GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Arcobacter nitrofigilis DSM 7299

Best path

rocE, adiA, speB, patA, patD, gabT, gabD

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 (34 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rocE L-arginine permease
adiA arginine decarboxylase (AdiA/SpeA) ARNIT_RS09805
speB agmatinase ARNIT_RS07020 ARNIT_RS01640
patA putrescine aminotransferase (PatA/SpuC) ARNIT_RS11930 ARNIT_RS06120
patD gamma-aminobutyraldehyde dehydrogenase ARNIT_RS13950 ARNIT_RS05955
gabT gamma-aminobutyrate transaminase ARNIT_RS06120 ARNIT_RS11930
gabD succinate semialdehyde dehydrogenase ARNIT_RS06115 ARNIT_RS05955
Alternative steps:
AAP3 L-arginine transporter AAP3
aguA agmatine deiminase
aguB N-carbamoylputrescine hydrolase
arcA arginine deiminase
arcB ornithine carbamoyltransferase ARNIT_RS08310 ARNIT_RS13870
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 ARNIT_RS14270 ARNIT_RS16495
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) ARNIT_RS01645 ARNIT_RS13580
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA ARNIT_RS01655 ARNIT_RS13590
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) ARNIT_RS13580 ARNIT_RS16500
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH L-arginine:pyruvate transaminase ARNIT_RS10285
aruI 2-ketoarginine decarboxylase
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase ARNIT_RS13880 ARNIT_RS12320
astD succinylglutamate semialdehyde dehydrogenase ARNIT_RS13950 ARNIT_RS00055
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase ARNIT_RS06730
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) ARNIT_RS06925 ARNIT_RS08960
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) ARNIT_RS06930 ARNIT_RS08955
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) ARNIT_RS08950 ARNIT_RS06935
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) ARNIT_RS08945 ARNIT_RS06940
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase ARNIT_RS00055 ARNIT_RS05955
davT 5-aminovalerate aminotransferase ARNIT_RS12320 ARNIT_RS06120
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase ARNIT_RS06725
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase ARNIT_RS06725 ARNIT_RS11565
gbamidase guanidinobutyramidase
gbuA guanidinobutyrase ARNIT_RS01640 ARNIT_RS07020
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase ARNIT_RS13950 ARNIT_RS05955
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) ARNIT_RS06065
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
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase ARNIT_RS06080
PRO3 pyrroline-5-carboxylate reductase ARNIT_RS04145
puo putrescine oxidase
put1 proline dehydrogenase
putA L-glutamate 5-semialdeyde dehydrogenase ARNIT_RS08940 ARNIT_RS05955
puuA glutamate-putrescine ligase ARNIT_RS13175
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase ARNIT_RS13950 ARNIT_RS05955
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase ARNIT_RS08940 ARNIT_RS05955
rocD ornithine aminotransferase ARNIT_RS13880 ARNIT_RS11930
rocF arginase ARNIT_RS07020

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