GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Hippea alviniae EP5-r

Best path

rocE, 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 (36 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rocE L-arginine permease
rocF arginase G415_RS0101040
rocD ornithine aminotransferase G415_RS0106790
PRO3 pyrroline-5-carboxylate reductase G415_RS0103995
put1 proline dehydrogenase G415_RS0108290
putA L-glutamate 5-semialdeyde dehydrogenase G415_RS0108295 G415_RS0101870
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) G415_RS0101045 G415_RS0101050
aguA agmatine deiminase
aguB N-carbamoylputrescine hydrolase
arcA arginine deiminase
arcB ornithine carbamoyltransferase G415_RS0107525 G415_RS0104265
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 G415_RS0100530
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) G415_RS0100535
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA G415_RS0100540 G415_RS0105700
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) G415_RS0100535
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH L-arginine:pyruvate transaminase G415_RS0104595
aruI 2-ketoarginine decarboxylase G415_RS0101065
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase G415_RS0106790 G415_RS0101830
astD succinylglutamate semialdehyde dehydrogenase G415_RS0101870
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase G415_RS0109095
bgtB L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) G415_RS0100535
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) G415_RS0108260 G415_RS0107490
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) G415_RS0108700 G415_RS0108255
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) G415_RS0107500 G415_RS0108250
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) G415_RS0108245 G415_RS0107505
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase G415_RS0101870
davT 5-aminovalerate aminotransferase G415_RS0106790 G415_RS0101830
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase G415_RS0105565 G415_RS0104835
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase G415_RS0100670
gabD succinate semialdehyde dehydrogenase G415_RS0101870
gabT gamma-aminobutyrate transaminase G415_RS0101830 G415_RS0106790
gbamidase guanidinobutyramidase
gbuA guanidinobutyrase G415_RS0101040
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase G415_RS0100700
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase G415_RS0101870
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
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) G415_RS0106790
patD gamma-aminobutyraldehyde dehydrogenase G415_RS0101870
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 G415_RS0104980
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase G415_RS0101870
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase G415_RS0108295 G415_RS0101870
speB agmatinase G415_RS0101040

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 Apr 09 2024. 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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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:

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