GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Sphingomonas koreensis DSMZ 15582

Best path

rocE, astA, astB, astC, astD, astE

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 (35 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rocE L-arginine permease
astA arginine N-succinyltransferase Ga0059261_3996
astB N-succinylarginine dihydrolase Ga0059261_3995
astC succinylornithine transaminase Ga0059261_3205 Ga0059261_4131
astD succinylglutamate semialdehyde dehydrogenase Ga0059261_4132 Ga0059261_1495
astE succinylglutamate desuccinylase
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA)
aguA agmatine deiminase Ga0059261_1981
aguB N-carbamoylputrescine hydrolase Ga0059261_1979
arcA arginine deiminase
arcB ornithine carbamoyltransferase Ga0059261_3206 Ga0059261_0076
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 Ga0059261_3653 Ga0059261_0341
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ)
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) Ga0059261_3996
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) Ga0059261_3996
aruH L-arginine:pyruvate transaminase Ga0059261_2226 Ga0059261_1288
aruI 2-ketoarginine decarboxylase Ga0059261_1674 Ga0059261_0285
atoB acetyl-CoA C-acetyltransferase Ga0059261_0982 Ga0059261_2888
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) Ga0059261_2556
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) Ga0059261_2542 Ga0059261_0484
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1 Ga0059261_1577
davD glutarate semialdehyde dehydrogenase Ga0059261_0516 Ga0059261_1680
davT 5-aminovalerate aminotransferase Ga0059261_4131 Ga0059261_3205
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Ga0059261_3685 Ga0059261_2668
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Ga0059261_2816 Ga0059261_0837
gabD succinate semialdehyde dehydrogenase Ga0059261_1006 Ga0059261_1680
gabT gamma-aminobutyrate transaminase Ga0059261_4131 Ga0059261_3205
gbamidase guanidinobutyramidase Ga0059261_3603
gbuA guanidinobutyrase
gcdG succinyl-CoA:glutarate CoA-transferase Ga0059261_2166 Ga0059261_2807
gcdH glutaryl-CoA dehydrogenase Ga0059261_2164 Ga0059261_4052
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase Ga0059261_3374 Ga0059261_1680
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase Ga0059261_3753
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) Ga0059261_4131 Ga0059261_3205
patD gamma-aminobutyraldehyde dehydrogenase Ga0059261_3374 Ga0059261_1680
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 Ga0059261_3321 Ga0059261_3808
puo putrescine oxidase
put1 proline dehydrogenase Ga0059261_3926
putA L-glutamate 5-semialdeyde dehydrogenase Ga0059261_3926 Ga0059261_3374
puuA glutamate-putrescine ligase
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase Ga0059261_3374 Ga0059261_1680
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase Ga0059261_3926 Ga0059261_3374
rocD ornithine aminotransferase Ga0059261_3205 Ga0059261_4131
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.

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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