GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Caulobacter crescentus NA1000

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 (41 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rocE L-arginine permease
adiA arginine decarboxylase (AdiA/SpeA)
aguA agmatine deiminase CCNA_00211
aguB N-carbamoylputrescine hydrolase CCNA_00212
puuA glutamate-putrescine ligase CCNA_03230 CCNA_03240
puuB gamma-glutamylputrescine oxidase CCNA_03229
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase CCNA_03243 CCNA_03695
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase CCNA_03234
gabT gamma-aminobutyrate transaminase CCNA_03233 CCNA_03245
gabD succinate semialdehyde dehydrogenase CCNA_03242 CCNA_03243
Alternative steps:
AAP3 L-arginine transporter AAP3
arcA arginine deiminase
arcB ornithine carbamoyltransferase CCNA_02325 CCNA_02525
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 CCNA_01508
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) CCNA_01507
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA CCNA_01506 CCNA_02751
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) CCNA_01507
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) CCNA_01678 CCNA_00617
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) CCNA_00617 CCNA_01678
aruH L-arginine:pyruvate transaminase CCNA_01603 CCNA_00775
aruI 2-ketoarginine decarboxylase CCNA_02185
astA arginine N-succinyltransferase CCNA_01678 CCNA_00617
astB N-succinylarginine dihydrolase CCNA_01680 CCNA_00619
astC succinylornithine transaminase CCNA_00620 CCNA_02326
astD succinylglutamate semialdehyde dehydrogenase CCNA_01679 CCNA_00618
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase CCNA_00820 CCNA_00544
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) CCNA_03714 CCNA_01670
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1 CCNA_01242 CCNA_00435
davD glutarate semialdehyde dehydrogenase CCNA_03242 CCNA_03243
davT 5-aminovalerate aminotransferase CCNA_00620 CCNA_02326
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase CCNA_00006 CCNA_01794
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase CCNA_00123 CCNA_03293
gbamidase guanidinobutyramidase CCNA_00871
gbuA guanidinobutyrase
gcdG succinyl-CoA:glutarate CoA-transferase CCNA_03677 CCNA_02410
gcdH glutaryl-CoA dehydrogenase CCNA_02254 CCNA_01412
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase CCNA_03243 CCNA_03695
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) CCNA_03278
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase CCNA_00365
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) CCNA_03233 CCNA_03245
patD gamma-aminobutyraldehyde dehydrogenase CCNA_03243 CCNA_03695
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 CCNA_00528
puo putrescine oxidase
put1 proline dehydrogenase CCNA_00846
putA L-glutamate 5-semialdeyde dehydrogenase CCNA_00846 CCNA_00865
rocA 1-pyrroline-5-carboxylate dehydrogenase CCNA_00846 CCNA_00865
rocD ornithine aminotransferase CCNA_03233 CCNA_02326
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.

Links

Downloads

Related tools

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