GapMind for catabolism of small carbon sources

 

L-tryptophan catabolism in Pseudomonas fluorescens FW300-N1B4

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 Pf1N1B4_3559 Pf1N1B4_801
kynA tryptophan 2,3-dioxygenase
kynB kynurenine formamidase
kyn kynureninase
antA anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA Pf1N1B4_5800
antB anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB Pf1N1B4_5799
antC anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC Pf1N1B4_5798
catA catechol 1,2-dioxygenase Pf1N1B4_5803
catB muconate cycloisomerase Pf1N1B4_5805
catC muconolactone isomerase Pf1N1B4_5804
pcaD 3-oxoadipate enol-lactone hydrolase Pf1N1B4_3238 Pf1N1B4_549
catI 3-oxoadipate CoA-transferase subunit A (CatI) Pf1N1B4_3232
catJ 3-oxoadipate CoA-transferase subunit B (CatJ) Pf1N1B4_3233
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase Pf1N1B4_3234 Pf1N1B4_5835
Alternative steps:
ackA acetate kinase Pf1N1B4_879
acs acetyl-CoA synthetase, AMP-forming Pf1N1B4_3430 Pf1N1B4_2849
adh acetaldehyde dehydrogenase (not acylating) Pf1N1B4_4502 Pf1N1B4_2673
ald-dh-CoA acetaldehyde dehydrogenase, acylating
andAa anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin--NAD(+) reductase component AndAa Pf1N1B4_4393 Pf1N1B4_5042
andAb anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin subunit AndAb Pf1N1B4_5586
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 Pf1N1B4_4352 Pf1N1B4_2210
ecfA2 energy-coupling factor transporter, ATPase 2 (A2) component Pf1N1B4_2210 Pf1N1B4_3175
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 Pf1N1B4_5694
nbaC 3-hydroxyanthranilate 3,4-dioxygenase
nbaD 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
nbaE 2-aminomuconate 6-semialdehyde dehydrogenase Pf1N1B4_2417 Pf1N1B4_171
nbaF 2-aminomuconate deaminase Pf1N1B4_1101
nbaG 2-oxo-3-hexenedioate decarboxylase
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) Pf1N1B4_5833
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) Pf1N1B4_5834
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase Pf1N1B4_2417 Pf1N1B4_4355
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase
pta phosphate acetyltransferase Pf1N1B4_1055
sibC L-kynurenine 3-monooxygenase
TAT tryptophan permease Pf1N1B4_1639 Pf1N1B4_801
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 Pf1N1B4_4192

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