GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Escherichia coli BW25113

Best path

artJ, artM, artP, artQ, adiA, speB, 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 (48 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 b2309 b2310
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) b2307 b0861
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA b2306 b0864
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) b0862 b2308
adiA arginine decarboxylase (AdiA/SpeA) b4117 b2938
speB agmatinase b2937
puuA glutamate-putrescine ligase b1297 b3870
puuB gamma-glutamylputrescine oxidase b1301
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase b1300 b3588
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase b1298
gabT gamma-aminobutyrate transaminase b2662 b1302
gabD succinate semialdehyde dehydrogenase b1300 b2661
Alternative steps:
AAP3 L-arginine transporter AAP3
aguA agmatine deiminase
aguB N-carbamoylputrescine hydrolase
arcA arginine deiminase
arcB ornithine carbamoyltransferase b0273 b4254
arcC carbamate kinase b0521 b2874
arg-monooxygenase arginine 2-monooxygenase
aroD L-arginine oxidase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) b1747
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) b1747
aruH L-arginine:pyruvate transaminase b0600
aruI 2-ketoarginine decarboxylase b3671 b0077
astA arginine N-succinyltransferase b1747
astB N-succinylarginine dihydrolase b1745
astC succinylornithine transaminase b1748 b3359
astD succinylglutamate semialdehyde dehydrogenase b1746 b2661
astE succinylglutamate desuccinylase b1744
atoB acetyl-CoA C-acetyltransferase b2224 b2844
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 b3460 b3458
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) b3457
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) b3456
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) b3455
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) b3454 b3455
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase b2661 b1415
davT 5-aminovalerate aminotransferase b2662 b1302
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase b1393 b3846
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase b3846 b2341
gbamidase guanidinobutyramidase
gbuA guanidinobutyrase b2937
gcdG succinyl-CoA:glutarate CoA-transferase b2371 b2374
gcdH glutaryl-CoA dehydrogenase
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD) b2659
kauB 4-guanidinobutyraldehyde dehydrogenase b1300 b3588
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) b2660
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase b0693 b2965
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) b3073 b1302
patD gamma-aminobutyraldehyde dehydrogenase b1444 b1300
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 b0386
puo putrescine oxidase b1386
put1 proline dehydrogenase b1014
putA L-glutamate 5-semialdeyde dehydrogenase b1014 b1415
rocA 1-pyrroline-5-carboxylate dehydrogenase b1014 b1415
rocD ornithine aminotransferase b1302 b2662
rocE L-arginine permease b0260 b2156
rocF arginase

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