GapMind for catabolism of small carbon sources

 

L-tryptophan catabolism in Cupriavidus basilensis 4G11

Best path

aroP, kynA, kynB, kyn, antA, antB, antC, xylE, praB, praC, praD, mhpD, mhpE, adh, ackA, pta

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 (39 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aroP tryptophan:H+ symporter AroP RR42_RS33495 RR42_RS05070
kynA tryptophan 2,3-dioxygenase RR42_RS15390
kynB kynurenine formamidase RR42_RS15380 RR42_RS16840
kyn kynureninase RR42_RS15385
antA anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA RR42_RS23500
antB anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB RR42_RS23495
antC anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC RR42_RS23490 RR42_RS32665
xylE catechol 2,3-dioxygenase RR42_RS32655 RR42_RS34600
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase RR42_RS05110 RR42_RS32650
praC 2-hydroxymuconate tautomerase RR42_RS32635 RR42_RS15120
praD 2-oxohex-3-enedioate decarboxylase RR42_RS32640 RR42_RS32645
mhpD 2-hydroxypentadienoate hydratase RR42_RS27885 RR42_RS32645
mhpE 4-hydroxy-2-oxovalerate aldolase RR42_RS27900 RR42_RS32625
adh acetaldehyde dehydrogenase (not acylating) RR42_RS34255 RR42_RS25005
ackA acetate kinase RR42_RS03800 RR42_RS22745
pta phosphate acetyltransferase RR42_RS33690 RR42_RS03805
Alternative steps:
acs acetyl-CoA synthetase, AMP-forming RR42_RS13880 RR42_RS10650
ald-dh-CoA acetaldehyde dehydrogenase, acylating RR42_RS27895 RR42_RS32630
andAa anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin--NAD(+) reductase component AndAa RR42_RS26430 RR42_RS29850
andAb anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin subunit AndAb RR42_RS26435 RR42_RS33940
andAc anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AndAc RR42_RS26425 RR42_RS33930
andAd athranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AndAd RR42_RS33935 RR42_RS26420
catA catechol 1,2-dioxygenase RR42_RS23505 RR42_RS32880
catB muconate cycloisomerase RR42_RS21835
catC muconolactone isomerase RR42_RS21840 RR42_RS10025
catI 3-oxoadipate CoA-transferase subunit A (CatI)
catJ 3-oxoadipate CoA-transferase subunit B (CatJ) RR42_RS31950
ecfA1 energy-coupling factor transporter, ATPase 1 (A1) component RR42_RS27115 RR42_RS09480
ecfA2 energy-coupling factor transporter, ATPase 2 (A2) component RR42_RS16445 RR42_RS30240
ecfT energy-coupling factor transporter, transmembrane (T) component
hpaH anthranilate 3-monooxygenase (hydroxylase), FADH2-dependent
nbaC 3-hydroxyanthranilate 3,4-dioxygenase RR42_RS05080
nbaD 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase RR42_RS05075
nbaE 2-aminomuconate 6-semialdehyde dehydrogenase RR42_RS05110 RR42_RS32650
nbaF 2-aminomuconate deaminase RR42_RS05085 RR42_RS07975
nbaG 2-oxo-3-hexenedioate decarboxylase RR42_RS32640 RR42_RS32645
pcaD 3-oxoadipate enol-lactone hydrolase RR42_RS21850 RR42_RS32050
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase RR42_RS35915 RR42_RS26090
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) RR42_RS35925 RR42_RS10005
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) RR42_RS35920 RR42_RS10010
sibC L-kynurenine 3-monooxygenase
TAT tryptophan permease RR42_RS11100 RR42_RS05070
tnaA tryptophanase
tnaB tryptophan:H+ symporter TnaB
tnaT tryptophan:Na+ symporter TnaT
trpP energy-coupling factor transporter, tryptophan-specific (S) component TrpP
xylF 2-hydroxymuconate semialdehyde hydrolase RR42_RS27870 RR42_RS31825

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