GapMind for catabolism of small carbon sources

 

L-tryptophan catabolism in Alicycliphilus denitrificans K601

Best path

aroP, tnaA

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 ALIDE2_RS12155
tnaA tryptophanase ALIDE2_RS06575
Alternative steps:
ackA acetate kinase ALIDE2_RS13490 ALIDE2_RS21910
acs acetyl-CoA synthetase, AMP-forming ALIDE2_RS18585 ALIDE2_RS17850
adh acetaldehyde dehydrogenase (not acylating) ALIDE2_RS18640 ALIDE2_RS22625
ald-dh-CoA acetaldehyde dehydrogenase, acylating ALIDE2_RS01400
andAa anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin--NAD(+) reductase component AndAa ALIDE2_RS12885
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 ALIDE2_RS19345 ALIDE2_RS01360
catA catechol 1,2-dioxygenase
catB muconate cycloisomerase
catC muconolactone isomerase ALIDE2_RS18195
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 ALIDE2_RS13130 ALIDE2_RS18590
ecfA2 energy-coupling factor transporter, ATPase 2 (A2) component ALIDE2_RS13080 ALIDE2_RS01630
ecfT energy-coupling factor transporter, transmembrane (T) component
hpaH anthranilate 3-monooxygenase (hydroxylase), FADH2-dependent
kyn kynureninase
kynA tryptophan 2,3-dioxygenase
kynB kynurenine formamidase ALIDE2_RS17595
mhpD 2-hydroxypentadienoate hydratase ALIDE2_RS01395 ALIDE2_RS01410
mhpE 4-hydroxy-2-oxovalerate aldolase ALIDE2_RS02575 ALIDE2_RS08535
nbaC 3-hydroxyanthranilate 3,4-dioxygenase
nbaD 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
nbaE 2-aminomuconate 6-semialdehyde dehydrogenase ALIDE2_RS01385 ALIDE2_RS07670
nbaF 2-aminomuconate deaminase ALIDE2_RS17215 ALIDE2_RS01195
nbaG 2-oxo-3-hexenedioate decarboxylase ALIDE2_RS01410 ALIDE2_RS01395
pcaD 3-oxoadipate enol-lactone hydrolase ALIDE2_RS01390
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase ALIDE2_RS19480 ALIDE2_RS21130
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) ALIDE2_RS19470 ALIDE2_RS18185
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) ALIDE2_RS19475 ALIDE2_RS18190
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase ALIDE2_RS01385 ALIDE2_RS07695
praC 2-hydroxymuconate tautomerase ALIDE2_RS01420 ALIDE2_RS22035
praD 2-oxohex-3-enedioate decarboxylase ALIDE2_RS01410 ALIDE2_RS01395
pta phosphate acetyltransferase ALIDE2_RS21905 ALIDE2_RS23320
sibC L-kynurenine 3-monooxygenase
TAT tryptophan permease
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 ALIDE2_RS01370 ALIDE2_RS21205
xylF 2-hydroxymuconate semialdehyde hydrolase ALIDE2_RS01390 ALIDE2_RS00495

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 Apr 09 2024. 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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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:

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