GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Pseudomonas fluorescens FW300-N2E2

Best path

artJ, artM, artP, artQ, arcA, arcB, arcC, aruF, aruG, astC, astD, astE

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 (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 Pf6N2E2_5660 Pf6N2E2_3856
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) Pf6N2E2_5662 Pf6N2E2_3858
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA Pf6N2E2_5663 Pf6N2E2_3855
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) Pf6N2E2_5661 Pf6N2E2_3857
arcA arginine deiminase Pf6N2E2_2908
arcB ornithine carbamoyltransferase Pf6N2E2_2909 Pf6N2E2_5579
arcC carbamate kinase Pf6N2E2_2910
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) Pf6N2E2_5666 Pf6N2E2_2180
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) Pf6N2E2_5667 Pf6N2E2_2181
astC succinylornithine transaminase Pf6N2E2_5665 Pf6N2E2_5326
astD succinylglutamate semialdehyde dehydrogenase Pf6N2E2_5668 Pf6N2E2_1370
astE succinylglutamate desuccinylase Pf6N2E2_5671
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) Pf6N2E2_3504
aguA agmatine deiminase Pf6N2E2_3876
aguB N-carbamoylputrescine hydrolase Pf6N2E2_4777
arg-monooxygenase arginine 2-monooxygenase Pf6N2E2_4778
aroD L-arginine oxidase
aruH L-arginine:pyruvate transaminase Pf6N2E2_462 Pf6N2E2_3173
aruI 2-ketoarginine decarboxylase Pf6N2E2_5475 Pf6N2E2_5839
astA arginine N-succinyltransferase Pf6N2E2_5667 Pf6N2E2_2181
astB N-succinylarginine dihydrolase Pf6N2E2_5669
atoB acetyl-CoA C-acetyltransferase Pf6N2E2_2113 Pf6N2E2_1145
bgtB L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) Pf6N2E2_1799
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC Pf6N2E2_3580 Pf6N2E2_2921
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) Pf6N2E2_3579 Pf6N2E2_2923
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) Pf6N2E2_2924 Pf6N2E2_3578
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) Pf6N2E2_3577 Pf6N2E2_2925
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) Pf6N2E2_3576 Pf6N2E2_2926
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase Pf6N2E2_4014 Pf6N2E2_368
davT 5-aminovalerate aminotransferase Pf6N2E2_4013 Pf6N2E2_373
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Pf6N2E2_1147 Pf6N2E2_1834
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Pf6N2E2_2290 Pf6N2E2_1922
gabD succinate semialdehyde dehydrogenase Pf6N2E2_4014 Pf6N2E2_1919
gabT gamma-aminobutyrate transaminase Pf6N2E2_4512 Pf6N2E2_4013
gbamidase guanidinobutyramidase Pf6N2E2_4777
gbuA guanidinobutyrase Pf6N2E2_2655
gcdG succinyl-CoA:glutarate CoA-transferase Pf6N2E2_4035 Pf6N2E2_3139
gcdH glutaryl-CoA dehydrogenase Pf6N2E2_4036 Pf6N2E2_2191
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase Pf6N2E2_4383 Pf6N2E2_1381
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) Pf6N2E2_261
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase Pf6N2E2_3334
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) Pf6N2E2_4512 Pf6N2E2_1742
patD gamma-aminobutyraldehyde dehydrogenase Pf6N2E2_3131 Pf6N2E2_3126
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase Pf6N2E2_681 Pf6N2E2_671
PRO3 pyrroline-5-carboxylate reductase Pf6N2E2_4600
puo putrescine oxidase
put1 proline dehydrogenase Pf6N2E2_3685
putA L-glutamate 5-semialdeyde dehydrogenase Pf6N2E2_3685 Pf6N2E2_3298
puuA glutamate-putrescine ligase Pf6N2E2_4509 Pf6N2E2_4511
puuB gamma-glutamylputrescine oxidase Pf6N2E2_80 Pf6N2E2_4388
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase Pf6N2E2_4383 Pf6N2E2_1381
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase Pf6N2E2_4510
rocA 1-pyrroline-5-carboxylate dehydrogenase Pf6N2E2_3685 Pf6N2E2_3298
rocD ornithine aminotransferase Pf6N2E2_5326 Pf6N2E2_373
rocE L-arginine permease Pf6N2E2_4959 Pf6N2E2_5459
rocF arginase Pf6N2E2_2655
speB agmatinase Pf6N2E2_2655

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, the preprint 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