GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Phaeobacter inhibens BS107

Best path

artJ, artM, artP, artQ, rocF, ocd, 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 (42 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 PGA1_262p02360 PGA1_c11570
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) PGA1_c11550 PGA1_262p02380
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA PGA1_262p02350 PGA1_c11580
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) PGA1_262p02370 PGA1_c11560
rocF arginase PGA1_c16370 PGA1_c19920
ocd ornithine cyclodeaminase PGA1_c16390
put1 proline dehydrogenase PGA1_c11750 PGA1_c23300
putA L-glutamate 5-semialdeyde dehydrogenase PGA1_c11750 PGA1_c05130
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) PGA1_c03800 PGA1_c14480
aguA agmatine deiminase PGA1_c26490
aguB N-carbamoylputrescine hydrolase
arcA arginine deiminase
arcB ornithine carbamoyltransferase PGA1_c24220 PGA1_c03060
arcC carbamate kinase
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 PGA1_262p02330 PGA1_c21250
aruI 2-ketoarginine decarboxylase PGA1_262p02320 PGA1_c19360
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase PGA1_c24230 PGA1_c28750
astD succinylglutamate semialdehyde dehydrogenase PGA1_c32120 PGA1_262p01460
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase PGA1_c03400 PGA1_c33180
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) PGA1_c02590
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) PGA1_c32620 PGA1_c02610
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) PGA1_c02620 PGA1_c32560
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase PGA1_c29650 PGA1_c23170
davT 5-aminovalerate aminotransferase PGA1_c24230 PGA1_c28750
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase PGA1_c36500 PGA1_262p01980
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase PGA1_c04110 PGA1_c11320
gabD succinate semialdehyde dehydrogenase PGA1_c29650 PGA1_c23170
gabT gamma-aminobutyrate transaminase PGA1_c34400 PGA1_c09350
gbamidase guanidinobutyramidase
gbuA guanidinobutyrase PGA1_c19920 PGA1_c00310
gcdG succinyl-CoA:glutarate CoA-transferase PGA1_c27870 PGA1_c12340
gcdH glutaryl-CoA dehydrogenase PGA1_c15710 PGA1_c10280
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase PGA1_c32250 PGA1_c21670
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
odc L-ornithine decarboxylase PGA1_c11650 PGA1_c03800
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 PGA1_c17610
ortA 2-amino-4-oxopentanoate thiolase, alpha subunit
ortB 2-amino-4-oxopentanoate thiolase, beta subunit
patA putrescine aminotransferase (PatA/SpuC) PGA1_c34400 PGA1_c09350
patD gamma-aminobutyraldehyde dehydrogenase PGA1_c21670 PGA1_c32250
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase PGA1_262p00280 PGA1_c05120
PRO3 pyrroline-5-carboxylate reductase PGA1_c24700
puo putrescine oxidase
puuA glutamate-putrescine ligase PGA1_c11520 PGA1_c11540
puuB gamma-glutamylputrescine oxidase PGA1_c11510 PGA1_78p00350
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PGA1_c32250 PGA1_c21670
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase PGA1_c09920 PGA1_c28350
rocA 1-pyrroline-5-carboxylate dehydrogenase PGA1_c11750 PGA1_c05130
rocD ornithine aminotransferase PGA1_c28770 PGA1_c09350
rocE L-arginine permease
speB agmatinase PGA1_c19930 PGA1_c19920

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, 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