Definition of citrate catabolism
As rules and steps, or see full text
Rules
Overview: Citrate is utilized via ATP-citrate lyase (link) or by oxidation to 2-oxoglutarate (part of the the TCA cycle, link). MetaCyc does not explicitly represent the TCA cycle as a means for catabolizing citrate, but it is expected to function under respiratory conditions. Fitness data confirms that in diverse bacteria, ATP-citrate lyase is not necessary for aerobic utilization of citrate.
- all:
- citrate-transport, citD, citE and citF
- or citrate-transport, acn and icd
- Comment: ATP-citrate lyase (citDEF) produces oxaloacetate (a central metabolite) and acetate. Because this is often a fermentative pathway, the acetate may be excreted, so activation to acetyl-CoA is not represented. Or, citrate is isomerized to isocitrate by acn and oxidized to 2-oxoglutarate by icd.
- citrate-transport:
Steps
fecB: ferric citrate ABC transporter, substrate-binding component FecB
- Curated sequence P15028: Fe(3+) dicitrate-binding periplasmic protein; Iron(III) dicitrate-binding periplasmic protein. FecB aka B4290, component of Iron (Fe3+) or ferric-dicitrate porter. ferric citrate ABC transporter periplasmic binding protein (EC 7.2.2.18). ferric citrate ABC transporter periplasmic binding protein (EC 7.2.2.18)
- Total: 1 characterized proteins
fecC: ferric citrate ABC transporter, permease component 1 (FecC)
- Curated sequence P15030: Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC. FecC aka B4289, component of Iron (Fe3+) or ferric-dicitrate porter. ferric citrate ABC transporter membrane subunit FecC (EC 7.2.2.18). ferric citrate ABC transporter membrane subunit FecC (EC 7.2.2.18)
- Total: 1 characterized proteins
fecD: ferric citrate ABC transporter, permease component 2 (FecD)
- Curated sequence CH_004160: iron(III) dicitrate transport system permease protein FecD. Fe(3+) dicitrate transport system permease protein FecD; Iron(III) dicitrate transport system permease protein FecD. FecD aka B4288, component of Iron (Fe3+) or ferric-dicitrate porter. ferric citrate ABC transporter membrane subunit FecD (EC 7.2.2.18). ferric citrate ABC transporter membrane subunit FecD (EC 7.2.2.18)
- Total: 1 characterized proteins
fecE: ferric citrate ABC transporter, ATPase component FecE
- Curated sequence CH_088321: iron(III) dicitrate transport ATP-binding protein FecE. Fe(3+) dicitrate transport ATP-binding protein FecE; Iron(III) dicitrate transport ATP-binding protein FecE. Fe(3+) dicitrate transport ATP-binding protein FecE, component of Iron (Fe3+) or ferric-dicitrate porter. ferric citrate ABC transporter ATP binding subunit (EC 7.2.2.18). ferric citrate ABC transporter ATP binding subunit (EC 7.2.2.18)
- Total: 1 characterized proteins
tctA: citrate/Na+ symporter, large transmembrane component TctA
- Curated sequence S5Y5N9: Citrate uptake transporter, membrane subunit, component of Pmf-dependent citrate uptake porter, TctABC
- Curated sequence Q9FA44: TctA, component of The tricarboxylate transporter, TctABC
- Curated sequence 3609738: Tricarboxylate transport membrane protein TctA
- UniProt sequence E4PJQ9: SubName: Full=Tricarboxylic transport TctA {ECO:0000313|EMBL:ADP98423.1};
- Comment: TctABC is also studied in S. typhimurium and D. shibae but was missed by the query. Fitness data confirms that HP15_2659:HP15_2661 (E4PJQ9,E4PJR0,E4PJR1) in Marinobacter adhaerens are tctABC
- Total: 4 characterized proteins
tctB: citrate/Na+ symporter, small transmembrane component TctB
- Curated sequence S5XH28: Citrate uptake transporter, membrane subunit, component of Pmf-dependent citrate uptake porter, TctABC
- Curated sequence Q9FA45: TctB aka STM2787, component of The tricarboxylate transporter, TctABC
- Curated sequence 3609739: Tricarboxylate transport protein TctB
- UniProt sequence E4PJR0: SubName: Full=Tricarboxylic transport membrane protein {ECO:0000313|EMBL:ADP98424.1};
- Total: 4 characterized proteins
tctC: citrate/Na+ symporter, substrate-binding component TctC
- Curated sequence S5XTE7: Citrate uptake transporter, substrate binding protein, component of Pmf-dependent citrate uptake porter, TctABC
- Curated sequence Q9FA46: TctC aka STM2786, component of The tricarboxylate transporter, TctABC
- Curated sequence 3609740: Tricarboxylate transport protein TctC
- UniProt sequence E4PJR1: SubName: Full=Tricarboxylic transport TctC {ECO:0000313|EMBL:ADP98425.1};
- Total: 4 characterized proteins
SLC13A5: citrate:Na+ symporter
- Curated sequence CH_091173: tonoplast dicarboxylate transporter. Tonoplast dicarboxylate transporter; AttDT; Sodium-dicarboxylate cotransporter-like; AtSDAT; Vacuolar malate transporter. The tonoplast dicarboxylate (malate) transporter, AtDCT
- Curated sequence Q86YT5: Solute carrier family 13 member 5; Na(+)/citrate cotransporter; NaCT; Sodium-coupled citrate transporter; Sodium-dependent citrate transporter. Na+-coupled citrate transporter (NaCT) (Km=20 μM) (also may transport dicarboxylates and other tricarboxylates with lower affinity) (Inoue et al., 2002b; Bergeron et al. 2013). Na+:citrate = 3-4:1 (Bergeron et al. 2013). Na+:citrate = 3-4:1
- Curated sequence Q8CJ44: Solute carrier family 13 member 5; Na(+)/citrate cotransporter; NaCT; Sodium-coupled citrate transporter; Sodium-dependent citrate transporter
- Curated sequence Q13183: Solute carrier family 13 member 2 (Na /di- and tricarboxylate cotransporter 1) (NaDC-1) (Renal sodium/dicarboxylate cotransporter)
- Total: 4 characterized proteins
citA: citrate:H+ symporter CitA
- Curated sequence CH_014606: citrate transporter
- Curated sequence P0A2G3: Citrate-proton symporter; Citrate carrier protein; Citrate transporter; Citrate utilization determinant; Citrate utilization protein A. The citrate/tricarballylate:H+ symporter (CitA or TcuC); probably orthologous to 2.A.1.6.1
- Curated sequence P16482: Citrate:H+ symporter
- Total: 3 characterized proteins
cimH: citrate:H+ symporter CimH
citW: citrate exchange transporter CitW (with lactate or acetate)
- Curated sequence Q8VS41: citrate lyase holo-[acyl-carrier protein] synthase (EC 2.7.7.61). Citrate:acetate antiporter, CitW
- Curated sequence P21608: Electrogenic citrate:L-lactate exchanger, CitP or CitN
- Total: 2 characterized proteins
cit1: citrate:H+ symporter Cit1
citT: citrate:succinate antiporter CitT
- Curated sequence P0AE74: Citrate/succinate antiporter; Citrate carrier; Citrate transporter. Citrate:succinate antiporter. citrate:succinate antiporter. citrate:succinate antiporter
- Total: 1 characterized proteins
citM: citrate:cation:H+ symporter CitM
- Curated sequence P55069: Mg(2+)/citrate complex secondary transporter. [Citrate or D-isocitrate]•M2+ (Mg2+ preferring):H+ symporter, CitM (transports Mg2+, Mn2+, Ni2+, Co2+ & Zn2+)
- Curated sequence A4QA05: Citrate-inducible divalent cation:citrate uptake transporter, CitH
- Curated sequence P42308: [Citrate]•M2+ (Ca2+ preferring):H+ symporter, CitH (transports Ca2+, Ba2+ & Sr2+)
- Curated sequence Q9S242: Citrate-M2+ (Fe3+ preferring): H+ symporter, Cit (transports Fe3+, Ca2+, Pb2+, Ba2+ and Mn2+, but not Mg2+, Ni2+ or Co2+)
- Curated sequence Q8DUC7: Citrate•Me2+ (Fe2+/Mn2+ preferring):H+ symporter, CitM
- Comment: (Some of these were missed by the query, probably because the substrate field in TCDB mentions the cation only)
- Total: 5 characterized proteins
citS: citrate:Na+ symporter CitS
citD: citrate lyase, acyl carrier component CitD
- Curated sequence MONOMER-17000: citrate lyase γ subunit
- Curated sequence ACPSUB-MONOMER: citrate lyase gamma chain. Citrate lyase acyl carrier protein; Citrate lyase gamma chain. citrate lyase acyl carrier protein. citrate lyase acyl carrier protein
- Comment: Citrate lyase has 3 subunits citDEF; activity also requires acetylation by citrate lyase synthetase (citC); this is not represented here.
- Total: 2 characterized proteins
citE: citrate lyase, citryl-ACP lyase component CitE
- Curated sequence Q037K5: citrate (pro-3S)-lyase (EC 4.1.3.6)
- Curated sequence P0A9I1: Citrate lyase subunit beta; Citrase beta chain; Citrate (pro-3S)-lyase subunit beta; Citryl-CoA lyase subunit; EC 4.1.3.6; EC 4.1.3.34. citrate lyase β subunit
- Curated sequence MONOMER-16999: citrate lyase β subunit (EC 4.1.3.34)
- Total: 3 characterized proteins
citF: citrate lyase, citrate-ACP transferase component CitF
- Curated sequence P75726: Citrate lyase alpha chain; Citrase alpha chain; Citrate (pro-3S)-lyase alpha chain; Citrate CoA-transferase subunit; EC 4.1.3.6; EC 2.8.3.10. citrate lyase α subunit
- Total: 1 characterized proteins
acn: aconitase
icd: isocitrate dehydrogenase
- Curated proteins or TIGRFams with EC 1.1.1.41
- Curated proteins or TIGRFams with EC 1.1.1.42
- Curated proteins or TIGRFams with EC 1.1.1.286
- Comment: Eukaryotic icd is heteromeric, but the regulatory subunits are similar to the enzymatic subunits, so this is not represented here
- Total: 4 HMMs and 74 characterized proteins
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About GapMind
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using
ublast (a fast alternative to protein BLAST)
against a database of manually-curated proteins (most of which are experimentally characterized) or by using
HMMer with enzyme models (usually from
TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
- ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
- HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.
where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").
Otherwise, a candidate is "medium confidence" if either:
- ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
- ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
- HMMer finds a hit (regardless of coverage or other bits).
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps."
For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways.
For diverse bacteria and archaea that can utilize a carbon source, there is a complete
high-confidence catabolic pathway (including a transporter) just 38% of the time, and
there is a complete medium-confidence pathway 63% of the time.
Gaps may be due to:
- our ignorance of proteins' functions,
- omissions in the gene models,
- frame-shift errors in the genome sequence, or
- the organism lacks the pathway.
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory