GapMind for catabolism of small carbon sources

 

L-tryptophan catabolism in Dyella japonica UNC79MFTsu3.2

Best path

aroP, kynA, kynB, sibC, kyn, nbaC, nbaD, nbaE, nbaF, nbaG, mhpD, mhpE, adh, acs

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 (23 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aroP tryptophan:H+ symporter AroP N515DRAFT_3653 N515DRAFT_2630
kynA tryptophan 2,3-dioxygenase N515DRAFT_0357
kynB kynurenine formamidase
sibC L-kynurenine 3-monooxygenase N515DRAFT_2874
kyn kynureninase N515DRAFT_3776
nbaC 3-hydroxyanthranilate 3,4-dioxygenase N515DRAFT_2922
nbaD 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase N515DRAFT_3778
nbaE 2-aminomuconate 6-semialdehyde dehydrogenase N515DRAFT_3729 N515DRAFT_0379
nbaF 2-aminomuconate deaminase N515DRAFT_3727 N515DRAFT_4323
nbaG 2-oxo-3-hexenedioate decarboxylase
mhpD 2-hydroxypentadienoate hydratase
mhpE 4-hydroxy-2-oxovalerate aldolase N515DRAFT_0574
adh acetaldehyde dehydrogenase (not acylating) N515DRAFT_0465 N515DRAFT_3729
acs acetyl-CoA synthetase, AMP-forming N515DRAFT_3075 N515DRAFT_0016
Alternative steps:
ackA acetate kinase N515DRAFT_2456
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
antA anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA
antB anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB
antC anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC N515DRAFT_3403
catA catechol 1,2-dioxygenase
catB muconate cycloisomerase N515DRAFT_2119
catC muconolactone isomerase
catI 3-oxoadipate CoA-transferase subunit A (CatI)
catJ 3-oxoadipate CoA-transferase subunit B (CatJ)
ecfA1 energy-coupling factor transporter, ATPase 1 (A1) component N515DRAFT_1085 N515DRAFT_1562
ecfA2 energy-coupling factor transporter, ATPase 2 (A2) component N515DRAFT_1562 N515DRAFT_1085
ecfT energy-coupling factor transporter, transmembrane (T) component
hpaH anthranilate 3-monooxygenase (hydroxylase), FADH2-dependent
pcaD 3-oxoadipate enol-lactone hydrolase N515DRAFT_2628
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase N515DRAFT_2688 N515DRAFT_0938
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) N515DRAFT_1736
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) N515DRAFT_1736
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase N515DRAFT_3729 N515DRAFT_0379
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase
pta phosphate acetyltransferase N515DRAFT_2182
TAT tryptophan permease N515DRAFT_2630 N515DRAFT_3653
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, 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