GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Acidovorax sp. GW101-3H11

Best path

braC, braD, braE, braF, braG, 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 (41 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC Ac3H11_2396 Ac3H11_552
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) Ac3H11_1695 Ac3H11_1939
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) Ac3H11_1694 Ac3H11_1938
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) Ac3H11_4630 Ac3H11_1937
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) Ac3H11_1692 Ac3H11_1936
rocF arginase Ac3H11_701
ocd ornithine cyclodeaminase Ac3H11_4531
put1 proline dehydrogenase Ac3H11_2850
putA L-glutamate 5-semialdeyde dehydrogenase Ac3H11_2850 Ac3H11_3961
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) Ac3H11_2914 Ac3H11_650
aguA agmatine deiminase
aguB N-carbamoylputrescine hydrolase
arcA arginine deiminase
arcB ornithine carbamoyltransferase Ac3H11_1333 Ac3H11_3978
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 Ac3H11_2555 Ac3H11_3325
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) Ac3H11_3200 Ac3H11_2554
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA Ac3H11_3200 Ac3H11_3327
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) Ac3H11_3200 Ac3H11_3326
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH L-arginine:pyruvate transaminase Ac3H11_1602 Ac3H11_3135
aruI 2-ketoarginine decarboxylase Ac3H11_1601
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase Ac3H11_1332 Ac3H11_4342
astD succinylglutamate semialdehyde dehydrogenase Ac3H11_3961 Ac3H11_1480
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase Ac3H11_178 Ac3H11_2303
bgtB L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase Ac3H11_1480 Ac3H11_4184
davT 5-aminovalerate aminotransferase Ac3H11_4179 Ac3H11_1332
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Ac3H11_4006 Ac3H11_2775
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Ac3H11_1914 Ac3H11_4658
gabD succinate semialdehyde dehydrogenase Ac3H11_255 Ac3H11_1480
gabT gamma-aminobutyrate transaminase Ac3H11_4179 Ac3H11_4342
gbamidase guanidinobutyramidase Ac3H11_1207
gbuA guanidinobutyrase
gcdG succinyl-CoA:glutarate CoA-transferase Ac3H11_3532 Ac3H11_198
gcdH glutaryl-CoA dehydrogenase Ac3H11_3533 Ac3H11_2991
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase Ac3H11_1496 Ac3H11_1486
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) Ac3H11_4104
odc L-ornithine decarboxylase Ac3H11_2914
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) Ac3H11_4342 Ac3H11_1332
patD gamma-aminobutyraldehyde dehydrogenase Ac3H11_1496 Ac3H11_1486
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase Ac3H11_4170
PRO3 pyrroline-5-carboxylate reductase Ac3H11_788
puo putrescine oxidase
puuA glutamate-putrescine ligase Ac3H11_1551
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase Ac3H11_1496 Ac3H11_1486
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase Ac3H11_1167
rocA 1-pyrroline-5-carboxylate dehydrogenase Ac3H11_2850 Ac3H11_3961
rocD ornithine aminotransferase Ac3H11_4179 Ac3H11_1332
rocE L-arginine permease
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