GapMind for catabolism of small carbon sources

 

L-tryptophan catabolism in Tistlia consotensis USBA 355

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 (26 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
acs acetyl-CoA synthetase, AMP-forming B9O00_RS28395 B9O00_RS29560
adh acetaldehyde dehydrogenase (not acylating) B9O00_RS05420 B9O00_RS20310
ald-dh-CoA acetaldehyde dehydrogenase, acylating
andAa anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin--NAD(+) reductase component AndAa B9O00_RS19310 B9O00_RS20075
andAb anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin subunit AndAb B9O00_RS19310 B9O00_RS00245
andAc anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AndAc B9O00_RS19310
andAd athranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AndAd B9O00_RS19315
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 B9O00_RS26275
catA catechol 1,2-dioxygenase B9O00_RS04340 B9O00_RS08690
catB muconate cycloisomerase
catC muconolactone isomerase
catI 3-oxoadipate CoA-transferase subunit A (CatI)
catJ 3-oxoadipate CoA-transferase subunit B (CatJ) B9O00_RS14025
ecfA1 energy-coupling factor transporter, ATPase 1 (A1) component B9O00_RS13620 B9O00_RS00455
ecfA2 energy-coupling factor transporter, ATPase 2 (A2) component B9O00_RS13620 B9O00_RS18480
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 B9O00_RS07890
mhpD 2-hydroxypentadienoate hydratase B9O00_RS26015 B9O00_RS21380
mhpE 4-hydroxy-2-oxovalerate aldolase B9O00_RS08735 B9O00_RS30415
nbaC 3-hydroxyanthranilate 3,4-dioxygenase
nbaD 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
nbaE 2-aminomuconate 6-semialdehyde dehydrogenase B9O00_RS20310 B9O00_RS15630
nbaF 2-aminomuconate deaminase B9O00_RS22050 B9O00_RS19355
nbaG 2-oxo-3-hexenedioate decarboxylase B9O00_RS21380 B9O00_RS08695
pcaD 3-oxoadipate enol-lactone hydrolase B9O00_RS27950 B9O00_RS11125 with B9O00_RS15590
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase B9O00_RS13575 B9O00_RS06430
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) B9O00_RS13585
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) B9O00_RS13580
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase B9O00_RS20310 B9O00_RS10030
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase B9O00_RS21380 B9O00_RS08695
pta phosphate acetyltransferase B9O00_RS18815 B9O00_RS03595
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 B9O00_RS06940
xylF 2-hydroxymuconate semialdehyde hydrolase B9O00_RS01415 B9O00_RS20695

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