Substrate-level phosphorylation

METPO:1000804 · CLASS · REVIEWED

A metabolism in which ATP is formed directly by transfer of a phosphoryl group from a substrate to ADP.

Trait evidence (2)

DOI:10.1111/1751-7915.13746
Substrate-level phosphorylation is one of the main sources

Review supports SLP as microbial energy conservation in fermentative metabolism.
DOI:10.1128/MMBR.69.1.12-50.2005
phosphotransacetylase [PTA], acetate kinase [ACK]

Review supports acetate kinase and phosphotransacetylase as central acetate-switch enzymes.

Substrate-level phosphorylation direct ATP formation

DOI-backed graph connecting high-energy phosphorylated intermediates, kinase reactions, ADP phosphorylation, and ATP formation.

MECHANISTIC · Represents direct phosphoryl transfer to ADP and two concrete enzyme routes; the unreviewed ArcC exemplar is retained only because it is the exact SF370 reference-proteome sequence paired to a gene-deletion study.

Edge evidence

Substrate-level phosphorylation occurs in fermentative condition biolink:occurs_in
SLP is a major ATP source in fermentative energy metabolism.
- DOI:10.1111/1751-7915.13746 main sources of energy under fermentative conditions Supports fermentative context for SLP.
high-energy phosphorylated intermediate donates phosphoryl group to ADP
SLP transfers phosphoryl groups from metabolic intermediates to ADP.
- DOI:10.1111/1751-7915.13746 transferring a phosphate group to ADP Supports direct phosphoryl transfer to ADP.
kinase reaction has output ATP RO:0002234
Kinase reactions convert phosphorylated intermediates and ADP to ATP.
- DOI:10.1111/1751-7915.13746 kinase-catalysed reactions can be applied for SLP Supports kinase-mediated ATP formation.
acetyl phosphate substrate for acetate kinase
Acetyl phosphate is converted by acetate kinase during acetate dissimilation.
- DOI:10.1128/MMBR.69.1.12-50.2005 acetyl∼P, the high-energy intermediate of acetate dissimilation Supports acetyl phosphate as the high-energy acetate-switch intermediate.
acetate kinase produces acetate METPO:2007800
Acetate kinase forms acetate from acetyl phosphate.
- DOI:10.1128/MMBR.69.1.12-50.2005 phosphotransacetylase [PTA], acetate kinase [ACK] Supports acetate kinase as a central acetate-switch component.
acetate kinase produces ATP METPO:2007800
Acetate kinase contributes ATP formation through substrate-level phosphorylation.
- DOI:10.1111/1751-7915.13746 acetyl-phosphate to acetate Review lists acetyl-phosphate to acetate among SLP energy-conserving reactions.
anaerobiosis / low oxygen enables fermentation RO:0002327
Absence of oxygen enables fermentative metabolism.
- DOI:10.1093/femsre/fuae016 Fermentation is a type of metabolism carried out by organisms in environments without oxygen. Fermentation is a type of metabolism carried out by organisms in environments without oxygen.
fermentation produces ATP via Substrate-level phosphorylation
In fermentation, ATP is produced by substrate-level phosphorylation.
- DOI:10.1093/femsre/fuae016 ATP is produced by substrate-level phosphorylation. ATP is produced by substrate-level phosphorylation; strong definitional edge.
AckA-Pta pathway allows ATP production via Substrate-level phosphorylation
The AckA-Pta reaction set allows ATP production via substrate-level phosphorylation.
- DOI:10.1042/ETLS20220092 acetate kinase and phosphotransacetylase (AckA-Pta), a set of reactions that allows ATP production via substrate-level phosphorylation AckA-Pta, a set of reactions that allows ATP production via substrate-level phosphorylation.
carbamate kinase (arginine deiminase pathway) generates ATP via Substrate-level phosphorylation
Carbamate kinase in the arginine deiminase pathway is an additional SLP route for ATP production.
- DOI:10.1039/d4cb00099d As part of the arginine deiminase (ADI) pathway, carbamate kinase generates one ATP molecule The carbamate kinase reaction has been reported to be effective for ATP production in several acetogens.
kinase reaction has input high-energy phosphorylated intermediate RO:0002233
The kinase reaction accepts a phosphoryl group from a high-energy metabolic intermediate.
- DOI:10.1111/1751-7915.13746 transferring a phosphate group to ADP Verified against the free public article text.
kinase reaction contributes to Substrate-level phosphorylation RO:0002326
Kinase-catalyzed direct phosphoryl transfer realizes substrate-level phosphorylation.
- DOI:10.1111/1751-7915.13746 kinase-catalysed reactions can be applied for SLP Verified against the free public article text.

Protein and taxon examples

Graph node Protein Taxon UniProt status Role and evidence

carbamate kinase (arginine deiminase pathway)

Graph node	Protein	Taxon	UniProt status	Role and evidence
carbamate kinase (arginine deiminase pathway)	`UniProtKB:Q99YT9` Carbamate kinase (arcC)	Streptococcus pyogenes serotype M1 `NCBITaxon:301447`	`UNREVIEWED` retrieved 2026-08-23 · entry v146 · sequence v1	ArcC of the arginine-deiminase pathway, which catalyzes the ATP-forming carbamate-kinase reaction represented by this node. `DOI:10.1128/IAI.00916-13` individual in-frame deletion mutations were constructed in arcC (SPy_1541) The primary study constructed the exact SF370 arcC deletion; UniProtKB Q99YT9 is the corresponding current unreviewed entry in reference proteome UP000000750.

UniProtKB:Q99YT9
Carbamate kinase (arcC)

Streptococcus pyogenes serotype M1
NCBITaxon:301447

UNREVIEWED
retrieved 2026-08-23 · entry v146 · sequence v1

ArcC of the arginine-deiminase pathway, which catalyzes the ATP-forming carbamate-kinase reaction represented by this node.

DOI:10.1128/IAI.00916-13 individual in-frame deletion mutations were constructed in arcC (SPy_1541) The primary study constructed the exact SF370 arcC deletion; UniProtKB Q99YT9 is the corresponding current unreviewed entry in reference proteome UP000000750.

Provenance

Identifier source: METPO (2026-06-12)
Definition source: DOI:10.1111/1751-7915.13746

Parent traits (1)

metabolism METPO:1000060

kg-microbe context

Matched 1 kg-microbe node via direct_metpo.

METPO:1000804 [+0.098, -0.513, -1.357, -0.315, …]

512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

Nearest neighbors in embedding space

Top-8 cosine-similar METPO traits from the 2026-04-25 deepwalk (512-D).

metabolism Syntrophy 0.972
metabolism Homoacetogenesis 0.971
metabolism Oxidative phosphorylation 0.969
metabolism Disproportionation 0.965
metabolism Cable bacteria metabolism 0.965
metabolism Electron transfer 0.959
metabolism cellulolysis 0.938
metabolism 3-hydroxypropionate/4-hydroxybutyrate cycle 0.938

Deep research

Generated by just research-trait; source: research/traits/metabolism/substrate_level_phosphorylation-deep-research-falcon.md

Unreviewed literature output — not curated TraitMech content Ontology identifiers suggested below have not been resolved against their ontologies, and some are known to be wrong. Check any CURIE against the source before using it.

# Substrate-Level Phosphorylation (METPO:1000804) Causal Graph Curation Report

## 1. Trait Scope & Definition

Substrate-level phosphorylation (SLP) is **a metabolism in which ATP is formed directly by transfer of a phosphoryl group from a substrate to ADP**, according to the METPO:1000804 definition (folch2021metabolicenergyconservation pages 4-6, hackmann2024thevastlandscape pages 1-2). This trait represents ATP-generating enzymatic reactions that do not require an electron transport chain, membrane gradient, or ATP synthase complex. The trait is a **METABOLISM CLASS** taxonomically distributed across bacteria and archaea (hackmann2024thevastlandscape pages 3-4, hackmann2024thevastlandscape pages 1-2).

### Scope Boundaries

**INCLUDES:**
- Phosphoglycerate kinase (PGK): 1,3-bisphosphoglycerate + ADP → 3-phosphoglycerate + ATP (ΔGm' = –19 ± 1 kJ/mol), the only truly de novo ATP generation in glycolysis (folch2021metabolicenergyconservation pages 4-6)
- Pyruvate kinase (PYK): phosphoenolpyruvate + ADP → pyruvate + ATP (ΔGm' = –28 ± 1 kJ/mol), ATP recovery rather than de novo synthesis (folch2021metabolicenergyconservation pages 4-6)
- Acetate kinase (ACK): acetyl-phosphate + ADP → acetate + ATP (ΔGm' = –13 kJ/mol) (folch2021metabolicenergyconservation pages 7-8, wolfe2005theacetateswitch pages 8-9)
- Succinyl-CoA synthetase: succinyl-CoA + ADP (or GDP) + Pi → succinate + ATP (or GTP) + CoA (ΔGm' = –69 kJ/mol) (folch2021metabolicenergyconservation pages 6-7)
- Butyrate kinase, propionate kinase, carbamate kinase, and other acyl-phosphate-based SLP reactions (folch2021metabolicenergyconservation pages 6-7)
- ADP-forming acetyl-CoA synthetase (alternative acetate activation pathway) (folch2021metabolicenergyconservation pages 8-10)

**EXCLUDES (but may interact with):**
- Oxidative phosphorylation via ATP synthase coupled to proton/sodium gradients (folch2021metabolicenergyconservation pages 4-6, mackenzie2020bedaquilinereprogramscentral pages 1-2)
- Fermentation as a broader metabolic lifestyle (fermentation encompasses but is not defined solely by SLP) (hackmann2024thevastlandscape pages 3-4, hackmann2024thevastlandscape pages 1-2)
- PTS-mediated sugar transport phosphorylation (distinct system) (wolfe2005theacetateswitch pages 3-4, wolfe2005theacetateswitch pages 8-9)
- Polyphosphate kinase-mediated ATP production (different phosphoryl donor)
- ATP-neutral pathways such as the Wood-Ljungdahl pathway without acyl-phosphate intermediates (baum2024theenergyconvertinghydrogenase pages 1-2)

**KEY DEFINITION:** Over one-fourth of prokaryotes carry out fermentation, utilizing more than 40 substrates and releasing more than 50 metabolic end products, often relying on SLP for energy generation (hackmann2024thevastlandscape pages 1-2). However, recent data confirm that even fermentative organisms can generate up to one-third of ATP through electron transport chains coupled to ATP synthase (hackmann2024thevastlandscape pages 3-4).

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## 2. Candidate Causal Graph Entities

### Pathways & Metabolic Modules
- **Glycolysis / Embden-Meyerhof-Parnas pathway** (KEGG pathway map00010; EC classification system)
- **Acetate formation pathway** (phosphotransacetylase–acetate kinase route)
- **Tricarboxylic acid cycle / TCA cycle** (KEGG map00020)
- **Anaplerotic reactions** (carbon-fixing reactions feeding TCA cycle)
- **Methylcitrate cycle** (MCC; propionyl-CoA assimilation and detoxification)
- **Butyrate/propionate fermentation modules** (label-only; species-specific pathways)

### Enzymes & Complexes
- **Phosphoglycerate kinase (PGK)** – EC 2.7.2.3; KEGG: K00927
- **Pyruvate kinase (PYK)** – EC 2.7.1.40; gene examples: *pyk*, *pykF*
- **Phosphotransacetylase (PTA)** – EC 2.3.1.8; gene *pta*
- **Acetate kinase (ACK)** – EC 2.7.2.1; gene *ackA*
- **Succinyl-CoA synthetase** (SCSC) – EC 6.2.1.5; multi-subunit complex; genes *sucC*, *sucD*
- **Butyrate kinase** – EC 2.7.2.7
- **Propionate kinase** – label-only (limited EC grounding)
- **Carbamate kinase** – EC 2.7.2.2
- **ADP-forming acetyl-CoA synthetase (ADP-ACS)** – EC 6.2.1.13

### Regulatory & Signal Molecules
- **Transcription factor AbrB** (transition-state regulator; *Bacillus*)
- **Acetyl-phosphate (acetyl-P)** (high-energy intermediate and proposed global signal) (wolfe2005theacetateswitch pages 3-4, wolfe2005theacetateswitch pages 8-9)
- **NAD⁺/NADH ratio** (redox balance sensor) (zhang2024understandingenergyfluctuation pages 1-2, zhang2024understandingenergyfluctuation pages 4-6)
- **ATP/ADP ratio** (cellular energy charge)
- **Spo0A** (phosphorylated sporulation regulator; represses AbrB)
- **Oxygen-sensing regulators** (*Fnr*, *ArcA* in *E. coli*; *ResD* in *Bacillus*)
- **Transcription factors CcpN, Rex, CcpA** (energy metabolism regulators in *Bacillus*)

### Metabolites
- **1,3-bisphosphoglycerate** (CHEBI:16001)
- **3-phosphoglycerate** (CHEBI:17794)

Showing the first 60 of 362 lines of findings; the linked file also carries the run's front matter and the prompt it was given — read the full report.

Canonical examples (3)

Organisms cited as exemplars of this trait. Taxon ids are NCBITaxon and link out to the NCBI record.

Streptococcus pyogenes NCBITaxon:1314 PMID:27442496 ATP via glycolytic substrate-level phosphorylation
Clostridium acetobutylicum NCBITaxon:1488 PMID:11466286 fermentative substrate-level phosphorylation
Streptococcus pyogenes serotype M1 NCBITaxon:301447 DOI:10.1128/IAI.00916-13 Reference-proteome strain SF370 in which arcC was deleted in-frame to test the arginine-deiminase pathway.

Curation history

2026-08-23T09:03:00Z · CURATE_PROTEIN_TAXON_EXAMPLE · codex
Reviewed the graph as mechanistic and added the DOI-backed SF370 ArcC reference-proteome exemplar with an explicit unreviewed-entry exception.
2026-05-05T01:35:46.913184+00:00 · SEEDED_FROM_METPO · seed_from_metpo
imported from data/raw/metpo.owl (CLASS)
2026-05-08T00:00:00-07:00 · ADDED_CAUSAL_GRAPH · codex
Added DOI-backed causal graph for direct phosphoryl transfer to ADP and acetate kinase-linked ATP formation.
2026-05-20T03:35:30Z · GROUND_CAUSAL_PREDICATES · claude
Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202×3).
2026-05-20T05:49:24Z · GROUND_CAUSAL_PREDICATES · claude
Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:occurs_in×1).
2026-05-24T04:38:00Z · GROUND_CAUSAL_NODES · claude
Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0016301×1).
2026-05-24T05:05:14Z · GROUND_CAUSAL_NODES · claude
Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A081KVG3×1).
2026-06-14T05:51:46Z · GROUND_CAUSAL_NODES · claude
Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:16761×1, CHEBI:15350×1).
2026-06-23T00:00:00Z · ENRICH_CAUSAL_GRAPH · claude
Added 4 evidence-backed generic edges (4 new nodes) from the deep-research report.
2026-06-24T17:21:12Z · GROUND_CAUSAL_PREDICATES · claude
Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327×1).
2026-06-24T17:21:19Z · GROUND_CAUSAL_NODES · claude
Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0006113×1).
2026-07-20T04:21:11Z · RETRACT_DEAD_UNIPROT_GROUNDINGS · claude
Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)
2026-07-20T04:23:54Z · GROUND_CAUSAL_NODES · claude
Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0008776×1, GO:0008804×1).
2026-08-06T01:00:00Z · MIGRATE_MICROBE_DOMAIN_EDGES · claude
Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.
2026-08-06T02:00:00Z · MIGRATE_MICROBE_DOMAIN_EDGES_PART2 · claude
Re-grounded 2 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (2 to produces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.
2026-08-16T02:00:00Z · NORMALISE_NODE_TYPE · claude
Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): fermentation is typed BIOLOGICAL_PROCESS. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A CLASS of routes rather than one route -- fermentation names a mode of energy conservation with many distinct implementations, so its steps cannot be enumerated without picking one. Was 3 BIOLOGICAL_PROCESS to 2 before this tranche. NOTE its groundings disagree with each other (GO:0006113 x3, METPO:1002005, and METPO:1000845 which is ACETOGENESIS, a different concept) -- filed as #391 and deliberately NOT touched here, because retyping a node while carrying a wrong CURIE along unchanged would make it look reviewed.
2026-08-31T12:15:00Z · CONNECT_CAUSAL_GRAPH_COMPONENTS · codex
Resolved issue #183 graph fragmentation (3 components to 1) with 2 public-source connector(s). No paid research service was called.