GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Desulfobacter vibrioformis DSM 8776

Best path

rocE, rocF, rocD, rocA

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 (28 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rocE L-arginine permease
rocF arginase Q366_RS15985
rocD ornithine aminotransferase Q366_RS00665 Q366_RS12820
rocA 1-pyrroline-5-carboxylate dehydrogenase Q366_RS11500 Q366_RS10385
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) Q366_RS20030
aguA agmatine deiminase
aguB N-carbamoylputrescine hydrolase
arcA arginine deiminase
arcB ornithine carbamoyltransferase Q366_RS19245 Q366_RS13250
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 Q366_RS06940 Q366_RS03735
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
aruI 2-ketoarginine decarboxylase Q366_RS01295
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase Q366_RS19250 Q366_RS13500
astD succinylglutamate semialdehyde dehydrogenase Q366_RS13505 Q366_RS07005
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase Q366_RS09305 Q366_RS02505
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) Q366_RS04655
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) Q366_RS04650 Q366_RS00605
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) Q366_RS04645 Q366_RS13535
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) Q366_RS13540 Q366_RS04640
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase Q366_RS17050 Q366_RS13505
davT 5-aminovalerate aminotransferase Q366_RS13500 Q366_RS12820
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Q366_RS18135 Q366_RS13010
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Q366_RS00865 Q366_RS00395
gabD succinate semialdehyde dehydrogenase Q366_RS17050 Q366_RS13505
gabT gamma-aminobutyrate transaminase Q366_RS07000 Q366_RS13500
gbamidase guanidinobutyramidase
gbuA guanidinobutyrase
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase Q366_RS06780 Q366_RS11450
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase Q366_RS10385 Q366_RS13505
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) Q366_RS07000 Q366_RS19250
patD gamma-aminobutyraldehyde dehydrogenase Q366_RS07005 Q366_RS10385
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 Q366_RS04185
puo putrescine oxidase
put1 proline dehydrogenase Q366_RS04815
putA L-glutamate 5-semialdeyde dehydrogenase Q366_RS11500 Q366_RS10385
puuA glutamate-putrescine ligase
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase Q366_RS10385 Q366_RS13505
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
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 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