GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Desulfovibrio vulgaris Hildenborough

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 (31 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rocE L-arginine permease
rocF arginase
rocD ornithine aminotransferase DVU2559 DVU3168
PRO3 pyrroline-5-carboxylate reductase DVU2332
put1 proline dehydrogenase DVU3319
putA L-glutamate 5-semialdeyde dehydrogenase DVU3319 DVU3294
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) DVU0417
aguA agmatine deiminase
aguB N-carbamoylputrescine hydrolase
arcA arginine deiminase
arcB ornithine carbamoyltransferase DVU1096 DVU2901
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 DVU1238 DVU0386
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) DVU0387 DVU0967
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA DVU0105 DVU1236
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) DVU0967 DVU0387
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH L-arginine:pyruvate transaminase DVU3223 DVU1655
aruI 2-ketoarginine decarboxylase DVU0360 DVU1376
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase DVU2347 DVU2559
astD succinylglutamate semialdehyde dehydrogenase DVU3319
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase
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 DVU0547 DVU0712
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) DVU0548 DVU0713
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) DVU0549 DVU0714
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) DVU0550 DVU0715
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) DVU0551 DVU0716
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase DVU3294 DVU3319
davT 5-aminovalerate aminotransferase DVU2559 DVU2347
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase 206645
gabD succinate semialdehyde dehydrogenase DVU3294 DVU3319
gabT gamma-aminobutyrate transaminase DVU2559 DVU2347
gbamidase guanidinobutyramidase
gbuA guanidinobutyrase
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase DVU3319
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) DVU2559 DVU2347
patD gamma-aminobutyraldehyde dehydrogenase DVU3319 DVU3294
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 DVU3392
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase DVU3319 DVU3294
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase DVU3319 DVU3294
speB agmatinase DVU0421

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