A reusable cross-taxon model of protoporphyrin-dependent heme B biosynthesis. C5 glutamyl-tRNA and C4/Shemin reactions can independently supply 5-aminolevulinate (ALA); many organisms encode one route, while some encode both. A shared tetrapyrrole trunk then feeds independently selected oxygen-dependent or oxygen-independent coproporphyrinogen oxidases and HemJ-, HemG-, or HemY/PPOX-family protoporphyrinogen oxidases. All realizations converge at protoporphyrin IX, which a species-neutral ferrochelatase reaction converts to heme B.
Scope is CONCRETE because this document represents a chemically defined, leaf-grounded heme B biosynthetic pathway rather than a gene-free abstract motif; cross-taxon reuse does not make the pathway abstract. The boundary begins with route-specific ALA formation and ends with heme B. HemA/HemL and the trunk through uroporphyrinogen III can also supply sibling tetrapyrrole pathways, but siroheme-, corrin-, and cobalamin-specific enzymes remain outside. GltX supplies glutamyl-tRNA used by both translation and HemA and is upstream of the committed C5 entry chemistry. Coproheme synthesis, heme uptake, storage, degradation, and conversion of heme B to modified hemes are outside the boundary. A concrete organism or compartment may encode one or both ALA-entry systems and one or more enzymes on either late-oxidation axis; route enumeration describes minimal paths and therefore chooses one branch per axis. The catalog of late oxidation families is evidence-based but not a claim of universal cross-taxon completeness.
All recommended fields populated.
✓ present
✓ every leaf node grounds to a representative protein.
✓ every declared conforms_to bundle matches its template motif.
18 complete review(s) · 11 with deep research · 16 missing review · 8 reviewed but lacking deep research
| Gene | Review | Complete | Deep research |
|---|---|---|---|
| ALAD P13716 | ✓ | ✓ | ✗ |
| ALAS2 P22557 | ✓ | 39/40 | ✗ |
| CPOX P36551 | ✓ | ✓ | ✗ |
| FECH P22830 | ✓ | ✓ | ✗ |
| hemA Q88PW6 | ✓ | ✓ | ✓ |
| hemB Q88IT6 | ✓ | ✓ | ✓ |
| hemBB Q88HN1 | ✓ | ✓ | ✓ |
| hemC Q88RE5 | ✓ | ✓ | ✓ |
| hemD Q88RE4 | ✓ | ✓ | ✓ |
| hemE Q88CV6 | ✓ | ✓ | ✓ |
| hemF Q88RQ6 | ✓ | ✓ | ✓ |
| hemH Q88PV4 | ✓ | ✓ | ✓ |
| hemL Q88DP0 | ✓ | ✓ | ✓ |
| hemN Q88F35 | ✓ | ✓ | ✓ |
| HMBS P08397 | ✓ | ✓ | ✗ |
| E. coli hemC P06983 | ✗ | — | — |
| E. coli hemD P09126 | ✗ | — | — |
| E. coli hemA P0A6X1 | ✗ | — | — |
| E. coli hemB P0ACB2 | ✗ | — | — |
| E. coli hemG P0ACB4 | ✗ | — | — |
| human ALAS1 exemplar P13196 | ✗ | — | — |
| Rhodobacter capsulatus ALAS exemplar P18079 | ✗ | — | — |
| E. coli hemH P23871 | ✗ | — | — |
| E. coli hemL P23893 | ✗ | — | — |
| E. coli hemE P29680 | ✗ | — | — |
| E. coli hemN P32131 | ✗ | — | — |
| Rhodobacter sphaeroides HemN exemplar P33770 | ✗ | — | — |
| E. coli hemF P36553 | ✗ | — | — |
| Myxococcus xanthus pgoX/hemY P56601 | ✗ | — | — |
| PP_0431 Q88QQ7 | ✓ | ✓ | ✓ |
| PPOX P50336 | ✓ | ✓ | ✗ |
| Rhodobacter sphaeroides ALAS exemplar Q04512 | ✗ | — | — |
| Rhodobacter sphaeroides HemJ exemplar Q53229 | ✗ | — | — |
| UROD P06132 | ✓ | ✓ | ✗ |
| UROS P10746 | ✓ | ✓ | ✗ |
One or more ALA entry chemistries feed a shared trunk and independently selected late oxidation chemistry before the common ferrochelatase reaction.
Alternative C5 and C4 entry reactions form 5-aminolevulinate (ALA). One shared tetrapyrrole trunk and independently selected late oxidation chemistries then form protoporphyrin IX.
C5 glutamyl-tRNA and C4/Shemin chemistries independently form ALA. A concrete organism or compartment may use either route or both; entry chemistry does not determine which downstream oxidase families a taxon uses.
Commits glutamyl-tRNA-derived carbon to tetrapyrrole precursor synthesis.
Produces ALA from the HemA product.
Route-specific C4 formation of ALA.
HemF directly uses oxygen; HemN provides a radical-SAM, oxygen-independent alternative. A genome may encode both.
Direct oxygen-dependent route.
Oxygen-independent radical-SAM route.
HemJ uses a generic electron acceptor, HemG is an FMN enzyme that reduces quinone, and HemY/PPOX uses oxygen directly. Verified exemplars establish all three alternatives without claiming that any occurs in every taxon.
Acceptor-dependent route without asserting molecular oxygen as direct substrate.
Substantive quinone-linked HemG route.
Substantive oxygen-linked HemY route.
The common terminal chemistry has no generic mitochondrial or cytosolic location; localization belongs to concrete organismal realizations.
Final committed reaction producing heme B.