GapMind for catabolism of small carbon sources


L-tryptophan catabolism in Ruegeria conchae TW15

Best path

aroP, kynA, kynB, sibC, kyn, nbaC, nbaD, nbaE, nbaF, nbaG, mhpD, mhpE, adh, ackA, pta


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.

47 steps (27 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aroP tryptophan:H+ symporter AroP
kynA tryptophan 2,3-dioxygenase G7G_RS0116425
kynB kynurenine formamidase G7G_RS0116420
sibC L-kynurenine 3-monooxygenase
kyn kynureninase G7G_RS0117815
nbaC 3-hydroxyanthranilate 3,4-dioxygenase G7G_RS0110285
nbaD 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
nbaE 2-aminomuconate 6-semialdehyde dehydrogenase G7G_RS0111640 G7G_RS0120200
nbaF 2-aminomuconate deaminase G7G_RS0109455 G7G_RS0100965
nbaG 2-oxo-3-hexenedioate decarboxylase G7G_RS0121215 G7G_RS0111655
mhpD 2-hydroxypentadienoate hydratase G7G_RS0111655 G7G_RS0121215
mhpE 4-hydroxy-2-oxovalerate aldolase G7G_RS0111660 G7G_RS0100625
adh acetaldehyde dehydrogenase (not acylating) G7G_RS0104060 G7G_RS0111065
ackA acetate kinase G7G_RS0109955
pta phosphate acetyltransferase G7G_RS0111665 G7G_RS0104460
Alternative steps:
acs acetyl-CoA synthetase, AMP-forming G7G_RS0105955 G7G_RS0104455
ald-dh-CoA acetaldehyde dehydrogenase, acylating G7G_RS0121370 G7G_RS0107180
andAa anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin--NAD(+) reductase component AndAa G7G_RS0103740
andAb anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin subunit AndAb G7G_RS0111515
andAc anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AndAc
andAd athranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AndAd
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
catA catechol 1,2-dioxygenase G7G_RS0100815
catB muconate cycloisomerase G7G_RS0111610 G7G_RS0100610
catC muconolactone isomerase
catI 3-oxoadipate CoA-transferase subunit A (CatI)
catJ 3-oxoadipate CoA-transferase subunit B (CatJ)
ecfA1 energy-coupling factor transporter, ATPase 1 (A1) component G7G_RS0114935 G7G_RS0121115
ecfA2 energy-coupling factor transporter, ATPase 2 (A2) component G7G_RS0111050 G7G_RS0111535
ecfT energy-coupling factor transporter, transmembrane (T) component
hpaH anthranilate 3-monooxygenase (hydroxylase), FADH2-dependent
pcaD 3-oxoadipate enol-lactone hydrolase G7G_RS0102510 G7G_RS0122440
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase G7G_RS0102215 G7G_RS0116445
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) G7G_RS0111965
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) G7G_RS0111960
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase G7G_RS0111640 G7G_RS0120200
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase G7G_RS0121215 G7G_RS0111655
TAT tryptophan permease
tnaA tryptophanase
tnaB tryptophan:H+ symporter TnaB
tnaT tryptophan:Na+ symporter TnaT
trpP energy-coupling factor transporter, tryptophan-specific (S) component TrpP
xylE catechol 2,3-dioxygenase G7G_RS0100920
xylF 2-hydroxymuconate semialdehyde hydrolase

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.



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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