GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Pseudomonas stutzeri RCH2

Best path

artJ, artM, artP, artQ, 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 (44 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 Psest_0138
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) Psest_0136 Psest_0018
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA Psest_0139 Psest_0016
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) Psest_0137 Psest_0018
adiA arginine decarboxylase (AdiA/SpeA) Psest_3366 Psest_2075
aguA agmatine deiminase Psest_4291
aguB N-carbamoylputrescine hydrolase Psest_4290
puuA glutamate-putrescine ligase Psest_4288 Psest_4286
puuB gamma-glutamylputrescine oxidase Psest_1966 Psest_3795
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase Psest_4305 Psest_0905
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase Psest_4287
gabT gamma-aminobutyrate transaminase Psest_4285 Psest_3653
gabD succinate semialdehyde dehydrogenase Psest_4237 Psest_3654
Alternative steps:
AAP3 L-arginine transporter AAP3
arcA arginine deiminase Psest_0272
arcB ornithine carbamoyltransferase Psest_0271 Psest_1291
arcC carbamate kinase Psest_0270
arg-monooxygenase arginine 2-monooxygenase
aroD L-arginine oxidase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH L-arginine:pyruvate transaminase Psest_1268 Psest_1004
aruI 2-ketoarginine decarboxylase Psest_1181
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase Psest_2719 Psest_3653
astD succinylglutamate semialdehyde dehydrogenase Psest_3654 Psest_4305
astE succinylglutamate desuccinylase Psest_2717
atoB acetyl-CoA C-acetyltransferase Psest_1076 Psest_2446
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 Psest_1312
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) Psest_1311 Psest_1092
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) Psest_1310
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) Psest_1309 Psest_3853
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) Psest_1308 Psest_0563
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase Psest_4237 Psest_3654
davT 5-aminovalerate aminotransferase Psest_3653 Psest_2719
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Psest_2437 Psest_3109
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Psest_2654 Psest_4235
gbamidase guanidinobutyramidase
gbuA guanidinobutyrase
gcdG succinyl-CoA:glutarate CoA-transferase Psest_3829 Psest_2660
gcdH glutaryl-CoA dehydrogenase Psest_3830 Psest_2440
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase Psest_4305 Psest_0905
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) Psest_0232
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase Psest_3350 Psest_2075
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) Psest_4285 Psest_4306
patD gamma-aminobutyraldehyde dehydrogenase Psest_4305 Psest_2634
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 Psest_0283
puo putrescine oxidase
put1 proline dehydrogenase Psest_3079
putA L-glutamate 5-semialdeyde dehydrogenase Psest_3079 Psest_0375
rocA 1-pyrroline-5-carboxylate dehydrogenase Psest_3079 Psest_0375
rocD ornithine aminotransferase Psest_2719 Psest_3653
rocE L-arginine permease Psest_1697
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 Aug 02 2021. The underlying query database was built on Aug 02 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