GapMind for catabolism of small carbon sources

 

L-tryptophan catabolism in Herbaspirillum seropedicae SmR1

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 (27 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aroP tryptophan:H+ symporter AroP
kynA tryptophan 2,3-dioxygenase
kynB kynurenine formamidase HSERO_RS05590 HSERO_RS18245
kyn kynureninase
antA anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA HSERO_RS06550 HSERO_RS06720
antB anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB HSERO_RS06555
antC anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC HSERO_RS06560 HSERO_RS18275
catA catechol 1,2-dioxygenase HSERO_RS06545 HSERO_RS18295
catB muconate cycloisomerase HSERO_RS06540 HSERO_RS18290
catC muconolactone isomerase HSERO_RS06530
pcaD 3-oxoadipate enol-lactone hydrolase HSERO_RS06525 HSERO_RS19935
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) HSERO_RS20000 HSERO_RS23190
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) HSERO_RS19995 HSERO_RS23185
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase HSERO_RS19990 HSERO_RS20660
Alternative steps:
ackA acetate kinase HSERO_RS01305 HSERO_RS11090
acs acetyl-CoA synthetase, AMP-forming HSERO_RS07770 HSERO_RS23535
adh acetaldehyde dehydrogenase (not acylating) HSERO_RS05115 HSERO_RS09465
ald-dh-CoA acetaldehyde dehydrogenase, acylating
andAa anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin--NAD(+) reductase component AndAa HSERO_RS14545
andAb anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin subunit AndAb HSERO_RS18275
andAc anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AndAc HSERO_RS18285 HSERO_RS06720
andAd athranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AndAd HSERO_RS18280
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 HSERO_RS11630 HSERO_RS19345
ecfA2 energy-coupling factor transporter, ATPase 2 (A2) component HSERO_RS19345 HSERO_RS11450
ecfT energy-coupling factor transporter, transmembrane (T) component
hpaH anthranilate 3-monooxygenase (hydroxylase), FADH2-dependent
mhpD 2-hydroxypentadienoate hydratase HSERO_RS16775 HSERO_RS13395
mhpE 4-hydroxy-2-oxovalerate aldolase HSERO_RS01600 HSERO_RS14210
nbaC 3-hydroxyanthranilate 3,4-dioxygenase
nbaD 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
nbaE 2-aminomuconate 6-semialdehyde dehydrogenase HSERO_RS19755 HSERO_RS09465
nbaF 2-aminomuconate deaminase HSERO_RS09160 HSERO_RS02850
nbaG 2-oxo-3-hexenedioate decarboxylase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase HSERO_RS09465 HSERO_RS19755
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase
pta phosphate acetyltransferase HSERO_RS12030 HSERO_RS01300
sibC L-kynurenine 3-monooxygenase
TAT tryptophan permease
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 HSERO_RS08570

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