GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Pseudomonas fluorescens FW300-N1B4

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 (56 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 Pf1N1B4_3431 Pf1N1B4_1641
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) Pf1N1B4_3433 Pf1N1B4_4398
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA Pf1N1B4_3435 Pf1N1B4_1640
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) Pf1N1B4_3432 Pf1N1B4_4399
adiA arginine decarboxylase (AdiA/SpeA) Pf1N1B4_1296 Pf1N1B4_4600
aguA agmatine deiminase Pf1N1B4_1661 Pf1N1B4_4325
aguB N-carbamoylputrescine hydrolase Pf1N1B4_1662 Pf1N1B4_4326
puuA glutamate-putrescine ligase Pf1N1B4_4354 Pf1N1B4_2254
puuB gamma-glutamylputrescine oxidase Pf1N1B4_6047 Pf1N1B4_4356
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase Pf1N1B4_2132 Pf1N1B4_4355
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase Pf1N1B4_4353 Pf1N1B4_2255
gabT gamma-aminobutyrate transaminase Pf1N1B4_2257 Pf1N1B4_1733
gabD succinate semialdehyde dehydrogenase Pf1N1B4_1734 Pf1N1B4_5616
Alternative steps:
AAP3 L-arginine transporter AAP3
arcA arginine deiminase Pf1N1B4_615
arcB ornithine carbamoyltransferase Pf1N1B4_616 Pf1N1B4_762
arcC carbamate kinase Pf1N1B4_617
arg-monooxygenase arginine 2-monooxygenase Pf1N1B4_2505
aroD L-arginine oxidase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) Pf1N1B4_3442 Pf1N1B4_5856
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) Pf1N1B4_3443 Pf1N1B4_4797
aruH L-arginine:pyruvate transaminase Pf1N1B4_4996 Pf1N1B4_5070
aruI 2-ketoarginine decarboxylase Pf1N1B4_696 Pf1N1B4_3661
astA arginine N-succinyltransferase Pf1N1B4_3443 Pf1N1B4_4797
astB N-succinylarginine dihydrolase Pf1N1B4_3445
astC succinylornithine transaminase Pf1N1B4_3440 Pf1N1B4_2980
astD succinylglutamate semialdehyde dehydrogenase Pf1N1B4_3444 Pf1N1B4_3024
astE succinylglutamate desuccinylase Pf1N1B4_3447
atoB acetyl-CoA C-acetyltransferase Pf1N1B4_4786 Pf1N1B4_5835
bgtB L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) Pf1N1B4_4805
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC Pf1N1B4_1382 Pf1N1B4_3218
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) Pf1N1B4_1381 Pf1N1B4_3217
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) Pf1N1B4_3216 Pf1N1B4_1380
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) Pf1N1B4_1379 Pf1N1B4_3215
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) Pf1N1B4_1378 Pf1N1B4_3214
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase Pf1N1B4_1734 Pf1N1B4_4931
davT 5-aminovalerate aminotransferase Pf1N1B4_1733 Pf1N1B4_4910
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Pf1N1B4_4788 Pf1N1B4_3903
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Pf1N1B4_3903 Pf1N1B4_5134
gbamidase guanidinobutyramidase Pf1N1B4_2504
gbuA guanidinobutyrase Pf1N1B4_525 Pf1N1B4_4717
gcdG succinyl-CoA:glutarate CoA-transferase Pf1N1B4_1815 Pf1N1B4_5611
gcdH glutaryl-CoA dehydrogenase Pf1N1B4_1816 Pf1N1B4_3987
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase Pf1N1B4_2132 Pf1N1B4_4355
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) Pf1N1B4_4264
ocd ornithine cyclodeaminase Pf1N1B4_4977
odc L-ornithine decarboxylase Pf1N1B4_1136 Pf1N1B4_4600
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) Pf1N1B4_2257 Pf1N1B4_1239
patD gamma-aminobutyraldehyde dehydrogenase Pf1N1B4_3024 Pf1N1B4_3029
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase Pf1N1B4_5964 Pf1N1B4_5975
PRO3 pyrroline-5-carboxylate reductase Pf1N1B4_2341
puo putrescine oxidase
put1 proline dehydrogenase Pf1N1B4_1489
putA L-glutamate 5-semialdeyde dehydrogenase Pf1N1B4_1489 Pf1N1B4_1109
rocA 1-pyrroline-5-carboxylate dehydrogenase Pf1N1B4_1489 Pf1N1B4_1109
rocD ornithine aminotransferase Pf1N1B4_2980 Pf1N1B4_4910
rocE L-arginine permease Pf1N1B4_801 Pf1N1B4_1580
rocF arginase Pf1N1B4_525 Pf1N1B4_4717
speB agmatinase Pf1N1B4_4717 Pf1N1B4_525

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