GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Dyella japonica UNC79MFTsu3.2

Best path

rocE, rocF, rocD, PRO3, put1, putA

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 (34 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rocE L-arginine permease N515DRAFT_2630 N515DRAFT_3653
rocF arginase N515DRAFT_0348
rocD ornithine aminotransferase N515DRAFT_3630 N515DRAFT_3308
PRO3 pyrroline-5-carboxylate reductase N515DRAFT_1783
put1 proline dehydrogenase N515DRAFT_4232 N515DRAFT_0956
putA L-glutamate 5-semialdeyde dehydrogenase N515DRAFT_4232 N515DRAFT_3729
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) N515DRAFT_3000
aguA agmatine deiminase N515DRAFT_1539
aguB N-carbamoylputrescine hydrolase N515DRAFT_1536
arcA arginine deiminase
arcB ornithine carbamoyltransferase N515DRAFT_3763 N515DRAFT_1776
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
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM)
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA N515DRAFT_1085 N515DRAFT_1562
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ)
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH L-arginine:pyruvate transaminase N515DRAFT_1410 N515DRAFT_2186
aruI 2-ketoarginine decarboxylase N515DRAFT_0378
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase N515DRAFT_3308 N515DRAFT_1751
astD succinylglutamate semialdehyde dehydrogenase N515DRAFT_3729 N515DRAFT_4232
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase N515DRAFT_0938 N515DRAFT_2688
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) N515DRAFT_3950 N515DRAFT_3588
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1 N515DRAFT_2925 N515DRAFT_2924
davD glutarate semialdehyde dehydrogenase N515DRAFT_3729 N515DRAFT_2488
davT 5-aminovalerate aminotransferase N515DRAFT_3308 N515DRAFT_1751
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase N515DRAFT_1164 N515DRAFT_0416
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase N515DRAFT_2687 N515DRAFT_0416
gabD succinate semialdehyde dehydrogenase N515DRAFT_2488 N515DRAFT_3729
gabT gamma-aminobutyrate transaminase N515DRAFT_3308 N515DRAFT_1751
gbamidase guanidinobutyramidase
gbuA guanidinobutyrase
gcdG succinyl-CoA:glutarate CoA-transferase N515DRAFT_3223
gcdH glutaryl-CoA dehydrogenase N515DRAFT_0484 N515DRAFT_0492
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase N515DRAFT_3729 N515DRAFT_0379
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase
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) N515DRAFT_3308 N515DRAFT_1751
patD gamma-aminobutyraldehyde dehydrogenase N515DRAFT_3729 N515DRAFT_2488
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase N515DRAFT_0959
puo putrescine oxidase
puuA glutamate-putrescine ligase N515DRAFT_3024
puuB gamma-glutamylputrescine oxidase N515DRAFT_2697
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase N515DRAFT_3729 N515DRAFT_0379
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase N515DRAFT_4232 N515DRAFT_3729
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