GapMind for catabolism of small carbon sources

 

L-tryptophan catabolism in Pseudomonas stutzeri RCH2

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 (25 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aroP tryptophan:H+ symporter AroP Psest_1697
kynA tryptophan 2,3-dioxygenase
kynB kynurenine formamidase
kyn kynureninase
antA anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA Psest_2699
antB anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB Psest_2698
antC anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC Psest_2697 Psest_1174
catA catechol 1,2-dioxygenase Psest_2692
catB muconate cycloisomerase Psest_2694
catC muconolactone isomerase Psest_2693
pcaD 3-oxoadipate enol-lactone hydrolase Psest_3069
catI 3-oxoadipate CoA-transferase subunit A (CatI) Psest_3072
catJ 3-oxoadipate CoA-transferase subunit B (CatJ) Psest_3071
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase Psest_3070 Psest_1076
Alternative steps:
ackA acetate kinase Psest_3137 Psest_3213
acs acetyl-CoA synthetase, AMP-forming Psest_2657 Psest_2220
adh acetaldehyde dehydrogenase (not acylating) Psest_2276 Psest_0671
ald-dh-CoA acetaldehyde dehydrogenase, acylating
andAa anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin--NAD(+) reductase component AndAa Psest_2406 Psest_3834
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 Psest_4282 Psest_4314
ecfA2 energy-coupling factor transporter, ATPase 2 (A2) component Psest_4282 Psest_4063
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 Psest_1056
nbaC 3-hydroxyanthranilate 3,4-dioxygenase
nbaD 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
nbaE 2-aminomuconate 6-semialdehyde dehydrogenase Psest_0905 Psest_2276
nbaF 2-aminomuconate deaminase Psest_3329
nbaG 2-oxo-3-hexenedioate decarboxylase
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) Psest_1078
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) Psest_1077
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase Psest_0905 Psest_2634
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase
pta phosphate acetyltransferase Psest_3214
sibC L-kynurenine 3-monooxygenase
TAT tryptophan permease Psest_1697
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 (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