GapMind for catabolism of small carbon sources

 

Definition of L-tryptophan catabolism

As rules and steps, or see full text

Rules

Overview: Tryptophan degradation in GapMind is based on MetaCyc degradation pathways I via anthranilate (link), II via pyruvate (link), or IX via 3-hydroxyanthranilate (link). Pathway XII (link) overlaps with pathway I and is also represented. The other MetaCyc pathways do not yield fixed carbon or are not reported in prokaryotes, and are not included. For example, pathway IV yields indole-3-lactate, which could potentially be oxidized to indole-3-acetate, which has a known catabolic pathway, but no prokaryotes are known to consume tryptophan this way. Pathway VIII yields tryptophol (also known as indole-3-ethanol), which could potentially be oxidized to indole-3-acetate and consumed. Pathways X and XIII yield indole-3-propionate, which may spontaneously oxidize to kynurate, but kynurate catabolism is not reported.

Steps

trpP: energy-coupling factor transporter, tryptophan-specific (S) component TrpP

ecfA1: energy-coupling factor transporter, ATPase 1 (A1) component

ecfA2: energy-coupling factor transporter, ATPase 2 (A2) component

ecfT: energy-coupling factor transporter, transmembrane (T) component

aroP: tryptophan:H+ symporter AroP

tnaB: tryptophan:H+ symporter TnaB

TAT: tryptophan permease

tnaT: tryptophan:Na+ symporter TnaT

ald-dh-CoA: acetaldehyde dehydrogenase, acylating

adh: acetaldehyde dehydrogenase (not acylating)

acs: acetyl-CoA synthetase, AMP-forming

ackA: acetate kinase

pta: phosphate acetyltransferase

pcaI: 3-oxoadipate CoA-transferase subunit A (PcaI)

pcaJ: 3-oxoadipate CoA-transferase subunit B (PcaJ)

catI: 3-oxoadipate CoA-transferase subunit A (CatI)

catJ: 3-oxoadipate CoA-transferase subunit B (CatJ)

mhpD: 2-hydroxypentadienoate hydratase

mhpE: 4-hydroxy-2-oxovalerate aldolase

praB: 2-hydroxymuconate 6-semialdehyde dehydrogenase

praC: 2-hydroxymuconate tautomerase

praD: 2-oxohex-3-enedioate decarboxylase

xylF: 2-hydroxymuconate semialdehyde hydrolase

pcaF: succinyl-CoA:acetyl-CoA C-succinyltransferase

pcaD: 3-oxoadipate enol-lactone hydrolase

xylE: catechol 2,3-dioxygenase

catA: catechol 1,2-dioxygenase

catB: muconate cycloisomerase

catC: muconolactone isomerase

nbaC: 3-hydroxyanthranilate 3,4-dioxygenase

nbaD: 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase

nbaE: 2-aminomuconate 6-semialdehyde dehydrogenase

nbaF: 2-aminomuconate deaminase

nbaG: 2-oxo-3-hexenedioate decarboxylase

antA: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA

antB: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB

antC: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC

andAa: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin--NAD(+) reductase component AndAa

andAb: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin subunit AndAb

andAc: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AndAc

andAd: athranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AndAd

hpaH: anthranilate 3-monooxygenase (hydroxylase), FADH2-dependent

kynA: tryptophan 2,3-dioxygenase

kynB: kynurenine formamidase

kyn: kynureninase

tnaA: tryptophanase

sibC: L-kynurenine 3-monooxygenase

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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:

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:

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:

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