GapMind for catabolism of small carbon sources


L-arginine catabolism in Shewanella loihica PV-4

Best path

rocE, 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 (43 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rocE L-arginine permease
adiA arginine decarboxylase (AdiA/SpeA) Shew_1619
speB agmatinase Shew_1621
puuA glutamate-putrescine ligase Shew_0972 Shew_3554
puuB gamma-glutamylputrescine oxidase Shew_0977 Shew_0969
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase Shew_0967 Shew_3574
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase Shew_0971 Shew_2532
gabT gamma-aminobutyrate transaminase Shew_3172 Shew_0966
gabD succinate semialdehyde dehydrogenase Shew_3173 Shew_0967
Alternative steps:
AAP3 L-arginine transporter AAP3
aguA agmatine deiminase
aguB N-carbamoylputrescine hydrolase
arcA arginine deiminase
arcB ornithine carbamoyltransferase Shew_0204 Shew_1013
arcC carbamate kinase
arg-monooxygenase arginine 2-monooxygenase
aroD L-arginine oxidase
artJ L-arginine ABC transporter, periplasmic substrate-binding component ArtJ/HisJ/ArtI/AotJ/ArgT Shew_3166
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) Shew_3165
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA Shew_3164 Shew_0974
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) Shew_3165
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) Shew_0579
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) Shew_0579
aruH L-arginine:pyruvate transaminase
aruI 2-ketoarginine decarboxylase Shew_0289
astA arginine N-succinyltransferase Shew_0579
astB N-succinylarginine dihydrolase Shew_2225
astC succinylornithine transaminase Shew_0578 Shew_1718
astD succinylglutamate semialdehyde dehydrogenase Shew_0580 Shew_0967
astE succinylglutamate desuccinylase Shew_1924
atoB acetyl-CoA C-acetyltransferase Shew_1667 Shew_0018
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
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD)
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) Shew_2608
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) Shew_2611 Shew_1615
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) Shew_2606 Shew_3310
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase Shew_3173 Shew_0967
davT 5-aminovalerate aminotransferase Shew_3172 Shew_0578
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Shew_1670 Shew_0019
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Shew_0019 Shew_2425
gbamidase guanidinobutyramidase
gbuA guanidinobutyrase Shew_1621
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase Shew_0900 Shew_2570
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase Shew_0967 Shew_3574
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) Shew_0530
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase Shew_3392
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) Shew_0966 Shew_3172
patD gamma-aminobutyraldehyde dehydrogenase Shew_0967 Shew_3574
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase Shew_2363 Shew_2361
PRO3 pyrroline-5-carboxylate reductase Shew_1136 Shew_3016
puo putrescine oxidase
put1 proline dehydrogenase Shew_0615
putA L-glutamate 5-semialdeyde dehydrogenase Shew_0615 Shew_3574
rocA 1-pyrroline-5-carboxylate dehydrogenase Shew_0615 Shew_3574
rocD ornithine aminotransferase Shew_3172 Shew_1012
rocF arginase Shew_1621

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