GapMind for catabolism of small carbon sources

 

L-tryptophan catabolism in Pseudomonas fluorescens FW300-N2E3

Best path

aroP, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, catI, catJ, pcaF

Also see fitness data for the top candidates

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.

47 steps (27 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aroP tryptophan:H+ symporter AroP AO353_05930 AO353_05965
kynA tryptophan 2,3-dioxygenase AO353_05970
kynB kynurenine formamidase AO353_05975
kyn kynureninase AO353_05935
antA anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA AO353_05950 AO353_23535
antB anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB AO353_05955 AO353_23540
antC anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC AO353_05960 AO353_23545
catA catechol 1,2-dioxygenase AO353_23525
catB muconate cycloisomerase AO353_23515
catC muconolactone isomerase AO353_23520
pcaD 3-oxoadipate enol-lactone hydrolase AO353_17230 AO353_19350
catI 3-oxoadipate CoA-transferase subunit A (CatI) AO353_17195
catJ 3-oxoadipate CoA-transferase subunit B (CatJ) AO353_17200
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase AO353_17205 AO353_01065
Alternative steps:
ackA acetate kinase AO353_04410
acs acetyl-CoA synthetase, AMP-forming AO353_03060 AO353_14365
adh acetaldehyde dehydrogenase (not acylating) AO353_22390 AO353_06560
ald-dh-CoA acetaldehyde dehydrogenase, acylating
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
ecfA1 energy-coupling factor transporter, ATPase 1 (A1) component AO353_12265 AO353_29310
ecfA2 energy-coupling factor transporter, ATPase 2 (A2) component AO353_08875 AO353_11555
ecfT energy-coupling factor transporter, transmembrane (T) component
hpaH anthranilate 3-monooxygenase (hydroxylase), FADH2-dependent
mhpD 2-hydroxypentadienoate hydratase
mhpE 4-hydroxy-2-oxovalerate aldolase
nbaC 3-hydroxyanthranilate 3,4-dioxygenase
nbaD 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
nbaE 2-aminomuconate 6-semialdehyde dehydrogenase AO353_07805 AO353_19510
nbaF 2-aminomuconate deaminase AO353_05260 AO353_15115
nbaG 2-oxo-3-hexenedioate decarboxylase
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) AO353_27935
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) AO353_27940
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase AO353_07805 AO353_09195
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase
pta phosphate acetyltransferase AO353_05065
sibC L-kynurenine 3-monooxygenase
TAT tryptophan permease AO353_24825 AO353_05965
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
xylF 2-hydroxymuconate semialdehyde hydrolase AO353_04920 AO353_25150

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 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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