR MNELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHLELTEKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEACRWEHVMSEDVERRLVKVLNNPTTSPFGNPIPGLVELGVGPEPGADDANLVRLTELPAGSPVAVVVRQLTEHVQGDIDLITRLKDAGVVPNARVTVETTPGGGVTIVIPGHENVTLPHEMAHAVKVEKV