GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Pedobacter sp. GW460-11-11-14-LB5

Best path

rocE, rocF, rocD, PRO3, 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 (33 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rocE L-arginine permease
rocF arginase
rocD ornithine aminotransferase CA265_RS15205 CA265_RS18530
PRO3 pyrroline-5-carboxylate reductase CA265_RS18505
put1 proline dehydrogenase CA265_RS11605
putA L-glutamate 5-semialdeyde dehydrogenase CA265_RS16605 CA265_RS14635
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA)
aguA agmatine deiminase CA265_RS15455
aguB N-carbamoylputrescine hydrolase CA265_RS15465
arcA arginine deiminase CA265_RS10470
arcB ornithine carbamoyltransferase CA265_RS14660 CA265_RS18520
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 CA265_RS04345 CA265_RS07485
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 CA265_RS07515
aruI 2-ketoarginine decarboxylase CA265_RS15805
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase CA265_RS15205 CA265_RS18530
astD succinylglutamate semialdehyde dehydrogenase CA265_RS24850 CA265_RS19780
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase CA265_RS06590 CA265_RS17585
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)
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) CA265_RS25230 CA265_RS04345
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1 CA265_RS15000 CA265_RS17395
davD glutarate semialdehyde dehydrogenase CA265_RS14635 CA265_RS24850
davT 5-aminovalerate aminotransferase CA265_RS18530 CA265_RS15205
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase CA265_RS20005 CA265_RS09125
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase CA265_RS17590 CA265_RS07715
gabD succinate semialdehyde dehydrogenase CA265_RS24850 CA265_RS01080
gabT gamma-aminobutyrate transaminase CA265_RS14455 CA265_RS18530
gbamidase guanidinobutyramidase
gbuA guanidinobutyrase
gcdG succinyl-CoA:glutarate CoA-transferase CA265_RS08550
gcdH glutaryl-CoA dehydrogenase CA265_RS09630 CA265_RS14465
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase CA265_RS14635 CA265_RS24850
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) CA265_RS19300
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase
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) CA265_RS15205 CA265_RS18530
patD gamma-aminobutyraldehyde dehydrogenase CA265_RS14635 CA265_RS24850
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase CA265_RS05710
puo putrescine oxidase
puuA glutamate-putrescine ligase CA265_RS24865
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase CA265_RS14635 CA265_RS24850
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase CA265_RS24855
rocA 1-pyrroline-5-carboxylate dehydrogenase CA265_RS16605 CA265_RS14635
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