che1 Resolved · high auto-curated
H37Rv Rv2393 · MTBC0 - ·
281 aa · 2687128–2687973 (+) ·
RefSeq NP_216909.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ferrochelatase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Ferrochelatase. Pfam: CbiX (PF01903.23). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P71751
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Ferrochelatase Che1 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | cbiX |
| eggNOG description | CbiX |
| Orthologous group | COG2138 |
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 | 1.149 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 3 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 |
|---|---|---|---|---|
CbiX | PF01903.23 | 2.0e-19 | 53–151 | CbiX |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: cysH (phosphoadenosine phosphosulfate reductase), high confidence from genomic context alone (score 989 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2392 cysH |
phosphoadenosine phosphosulfate reductase | 990 | 989 ctx | neighborhood:881 coexpression:891 |
Rv2391 sirA |
sulfite reductase | 989 | 987 ctx | neighborhood:881 coexpression:871 |
Rv2394 ggtB |
gamma-glutamyltranspeptidase precursor GgtB | 946 | 946 ctx | neighborhood:662 coexpression:848 |
Rv2847c cysG |
multifunctional uroporphyrin-III C-methyltransferase/precorrin-2 oxidase/ferrochelatase | 955 | 935 | coexpression:909 |
Rv2677c hemY |
protoporphyrinogen oxidase | 559 | 509 | database:500 |
Rv1286 cysC |
adenylyl-sulfate kinase | 543 | 502 | coexpression:404 |
Rv0511 hemD |
uroporphyrin-III C-methyltransferase | 643 | 499 | coexpression:429 |
Rv1162 narH |
nitrate reductase subunit beta | 469 | 469 | coexpression:451 |
Rv2395 |
integral membrane protein | 460 | 460 ctx | neighborhood:443 |
Rv2633c hyp |
hypothetical protein | 450 | 429 | |
Rv1163 narJ |
nitrate reductase subunit delta | 424 | 424 | coexpression:404 |
Rv1164 narI |
nitrate reductase subunit gamma | 415 | 416 | |
Rv1285 cysD |
sulfate adenylyltransferase subunit 2 | 480 | 398 | |
Rv0255c cobQ1 |
cobyric acid synthase | 455 | 391 | |
Rv2072c cobL |
precorrin-6Y C(5,15)-methyltransferase | 567 | 359 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): ferrochelatase
- Pfam (hmmscan --cut_ga): CbiX PF01903.23 (E=2e-19)
- (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_216909.1)
- Domains: Pfam-A via hmmscan --cut_ga — CbiX (PF01903.23)
- 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
COG2138 - Curated reference: UniProt P71751 (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 —
18 functional partner(s); context anchor
cysH - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2393|che1 MTAPATMQSAAMLRSGAIEAPPATMQSAAMRWGHLPLAEESGTIAPQLVLTAHGSKDPRSAANARAIAGRLARMRPGLDVRVAFCELNSPNLVDVLNRCRGAAVVTPLLLADAYHARVDIPAQIASCRVGHRVRQASVLGEDIRLVSALHERLTELGVSPFDHTLGVVVLAIGSSHPAANARTSTVASRLAEGTQWAAVTTAFITRPEASLADATDRLRRHGARRMVIAPWLLAPGILSDRVRGYAREAGIAMAQPLGAHPMVAATMWDRYRQAVAGRIAA