GapMind for catabolism of small carbon sources

 

L-tryptophan catabolism in Paraburkholderia bryophila 376MFSha3.1

Best path

aroP, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, pcaI, pcaJ, 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 (33 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aroP tryptophan:H+ symporter AroP H281DRAFT_04042 H281DRAFT_01668
kynA tryptophan 2,3-dioxygenase H281DRAFT_04144
kynB kynurenine formamidase H281DRAFT_04142
kyn kynureninase H281DRAFT_04143
antA anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA H281DRAFT_01075 H281DRAFT_01653
antB anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB H281DRAFT_01076
antC anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC H281DRAFT_01077 H281DRAFT_04056
catA catechol 1,2-dioxygenase H281DRAFT_01074 H281DRAFT_01643
catB muconate cycloisomerase H281DRAFT_01072 H281DRAFT_01645
catC muconolactone isomerase H281DRAFT_01644 H281DRAFT_01071
pcaD 3-oxoadipate enol-lactone hydrolase H281DRAFT_01594 H281DRAFT_02073
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) H281DRAFT_01597 H281DRAFT_04495
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) H281DRAFT_01596 H281DRAFT_04496
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase H281DRAFT_01504 H281DRAFT_05723
Alternative steps:
ackA acetate kinase H281DRAFT_00303 H281DRAFT_01409
acs acetyl-CoA synthetase, AMP-forming H281DRAFT_04953 H281DRAFT_05523
adh acetaldehyde dehydrogenase (not acylating) H281DRAFT_01117 H281DRAFT_02299
ald-dh-CoA acetaldehyde dehydrogenase, acylating H281DRAFT_01665
andAa anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin--NAD(+) reductase component AndAa H281DRAFT_03846 H281DRAFT_03646
andAb anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin subunit AndAb H281DRAFT_03634
andAc anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AndAc
andAd athranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AndAd
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 H281DRAFT_03194 H281DRAFT_05181
ecfA2 energy-coupling factor transporter, ATPase 2 (A2) component H281DRAFT_04267 H281DRAFT_02573
ecfT energy-coupling factor transporter, transmembrane (T) component
hpaH anthranilate 3-monooxygenase (hydroxylase), FADH2-dependent
mhpD 2-hydroxypentadienoate hydratase H281DRAFT_01663 H281DRAFT_05455
mhpE 4-hydroxy-2-oxovalerate aldolase H281DRAFT_01666 H281DRAFT_03252
nbaC 3-hydroxyanthranilate 3,4-dioxygenase
nbaD 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
nbaE 2-aminomuconate 6-semialdehyde dehydrogenase H281DRAFT_03256 H281DRAFT_02464
nbaF 2-aminomuconate deaminase H281DRAFT_03959 H281DRAFT_06113
nbaG 2-oxo-3-hexenedioate decarboxylase H281DRAFT_01664 H281DRAFT_03253
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase H281DRAFT_03256 H281DRAFT_02464
praC 2-hydroxymuconate tautomerase H281DRAFT_01655 H281DRAFT_05328
praD 2-oxohex-3-enedioate decarboxylase H281DRAFT_01664 H281DRAFT_03253
pta phosphate acetyltransferase H281DRAFT_01410 H281DRAFT_06308
sibC L-kynurenine 3-monooxygenase
TAT tryptophan permease H281DRAFT_04042 H281DRAFT_01668
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 H281DRAFT_00703
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