hemQ Resolved · high auto-curated
H37Rv Rv2676c · MTBC0 mtbc0_002850 ·
231 aa · 3014246–3014941 (-) ·
RefSeq NP_217192.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hydrogen peroxide-dependent heme synthase |
| Revised (this work) | Hydrogen peroxide-dependent heme synthase. Pfam: Chlor_dismutase (PF06778.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WL45
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Coproheme decarboxylase |
| EC (curated) |
EC 1.3.98.5
|
| Curated function | Involved in coproporphyrin-dependent heme b biosynthesis. Catalyzes the decarboxylation of Fe-coproporphyrin III (coproheme) to heme b (protoheme IX), the last step of the pathway. The reaction occurs in a stepwise manner with a three-propionate intermediate (By similarity). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | cld |
| eggNOG description | chlorite dismutase |
| Orthologous group | COG3253 |
| Gene Ontology (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, GO:0044464, GO:0071944
|
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 | 0.083 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 1 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 |
|---|---|---|---|---|
Chlor_dismutase | PF06778.19 | 3.3e-76 | 32–221 | Chlorite dismutase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: hemZ (ferrochelatase), high confidence from genomic context alone (score 958 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1485 hemZ |
ferrochelatase | 964 | 958 ctx | fusion:881 coexpression:458 |
Rv2678c hemE |
uroporphyrinogen decarboxylase | 927 | 924 ctx | neighborhood:881 |
Rv2677c hemY |
protoporphyrinogen oxidase | 931 | 921 ctx | neighborhood:881 |
Rv2680 hyp |
hypothetical protein | 822 | 822 ctx | neighborhood:694 cooccurence:434 |
Rv2679 echA15 |
enoyl-CoA hydratase EchA15 | 790 | 791 ctx | neighborhood:788 |
Rv2675c hyp |
hypothetical protein | 787 | 786 ctx | neighborhood:773 |
Rv2681 hyp |
hypothetical protein | 696 | 697 ctx | neighborhood:694 |
Rv2199c ctaF |
cytochrome c oxidase polypeptide 4 | 615 | 616 ctx | cooccurence:614 |
Rv2194 qcrC |
ubiquinol-cytochrome C reductase cytochrome subunit C | 629 | 611 ctx | cooccurence:605 |
Rv1423 whiA |
transcriptional regulator WhiA | 600 | 600 ctx | cooccurence:595 |
Rv3610c ftsH |
zinc metalloprotease FtsH | 588 | 588 | coexpression:580 |
Rv2699c hyp |
hypothetical protein | 558 | 558 ctx | cooccurence:557 |
Rv0811c hyp |
hypothetical protein | 525 | 526 ctx | cooccurence:512 |
Rv2206 |
transmembrane protein | 508 | 508 ctx | cooccurence:505 |
Rv2256c hyp |
hypothetical protein | 504 | 504 ctx | cooccurence:489 |
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: hypothetical protein
- MTBC0 PGAP product: hydrogen peroxide-dependent heme synthase
- Pfam (hmmscan --cut_ga): Chlor_dismutase PF06778.19 (E=3e-76)
- (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_217192.1)
- Domains: Pfam-A via hmmscan --cut_ga — Chlor_dismutase (PF06778.19)
- 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
COG3253 - Curated reference: UniProt P9WL45 (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 —
35 functional partner(s); context anchor
hemZ - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002850|Rv2676c|hemQ MARLDYDALNATLRYLMFSVFSVSPGALGDQRDAIIDDASTFFKQQEERGVVVRGLYDVAGLRADADFMVWTHAERVEALQATYADFRRTTTLGRACTPVWSGVGLHRPAEFNKSHIPAFLAGEEPGAYICVYPFVRSYEWYLLPDEERRRMLAEHGMAARGYKDVRANTVPAFALGDYEWILAFEAPELDRIVDLMRELRATDARRHTRAETPFFTGPRVPVEQLVHSLP