GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Erythrobacter gangjinensis K7-2

Best path

rocE, astA, astB, astC, astD, astE

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 (32 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rocE L-arginine permease
astA arginine N-succinyltransferase AAW01_RS05075
astB N-succinylarginine dihydrolase AAW01_RS05080
astC succinylornithine transaminase AAW01_RS09055
astD succinylglutamate semialdehyde dehydrogenase AAW01_RS11975 AAW01_RS11260
astE succinylglutamate desuccinylase
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA)
aguA agmatine deiminase AAW01_RS07635
aguB N-carbamoylputrescine hydrolase AAW01_RS09855
arcA arginine deiminase
arcB ornithine carbamoyltransferase AAW01_RS09060 AAW01_RS06590
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 AAW01_RS11525 AAW01_RS01810
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ)
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) AAW01_RS05075
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) AAW01_RS05075
aruH L-arginine:pyruvate transaminase
aruI 2-ketoarginine decarboxylase AAW01_RS01900
atoB acetyl-CoA C-acetyltransferase AAW01_RS02970 AAW01_RS00830
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) AAW01_RS12520
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) AAW01_RS09360 AAW01_RS06340
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase AAW01_RS09770 AAW01_RS04300
davT 5-aminovalerate aminotransferase AAW01_RS09055 AAW01_RS12605
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase AAW01_RS13205 AAW01_RS11465
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase AAW01_RS00825 AAW01_RS06205
gabD succinate semialdehyde dehydrogenase AAW01_RS09770 AAW01_RS04390
gabT gamma-aminobutyrate transaminase AAW01_RS09055 AAW01_RS12605
gbamidase guanidinobutyramidase
gbuA guanidinobutyrase
gcdG succinyl-CoA:glutarate CoA-transferase AAW01_RS11415 AAW01_RS11420
gcdH glutaryl-CoA dehydrogenase AAW01_RS11555 AAW01_RS07145
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase AAW01_RS09770 AAW01_RS13220
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) AAW01_RS09055 AAW01_RS12605
patD gamma-aminobutyraldehyde dehydrogenase AAW01_RS09770 AAW01_RS04390
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 AAW01_RS05825
puo putrescine oxidase
put1 proline dehydrogenase AAW01_RS11260
putA L-glutamate 5-semialdeyde dehydrogenase AAW01_RS11260 AAW01_RS09770
puuA glutamate-putrescine ligase AAW01_RS06010
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase AAW01_RS09770 AAW01_RS13220
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase AAW01_RS11260 AAW01_RS09770
rocD ornithine aminotransferase AAW01_RS12605 AAW01_RS09055
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 24 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 (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