GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Dechlorosoma suillum PS

Best path

rocE, rocF, rocD, rocA

Also see fitness data for the top candidates

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 Dsui_0671
rocD ornithine aminotransferase Dsui_3250 Dsui_0023
rocA 1-pyrroline-5-carboxylate dehydrogenase Dsui_0437 Dsui_1464
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) Dsui_1245
aguA agmatine deiminase
aguB N-carbamoylputrescine hydrolase
arcA arginine deiminase
arcB ornithine carbamoyltransferase Dsui_3249
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) Dsui_0637 Dsui_0636
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA Dsui_0638 Dsui_2877
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) Dsui_0636 Dsui_0637
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH L-arginine:pyruvate transaminase Dsui_3376 Dsui_0132
aruI 2-ketoarginine decarboxylase Dsui_1925
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase Dsui_3250 Dsui_0023
astD succinylglutamate semialdehyde dehydrogenase Dsui_0105 Dsui_0437
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase Dsui_0976 Dsui_3239
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 Dsui_0630
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) Dsui_0629 Dsui_2060
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) Dsui_0628 Dsui_2059
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) Dsui_0627 Dsui_2058
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) Dsui_0626 Dsui_2057
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase Dsui_0437 Dsui_0105
davT 5-aminovalerate aminotransferase Dsui_3250 Dsui_0023
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Dsui_1378 Dsui_0323
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Dsui_0318 Dsui_2330
gabD succinate semialdehyde dehydrogenase Dsui_0437 Dsui_0105
gabT gamma-aminobutyrate transaminase Dsui_3250 Dsui_0023
gbamidase guanidinobutyramidase
gbuA guanidinobutyrase
gcdG succinyl-CoA:glutarate CoA-transferase Dsui_0037 Dsui_1115
gcdH glutaryl-CoA dehydrogenase Dsui_3369 Dsui_0977
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase Dsui_1464 Dsui_0437
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) Dsui_2329
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase Dsui_1245
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) Dsui_3250 Dsui_0023
patD gamma-aminobutyraldehyde dehydrogenase Dsui_0105 Dsui_1464
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 Dsui_0602
puo putrescine oxidase
put1 proline dehydrogenase
putA L-glutamate 5-semialdeyde dehydrogenase Dsui_0437 Dsui_1464
puuA glutamate-putrescine ligase Dsui_1048
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase Dsui_1464 Dsui_0105
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase Dsui_3391 Dsui_3244
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 17 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 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, the preprint on GapMind for carbon sources, 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