GapMind for catabolism of small carbon sources

 

L-tryptophan catabolism in Pseudomonas simiae WCS417

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 (31 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aroP tryptophan:H+ symporter AroP PS417_23645 PS417_23700
kynA tryptophan 2,3-dioxygenase PS417_23705
kynB kynurenine formamidase PS417_23710
kyn kynureninase PS417_23650
antA anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA PS417_23685
antB anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB PS417_23690
antC anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC PS417_23695 PS417_08245
catA catechol 1,2-dioxygenase PS417_23660
catB muconate cycloisomerase PS417_23670
catC muconolactone isomerase PS417_23665
pcaD 3-oxoadipate enol-lactone hydrolase PS417_06735 PS417_06740 with PS417_20530
catI 3-oxoadipate CoA-transferase subunit A (CatI) PS417_06700
catJ 3-oxoadipate CoA-transferase subunit B (CatJ) PS417_06705
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase PS417_06710 PS417_10515
Alternative steps:
ackA acetate kinase PS417_22945
acs acetyl-CoA synthetase, AMP-forming PS417_21750 PS417_23925
adh acetaldehyde dehydrogenase (not acylating) PS417_17430 PS417_24810
ald-dh-CoA acetaldehyde dehydrogenase, acylating
andAa anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin--NAD(+) reductase component AndAa PS417_11105 PS417_14730
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 PS417_27400 PS417_27115
ecfA2 energy-coupling factor transporter, ATPase 2 (A2) component PS417_27400 PS417_00945
ecfT energy-coupling factor transporter, transmembrane (T) component
hpaH anthranilate 3-monooxygenase (hydroxylase), FADH2-dependent
mhpD 2-hydroxypentadienoate hydratase PS417_17860
mhpE 4-hydroxy-2-oxovalerate aldolase PS417_17865
nbaC 3-hydroxyanthranilate 3,4-dioxygenase
nbaD 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
nbaE 2-aminomuconate 6-semialdehyde dehydrogenase PS417_17840 PS417_26340
nbaF 2-aminomuconate deaminase PS417_05250 PS417_04240
nbaG 2-oxo-3-hexenedioate decarboxylase PS417_17860
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) PS417_10525
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) PS417_10520
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase PS417_17840 PS417_26340
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase PS417_17860
pta phosphate acetyltransferase PS417_03730
sibC L-kynurenine 3-monooxygenase
TAT tryptophan permease PS417_23700 PS417_05405
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

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