GapMind for catabolism of small carbon sources


L-arginine catabolism in Pseudomonas putida KT2440

Best path

artJ, artM, artP, artQ, adiA, speB, puuA, puuB, puuC, puuD, gabT, gabD

Also see fitness data for the top candidates


Overview: Arginine utilization in GapMind is based on MetaCyc pathways L-arginine degradation I via arginase (link); II via arginine succinyltransferase (link), III via arginine decarboxylase and agmatinase (link), IV via arginine decarboxylase and agmatine deiminase (link), V via arginine deiminase (link), VI (arginase 2, link), VII (arginase 3, link), VIII via arginase oxidase (link), IX via arginine:pyruvate transaminase (link), X via arginine monooxygenase (link), XIII via proline (link), and XIV via D-ornithine (link). Common intermediates are L-ornithine or L-proline. GapMind does not include pathways XI (link), which is poorly understood, or XII (link), which is not reported in prokaryotes.

71 steps (56 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
artJ L-arginine ABC transporter, periplasmic substrate-binding component ArtJ/HisJ/ArtI/AotJ/ArgT PP_4486 PP_0282
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) PP_4484 PP_0280
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA PP_4483 PP_0283
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) PP_4485 PP_0281
adiA arginine decarboxylase (AdiA/SpeA) PP_0567 PP_4140
speB agmatinase PP_2196 PP_4523
puuA glutamate-putrescine ligase PP_5184 PP_5299
puuB gamma-glutamylputrescine oxidase PP_2448 PP_3146
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PP_5278 PP_2589
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase PP_3598 PP_2179
gabT gamma-aminobutyrate transaminase PP_5182 PP_2180
gabD succinate semialdehyde dehydrogenase PP_0213 PP_3151
Alternative steps:
AAP3 L-arginine transporter AAP3
aguA agmatine deiminase PP_0266
aguB N-carbamoylputrescine hydrolase PP_0382
arcA arginine deiminase PP_1001
arcB ornithine carbamoyltransferase PP_1000 PP_1079
arcC carbamate kinase PP_0999
arg-monooxygenase arginine 2-monooxygenase PP_0383
aroD L-arginine oxidase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) PP_4480 PP_4479
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) PP_4479 PP_4480
aruH L-arginine:pyruvate transaminase PP_3721 PP_0858
aruI 2-ketoarginine decarboxylase PP_3723 PP_1394
astA arginine N-succinyltransferase PP_4480 PP_4479
astB N-succinylarginine dihydrolase PP_4477
astC succinylornithine transaminase PP_4481 PP_0372
astD succinylglutamate semialdehyde dehydrogenase PP_4478 PP_5278
astE succinylglutamate desuccinylase PP_4475
atoB acetyl-CoA C-acetyltransferase PP_2215 PP_4636
bgtB L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC PP_4867 PP_1141
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) PP_1140 PP_4866
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) PP_1139 PP_4865
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) PP_4864 PP_1138
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) PP_4863 PP_1137
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase PP_0213 PP_4422
davT 5-aminovalerate aminotransferase PP_0214 PP_4108
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase PP_2217 PP_3284
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase PP_2136 PP_3755
gbamidase guanidinobutyramidase PP_0382 PP_3846
gbuA guanidinobutyrase PP_4523 PP_2196
gcdG succinyl-CoA:glutarate CoA-transferase PP_0159 PP_3001
gcdH glutaryl-CoA dehydrogenase PP_0158 PP_4064
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD) PP_2909
kauB 4-guanidinobutyraldehyde dehydrogenase PP_5278 PP_2589
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) PP_2910
ocd ornithine cyclodeaminase PP_3533 PP_4431
odc L-ornithine decarboxylase PP_0864 PP_4140
oraE D-ornithine 4,5-aminomutase, beta (E) subunit
oraS D-ornithine 4,5-aminomutase, alpha (S) subunit
ord 2,4-diaminopentanoate dehydrogenase
orr ornithine racemase
ortA 2-amino-4-oxopentanoate thiolase, alpha subunit
ortB 2-amino-4-oxopentanoate thiolase, beta subunit
patA putrescine aminotransferase (PatA/SpuC) PP_5182 PP_2180
patD gamma-aminobutyraldehyde dehydrogenase PP_1481 PP_2801
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase PP_1258
PRO3 pyrroline-5-carboxylate reductase PP_5095 PP_3778
puo putrescine oxidase
put1 proline dehydrogenase PP_4947
putA L-glutamate 5-semialdeyde dehydrogenase PP_4947 PP_2694
rocA 1-pyrroline-5-carboxylate dehydrogenase PP_4947 PP_2694
rocD ornithine aminotransferase PP_0214 PP_4223
rocE L-arginine permease PP_3727 PP_0660
rocF arginase PP_4523 PP_2196

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 17 2021. The underlying query database was built on Sep 17 2021.



Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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