GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Shewanella sp. ANA-3

Best path

rocE, adiA, aguA, aguB, puuA, puuB, puuC, puuD, gabT, gabD

Also see fitness data for the top candidates

Rules

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 (39 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rocE L-arginine permease
adiA arginine decarboxylase (AdiA/SpeA) Shewana3_1624 Shewana3_3871
aguA agmatine deiminase Shewana3_3465
aguB N-carbamoylputrescine hydrolase
puuA glutamate-putrescine ligase Shewana3_3098 Shewana3_0300
puuB gamma-glutamylputrescine oxidase Shewana3_3093 Shewana3_3101
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase Shewana3_3105 Shewana3_0250
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase Shewana3_3099
gabT gamma-aminobutyrate transaminase Shewana3_3091 Shewana3_3106
gabD succinate semialdehyde dehydrogenase Shewana3_3092 Shewana3_3105
Alternative steps:
AAP3 L-arginine transporter AAP3
arcA arginine deiminase
arcB ornithine carbamoyltransferase Shewana3_3903 Shewana3_3070
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 Shewana3_0882
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) Shewana3_0881
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA Shewana3_0880 Shewana3_3192
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) Shewana3_0881
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) Shewana3_0611
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) Shewana3_0611
aruH L-arginine:pyruvate transaminase
aruI 2-ketoarginine decarboxylase Shewana3_0356
astA arginine N-succinyltransferase Shewana3_0611
astB N-succinylarginine dihydrolase Shewana3_1728
astC succinylornithine transaminase Shewana3_0610 Shewana3_3091
astD succinylglutamate semialdehyde dehydrogenase Shewana3_0612 Shewana3_0250
astE succinylglutamate desuccinylase Shewana3_2132
atoB acetyl-CoA C-acetyltransferase Shewana3_2771 Shewana3_0023
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)
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) Shewana3_2749
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) Shewana3_0673 Shewana3_3096
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase Shewana3_3092 Shewana3_3105
davT 5-aminovalerate aminotransferase Shewana3_3091 Shewana3_0610
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Shewana3_2768 Shewana3_0024
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Shewana3_0024 Shewana3_1461
gbamidase guanidinobutyramidase Shewana3_3642
gbuA guanidinobutyrase
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase Shewana3_1672 Shewana3_2769
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase Shewana3_3105 Shewana3_0250
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase Shewana3_3871 Shewana3_3682
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) Shewana3_3106 Shewana3_0610
patD gamma-aminobutyraldehyde dehydrogenase Shewana3_3105 Shewana3_0250
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase
PRO3 pyrroline-5-carboxylate reductase Shewana3_1193
puo putrescine oxidase
put1 proline dehydrogenase Shewana3_0819
putA L-glutamate 5-semialdeyde dehydrogenase Shewana3_0819 Shewana3_0250
rocA 1-pyrroline-5-carboxylate dehydrogenase Shewana3_0819 Shewana3_0250
rocD ornithine aminotransferase Shewana3_3091 Shewana3_2520
rocF arginase
speB agmatinase

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.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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