GapMind for catabolism of small carbon sources

 

L-tryptophan catabolism in Pseudomonas fluorescens GW456-L13

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 (32 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aroP tryptophan:H+ symporter AroP PfGW456L13_4286 PfGW456L13_4291
kynA tryptophan 2,3-dioxygenase PfGW456L13_4292
kynB kynurenine formamidase PfGW456L13_4293
kyn kynureninase PfGW456L13_4288
antA anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA PfGW456L13_2740 PfGW456L13_3819
antB anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB PfGW456L13_2739 PfGW456L13_3818
antC anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC PfGW456L13_2738 PfGW456L13_3817
catA catechol 1,2-dioxygenase PfGW456L13_3822
catB muconate cycloisomerase PfGW456L13_3824
catC muconolactone isomerase PfGW456L13_3823
pcaD 3-oxoadipate enol-lactone hydrolase PfGW456L13_4585 PfGW456L13_2295
catI 3-oxoadipate CoA-transferase subunit A (CatI) PfGW456L13_4592
catJ 3-oxoadipate CoA-transferase subunit B (CatJ) PfGW456L13_4591 PfGW456L13_2532
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase PfGW456L13_4590 PfGW456L13_2430
Alternative steps:
ackA acetate kinase PfGW456L13_4820
acs acetyl-CoA synthetase, AMP-forming PfGW456L13_1963 PfGW456L13_1517
adh acetaldehyde dehydrogenase (not acylating) PfGW456L13_3517 PfGW456L13_1342
ald-dh-CoA acetaldehyde dehydrogenase, acylating PfGW456L13_2505
andAa anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin--NAD(+) reductase component AndAa PfGW456L13_3417
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 PfGW456L13_3150 PfGW456L13_876
ecfA2 energy-coupling factor transporter, ATPase 2 (A2) component PfGW456L13_876 PfGW456L13_483
ecfT energy-coupling factor transporter, transmembrane (T) component
hpaH anthranilate 3-monooxygenase (hydroxylase), FADH2-dependent
mhpD 2-hydroxypentadienoate hydratase PfGW456L13_2504
mhpE 4-hydroxy-2-oxovalerate aldolase PfGW456L13_2506 PfGW456L13_3931
nbaC 3-hydroxyanthranilate 3,4-dioxygenase
nbaD 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
nbaE 2-aminomuconate 6-semialdehyde dehydrogenase PfGW456L13_1083 PfGW456L13_3737
nbaF 2-aminomuconate deaminase PfGW456L13_3117 PfGW456L13_3652
nbaG 2-oxo-3-hexenedioate decarboxylase PfGW456L13_2504
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI)
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ)
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase PfGW456L13_1083 PfGW456L13_1397
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase PfGW456L13_2504
pta phosphate acetyltransferase PfGW456L13_4990
sibC L-kynurenine 3-monooxygenase
TAT tryptophan permease PfGW456L13_3211 PfGW456L13_4291
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 PfGW456L13_2530
xylF 2-hydroxymuconate semialdehyde hydrolase PfGW456L13_2503

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, the preprint on GapMind for carbon sources, 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