GapMind for catabolism of small carbon sources

 

L-tryptophan catabolism in Pseudomonas benzenivorans DSM 8628

Best path

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

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
kynA tryptophan 2,3-dioxygenase
kynB kynurenine formamidase
kyn kynureninase
antA anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA BLS63_RS16825 BLS63_RS09975
antB anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB BLS63_RS16820
antC anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC BLS63_RS16815 BLS63_RS02485
xylE catechol 2,3-dioxygenase BLS63_RS02475 BLS63_RS10090
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase BLS63_RS10095 BLS63_RS02470
praC 2-hydroxymuconate tautomerase BLS63_RS02440 BLS63_RS10125
praD 2-oxohex-3-enedioate decarboxylase BLS63_RS02445 BLS63_RS10120
mhpD 2-hydroxypentadienoate hydratase BLS63_RS10105 BLS63_RS02460
mhpE 4-hydroxy-2-oxovalerate aldolase BLS63_RS10115 BLS63_RS17015
adh acetaldehyde dehydrogenase (not acylating) BLS63_RS17270 BLS63_RS19270
ackA acetate kinase BLS63_RS09000 BLS63_RS21520
pta phosphate acetyltransferase BLS63_RS21525
Alternative steps:
acs acetyl-CoA synthetase, AMP-forming BLS63_RS26090 BLS63_RS23690
ald-dh-CoA acetaldehyde dehydrogenase, acylating BLS63_RS02455 BLS63_RS17010
andAa anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin--NAD(+) reductase component AndAa BLS63_RS03865 BLS63_RS04540
andAb anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin subunit AndAb BLS63_RS09970
andAc anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AndAc
andAd athranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AndAd
catA catechol 1,2-dioxygenase BLS63_RS16790 BLS63_RS22780
catB muconate cycloisomerase BLS63_RS16800
catC muconolactone isomerase BLS63_RS16795
catI 3-oxoadipate CoA-transferase subunit A (CatI) BLS63_RS16775
catJ 3-oxoadipate CoA-transferase subunit B (CatJ) BLS63_RS16770
ecfA1 energy-coupling factor transporter, ATPase 1 (A1) component BLS63_RS14530 BLS63_RS14875
ecfA2 energy-coupling factor transporter, ATPase 2 (A2) component BLS63_RS11285 BLS63_RS25120
ecfT energy-coupling factor transporter, transmembrane (T) component
hpaH anthranilate 3-monooxygenase (hydroxylase), FADH2-dependent
nbaC 3-hydroxyanthranilate 3,4-dioxygenase
nbaD 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
nbaE 2-aminomuconate 6-semialdehyde dehydrogenase BLS63_RS10095 BLS63_RS02470
nbaF 2-aminomuconate deaminase BLS63_RS22440 BLS63_RS09930
nbaG 2-oxo-3-hexenedioate decarboxylase BLS63_RS02445 BLS63_RS10120
pcaD 3-oxoadipate enol-lactone hydrolase BLS63_RS16755 BLS63_RS15525
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase BLS63_RS16765 BLS63_RS22810
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) BLS63_RS21205 BLS63_RS25510
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) BLS63_RS21195 BLS63_RS25505
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
xylF 2-hydroxymuconate semialdehyde hydrolase BLS63_RS02465 BLS63_RS10100

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 24 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 (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