GapMind for catabolism of small carbon sources


L-arginine catabolism in Pseudomonas fluorescens FW300-N2E3

Best path

artJ, artM, artP, artQ, adiA, aguA, aguB, 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 (55 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 AO353_03055 AO353_11995
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) AO353_03045 AO353_27980
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA AO353_03040 AO353_12000
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) AO353_03050 AO353_27975
adiA arginine decarboxylase (AdiA/SpeA) AO353_13720 AO353_23560
aguA agmatine deiminase AO353_11915 AO353_28745
aguB N-carbamoylputrescine hydrolase AO353_11910 AO353_28740
puuA glutamate-putrescine ligase AO353_08595 AO353_29300
puuB gamma-glutamylputrescine oxidase AO353_20720 AO353_29290
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase AO353_09195 AO353_29295
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase AO353_29305
gabT gamma-aminobutyrate transaminase AO353_08585 AO353_15040
gabD succinate semialdehyde dehydrogenase AO353_11505 AO353_28230
Alternative steps:
AAP3 L-arginine transporter AAP3
arcA arginine deiminase AO353_03470
arcB ornithine carbamoyltransferase AO353_03475 AO353_04155
arcC carbamate kinase AO353_03480
arg-monooxygenase arginine 2-monooxygenase AO353_07420
aroD L-arginine oxidase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) AO353_03020 AO353_27915
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) AO353_03015 AO353_25630
aruH L-arginine:pyruvate transaminase AO353_24850 AO353_26890
aruI 2-ketoarginine decarboxylase AO353_24845 AO353_03865
astA arginine N-succinyltransferase AO353_03015 AO353_25630
astB N-succinylarginine dihydrolase AO353_03005
astC succinylornithine transaminase AO353_03025 AO353_10500
astD succinylglutamate semialdehyde dehydrogenase AO353_03010 AO353_09195
astE succinylglutamate desuccinylase AO353_02995
atoB acetyl-CoA C-acetyltransferase AO353_25685 AO353_27945
bgtB L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) AO353_25590
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC AO353_13340 AO353_17125
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) AO353_13345 AO353_17120
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) AO353_17115 AO353_13350
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) AO353_13355 AO353_17110
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) AO353_13360 AO353_17105
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase AO353_11505 AO353_28230
davT 5-aminovalerate aminotransferase AO353_11510 AO353_28215
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase AO353_25675 AO353_00510
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase AO353_00510 AO353_27535
gbamidase guanidinobutyramidase AO353_07425 AO353_28330
gbuA guanidinobutyrase AO353_18400
gcdG succinyl-CoA:glutarate CoA-transferase AO353_11105 AO353_23060
gcdH glutaryl-CoA dehydrogenase AO353_11100 AO353_20350
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase AO353_09195 AO353_29295
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
ocd ornithine cyclodeaminase AO353_25185
odc L-ornithine decarboxylase AO353_05445 AO353_23560
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) AO353_08585 AO353_15040
patD gamma-aminobutyraldehyde dehydrogenase AO353_04290 AO353_04265
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase AO353_14925 AO353_14880
PRO3 pyrroline-5-carboxylate reductase AO353_08165
puo putrescine oxidase
put1 proline dehydrogenase AO353_12810
putA L-glutamate 5-semialdeyde dehydrogenase AO353_12810 AO353_05300
rocA 1-pyrroline-5-carboxylate dehydrogenase AO353_12810 AO353_05300
rocD ornithine aminotransferase AO353_15640 AO353_28215
rocE L-arginine permease AO353_24825 AO353_05930
rocF arginase AO353_18400
speB agmatinase AO353_18400

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