GapMind for catabolism of small carbon sources

 

L-tryptophan catabolism in Novosphingobium aromaticivorans DSM 12444

Best path

aroP, kynA, kynB, kyn, andAa, andAb, andAc, andAd, xylE, xylF, mhpD, mhpE, adh, acs

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 (33 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 SARO_RS13615
kyn kynureninase
andAa anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin--NAD(+) reductase component AndAa SARO_RS16995 SARO_RS01080
andAb anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin subunit AndAb
andAc anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AndAc SARO_RS17145 SARO_RS17110
andAd athranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AndAd SARO_RS17105 SARO_RS17140
xylE catechol 2,3-dioxygenase SARO_RS17090 SARO_RS17130
xylF 2-hydroxymuconate semialdehyde hydrolase SARO_RS17095 SARO_RS17225
mhpD 2-hydroxypentadienoate hydratase SARO_RS17075 SARO_RS19315
mhpE 4-hydroxy-2-oxovalerate aldolase SARO_RS19305 SARO_RS17065
adh acetaldehyde dehydrogenase (not acylating) SARO_RS17045 SARO_RS05980
acs acetyl-CoA synthetase, AMP-forming SARO_RS13240 SARO_RS13225
Alternative steps:
ackA acetate kinase
ald-dh-CoA acetaldehyde dehydrogenase, acylating SARO_RS19310 SARO_RS17070
antA anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA SARO_RS17125 SARO_RS02680
antB anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB SARO_RS17120 SARO_RS02685
antC anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC SARO_RS17035
catA catechol 1,2-dioxygenase SARO_RS20025
catB muconate cycloisomerase SARO_RS20015
catC muconolactone isomerase SARO_RS20020
catI 3-oxoadipate CoA-transferase subunit A (CatI) SARO_RS19630
catJ 3-oxoadipate CoA-transferase subunit B (CatJ) SARO_RS19635
ecfA1 energy-coupling factor transporter, ATPase 1 (A1) component SARO_RS13360 SARO_RS02055
ecfA2 energy-coupling factor transporter, ATPase 2 (A2) component SARO_RS11475 SARO_RS14425
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 SARO_RS17080 SARO_RS17045
nbaF 2-aminomuconate deaminase SARO_RS03015 SARO_RS19950
nbaG 2-oxo-3-hexenedioate decarboxylase SARO_RS17060 SARO_RS17230
pcaD 3-oxoadipate enol-lactone hydrolase SARO_RS20005
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase SARO_RS20000 SARO_RS04040
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) SARO_RS19990 SARO_RS02835
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) SARO_RS19995 SARO_RS02825
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase SARO_RS17080 SARO_RS19930
praC 2-hydroxymuconate tautomerase SARO_RS17055
praD 2-oxohex-3-enedioate decarboxylase SARO_RS17060 SARO_RS17230
pta phosphate acetyltransferase SARO_RS16710
sibC L-kynurenine 3-monooxygenase SARO_RS18015
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

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