GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Magnetospirillum magneticum AMB-1

Best path

braC, braD, braE, braF, braG, rocF, rocD, PRO3, put1, putA

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
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC AMB_RS15010
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) AMB_RS09135 AMB_RS08455
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) AMB_RS09130 AMB_RS14460
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) AMB_RS09125 AMB_RS08465
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) AMB_RS09120 AMB_RS10230
rocF arginase
rocD ornithine aminotransferase AMB_RS04150 AMB_RS08515
PRO3 pyrroline-5-carboxylate reductase AMB_RS02820
put1 proline dehydrogenase AMB_RS12610
putA L-glutamate 5-semialdeyde dehydrogenase AMB_RS12610 AMB_RS04115
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) AMB_RS05630
aguA agmatine deiminase
aguB N-carbamoylputrescine hydrolase
arcA arginine deiminase
arcB ornithine carbamoyltransferase AMB_RS01610 AMB_RS18300
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 AMB_RS10565 AMB_RS06945
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 AMB_RS02875 AMB_RS07030
aruI 2-ketoarginine decarboxylase AMB_RS12840
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase AMB_RS01605 AMB_RS04150
astD succinylglutamate semialdehyde dehydrogenase AMB_RS06710 AMB_RS04115
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase AMB_RS18210 AMB_RS04295
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 AMB_RS06710 AMB_RS04160
davT 5-aminovalerate aminotransferase AMB_RS01605 AMB_RS04150
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase AMB_RS03265 AMB_RS13070
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase AMB_RS15050 AMB_RS19750
gabD succinate semialdehyde dehydrogenase AMB_RS06710 AMB_RS04160
gabT gamma-aminobutyrate transaminase AMB_RS08515 AMB_RS01605
gbamidase guanidinobutyramidase
gbuA guanidinobutyrase AMB_RS05595
gcdG succinyl-CoA:glutarate CoA-transferase AMB_RS08365 AMB_RS07510
gcdH glutaryl-CoA dehydrogenase AMB_RS16315 AMB_RS03480
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase AMB_RS04115 AMB_RS06710
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) AMB_RS19325
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase AMB_RS05630 AMB_RS07020
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) AMB_RS08515 AMB_RS04150
patD gamma-aminobutyraldehyde dehydrogenase AMB_RS06710 AMB_RS04115
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase
puo putrescine oxidase
puuA glutamate-putrescine ligase
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase AMB_RS04115 AMB_RS06710
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase AMB_RS20870
rocA 1-pyrroline-5-carboxylate dehydrogenase AMB_RS12610 AMB_RS04115
rocE L-arginine permease
speB agmatinase AMB_RS05595

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.

Links

Downloads

Related tools

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