GapMind for catabolism of small carbon sources

 

L-tryptophan catabolism in Klebsiella michiganensis M5al

Best path

aroP, tnaA

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 (31 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aroP tryptophan:H+ symporter AroP BWI76_RS04870 BWI76_RS07360
tnaA tryptophanase BWI76_RS03535
Alternative steps:
ackA acetate kinase BWI76_RS20235 BWI76_RS23200
acs acetyl-CoA synthetase, AMP-forming BWI76_RS02095 BWI76_RS17800
adh acetaldehyde dehydrogenase (not acylating) BWI76_RS21985 BWI76_RS15205
ald-dh-CoA acetaldehyde dehydrogenase, acylating BWI76_RS17250 BWI76_RS20790
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 BWI76_RS13705
andAd athranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AndAd
antA anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA BWI76_RS13705
antB anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB BWI76_RS13710
antC anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC BWI76_RS13715
catA catechol 1,2-dioxygenase BWI76_RS13700
catB muconate cycloisomerase BWI76_RS13690
catC muconolactone isomerase BWI76_RS13695
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 BWI76_RS22065 BWI76_RS23015
ecfA2 energy-coupling factor transporter, ATPase 2 (A2) component BWI76_RS08965 BWI76_RS18350
ecfT energy-coupling factor transporter, transmembrane (T) component
hpaH anthranilate 3-monooxygenase (hydroxylase), FADH2-dependent BWI76_RS03830 BWI76_RS15105
kyn kynureninase
kynA tryptophan 2,3-dioxygenase
kynB kynurenine formamidase
mhpD 2-hydroxypentadienoate hydratase BWI76_RS16910 BWI76_RS03850
mhpE 4-hydroxy-2-oxovalerate aldolase BWI76_RS16900 BWI76_RS19980
nbaC 3-hydroxyanthranilate 3,4-dioxygenase
nbaD 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
nbaE 2-aminomuconate 6-semialdehyde dehydrogenase BWI76_RS03865 BWI76_RS10695
nbaF 2-aminomuconate deaminase BWI76_RS07545 BWI76_RS10770
nbaG 2-oxo-3-hexenedioate decarboxylase BWI76_RS03850 BWI76_RS16910
pcaD 3-oxoadipate enol-lactone hydrolase BWI76_RS16125
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase BWI76_RS13135 BWI76_RS16135
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) BWI76_RS16145
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) BWI76_RS16140
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase BWI76_RS03865 BWI76_RS07615
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase BWI76_RS03850 BWI76_RS16910
pta phosphate acetyltransferase BWI76_RS20240 BWI76_RS20805
sibC L-kynurenine 3-monooxygenase
TAT tryptophan permease BWI76_RS19685 BWI76_RS06025
tnaB tryptophan:H+ symporter TnaB BWI76_RS25050 BWI76_RS03530
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 BWI76_RS16915

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