GapMind for catabolism of small carbon sources

 

L-tryptophan catabolism in Marinobacter guineae M3B

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 (23 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aroP tryptophan:H+ symporter AroP
tnaA tryptophanase
Alternative steps:
ackA acetate kinase CLH62_RS14355 CLH62_RS18460
acs acetyl-CoA synthetase, AMP-forming CLH62_RS16445 CLH62_RS02220
adh acetaldehyde dehydrogenase (not acylating) CLH62_RS14090 CLH62_RS07755
ald-dh-CoA acetaldehyde dehydrogenase, acylating CLH62_RS09585 CLH62_RS09690
andAa anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin--NAD(+) reductase component AndAa CLH62_RS13155 CLH62_RS10500
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 CLH62_RS09615 CLH62_RS09720
catA catechol 1,2-dioxygenase
catB muconate cycloisomerase
catC muconolactone isomerase
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 CLH62_RS09455 CLH62_RS06600
ecfA2 energy-coupling factor transporter, ATPase 2 (A2) component CLH62_RS02935 CLH62_RS07710
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
mhpD 2-hydroxypentadienoate hydratase CLH62_RS09590 CLH62_RS09705
mhpE 4-hydroxy-2-oxovalerate aldolase CLH62_RS09580 CLH62_RS09685
nbaC 3-hydroxyanthranilate 3,4-dioxygenase
nbaD 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
nbaE 2-aminomuconate 6-semialdehyde dehydrogenase CLH62_RS09600 CLH62_RS09710
nbaF 2-aminomuconate deaminase CLH62_RS05595
nbaG 2-oxo-3-hexenedioate decarboxylase CLH62_RS09575 CLH62_RS09700
pcaD 3-oxoadipate enol-lactone hydrolase
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase CLH62_RS05480 CLH62_RS07455
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) CLH62_RS11885 CLH62_RS15680
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) CLH62_RS15675 CLH62_RS11890
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase CLH62_RS09600 CLH62_RS09710
praC 2-hydroxymuconate tautomerase CLH62_RS09570 CLH62_RS09695
praD 2-oxohex-3-enedioate decarboxylase CLH62_RS09575 CLH62_RS09700
pta phosphate acetyltransferase CLH62_RS18455
sibC L-kynurenine 3-monooxygenase
TAT tryptophan permease
tnaB tryptophan:H+ symporter TnaB
tnaT tryptophan:Na+ symporter TnaT CLH62_RS16195
trpP energy-coupling factor transporter, tryptophan-specific (S) component TrpP
xylE catechol 2,3-dioxygenase CLH62_RS09715 CLH62_RS09605
xylF 2-hydroxymuconate semialdehyde hydrolase CLH62_RS09595

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