GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Shewanella oneidensis MR-1

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 (37 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rocE L-arginine permease
adiA arginine decarboxylase (AdiA/SpeA) SO1870
aguA agmatine deiminase SO_0887
aguB N-carbamoylputrescine hydrolase
puuA glutamate-putrescine ligase SO1268 SO4410
puuB gamma-glutamylputrescine oxidase SO1274 SO1264
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase SO3496 SO4480
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase SO1267
gabT gamma-aminobutyrate transaminase SO1276 SO3497
gabD succinate semialdehyde dehydrogenase SO1275 SO3496
Alternative steps:
AAP3 L-arginine transporter AAP3
arcA arginine deiminase
arcB ornithine carbamoyltransferase SO0277 SO1301
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 SO1044
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) SO1043
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA SO1042 SO4655
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) SO1043
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) SO0618
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) SO0618
aruH L-arginine:pyruvate transaminase
aruI 2-ketoarginine decarboxylase SO4347
astA arginine N-succinyltransferase SO0618
astB N-succinylarginine dihydrolase SO2706
astC succinylornithine transaminase SO0617 SO2741
astD succinylglutamate semialdehyde dehydrogenase SO0619 SO3496
astE succinylglutamate desuccinylase SO2338
atoB acetyl-CoA C-acetyltransferase SO1677 SO0020
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)
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) SO3960 SO1271
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase SO1275 SO3496
davT 5-aminovalerate aminotransferase SO1276 SO0617
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase SO3088 SO1680
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase SO0021 SO3088
gbamidase guanidinobutyramidase
gbuA guanidinobutyrase
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase SO1897 SO1679
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase SO3496 SO4480
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase SO0314 SO4136
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) SO3497 SO0617
patD gamma-aminobutyraldehyde dehydrogenase SO3496 SO4480
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 SO3354
puo putrescine oxidase
put1 proline dehydrogenase SO3774
putA L-glutamate 5-semialdeyde dehydrogenase SO3774 SO4480
rocA 1-pyrroline-5-carboxylate dehydrogenase SO3774 SO4480
rocD ornithine aminotransferase SO1276 SO0617
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