GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Shewanella amazonensis SB2B

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) Sama_1963 Sama_3334
aguA agmatine deiminase Sama_2521
aguB N-carbamoylputrescine hydrolase
puuA glutamate-putrescine ligase Sama_2644 Sama_1174
puuB gamma-glutamylputrescine oxidase Sama_2638 Sama_2647
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase Sama_2648 Sama_3435
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase Sama_0794 Sama_2645
gabT gamma-aminobutyrate transaminase Sama_2643 Sama_2636
gabD succinate semialdehyde dehydrogenase Sama_2637 Sama_2648
Alternative steps:
AAP3 L-arginine transporter AAP3
arcA arginine deiminase
arcB ornithine carbamoyltransferase Sama_0258 Sama_0840
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
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM)
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA Sama_1468 Sama_2641
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ)
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) Sama_3010 Sama_1627
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) Sama_3010 Sama_1627
aruH L-arginine:pyruvate transaminase
aruI 2-ketoarginine decarboxylase Sama_3281 Sama_2018
astA arginine N-succinyltransferase Sama_3010 Sama_1627
astB N-succinylarginine dihydrolase Sama_1321
astC succinylornithine transaminase Sama_1628 Sama_3011
astD succinylglutamate semialdehyde dehydrogenase Sama_3009 Sama_1626
astE succinylglutamate desuccinylase Sama_1708
atoB acetyl-CoA C-acetyltransferase Sama_1375 Sama_0031
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) Sama_3087 Sama_2641
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase Sama_2637 Sama_2648
davT 5-aminovalerate aminotransferase Sama_2636 Sama_1628
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Sama_1378 Sama_0032
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Sama_0032 Sama_2167
gbamidase guanidinobutyramidase Sama_0473
gbuA guanidinobutyrase
gcdG succinyl-CoA:glutarate CoA-transferase Sama_3300
gcdH glutaryl-CoA dehydrogenase Sama_2796 Sama_1362
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase Sama_2648 Sama_3435
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase Sama_3334 Sama_0410
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) Sama_2643 Sama_2649
patD gamma-aminobutyraldehyde dehydrogenase Sama_2648 Sama_3435
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase Sama_1530 Sama_1532
PRO3 pyrroline-5-carboxylate reductase Sama_2478
puo putrescine oxidase
put1 proline dehydrogenase Sama_2676
putA L-glutamate 5-semialdeyde dehydrogenase Sama_2676 Sama_2637
rocA 1-pyrroline-5-carboxylate dehydrogenase Sama_2676 Sama_2637
rocD ornithine aminotransferase Sama_2636 Sama_2643
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