GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Pseudomonas fluorescens FW300-N2C3

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 AO356_18700 AO356_09900
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) AO356_18710 AO356_09910
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA AO356_18715 AO356_09895
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) AO356_18705 AO356_09905
arcA arginine deiminase AO356_05270
arcB ornithine carbamoyltransferase AO356_05275 AO356_18275
arcC carbamate kinase AO356_05280
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) AO356_18730 AO356_01525
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) AO356_18735 AO356_01530
astC succinylornithine transaminase AO356_18725 AO356_17010
astD succinylglutamate semialdehyde dehydrogenase AO356_18740 AO356_27965
astE succinylglutamate desuccinylase AO356_18755
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) AO356_08155
aguA agmatine deiminase AO356_10030
aguB N-carbamoylputrescine hydrolase
arg-monooxygenase arginine 2-monooxygenase AO356_14230
aroD L-arginine oxidase
aruH L-arginine:pyruvate transaminase AO356_22880 AO356_25355
aruI 2-ketoarginine decarboxylase AO356_17755
astA arginine N-succinyltransferase AO356_18735 AO356_01530
astB N-succinylarginine dihydrolase AO356_18745
atoB acetyl-CoA C-acetyltransferase AO356_21640 AO356_26350
bgtB L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) AO356_29675
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC AO356_08500 AO356_05320
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) AO356_08495 AO356_05325
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) AO356_05330 AO356_08490
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) AO356_08485 AO356_05335
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) AO356_08480 AO356_05340
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase AO356_10720 AO356_29070
davT 5-aminovalerate aminotransferase AO356_10715 AO356_26715
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase AO356_26360 AO356_02330
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase AO356_02330 AO356_29995
gabD succinate semialdehyde dehydrogenase AO356_10720 AO356_30285
gabT gamma-aminobutyrate transaminase AO356_13150 AO356_26715
gbamidase guanidinobutyramidase AO356_14225
gbuA guanidinobutyrase AO356_04095
gcdG succinyl-CoA:glutarate CoA-transferase AO356_10845 AO356_06355
gcdH glutaryl-CoA dehydrogenase AO356_10850 AO356_01580
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase AO356_12580 AO356_09270
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) AO356_26445
ocd ornithine cyclodeaminase AO356_29450
odc L-ornithine decarboxylase AO356_07310
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) AO356_13150 AO356_28705
patD gamma-aminobutyraldehyde dehydrogenase AO356_06315 AO356_06290
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase AO356_09240 AO356_24960
PRO3 pyrroline-5-carboxylate reductase AO356_13420 AO356_00600
puo putrescine oxidase
put1 proline dehydrogenase AO356_09015
putA L-glutamate 5-semialdeyde dehydrogenase AO356_09015 AO356_07180
puuA glutamate-putrescine ligase AO356_13135 AO356_13145
puuB gamma-glutamylputrescine oxidase AO356_21495 AO356_12605
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase AO356_12580 AO356_09270
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase AO356_13140
rocA 1-pyrroline-5-carboxylate dehydrogenase AO356_09015 AO356_07180
rocD ornithine aminotransferase AO356_17010 AO356_26715
rocE L-arginine permease AO356_15120 AO356_17670
rocF arginase AO356_04095
speB agmatinase AO356_04095

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