GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Echinicola vietnamensis KMM 6221, DSM 17526

Best path

rocE, rocF, rocD, PRO3, put1, putA

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 (33 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rocE L-arginine permease
rocF arginase Echvi_2468
rocD ornithine aminotransferase Echvi_0577 Echvi_2919
PRO3 pyrroline-5-carboxylate reductase Echvi_2635 Echvi_2479
put1 proline dehydrogenase Echvi_0119
putA L-glutamate 5-semialdeyde dehydrogenase Echvi_1300 Echvi_0481
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA)
aguA agmatine deiminase
aguB N-carbamoylputrescine hydrolase
arcA arginine deiminase Echvi_0116
arcB ornithine carbamoyltransferase Echvi_4661 Echvi_3849
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 Echvi_4044 Echvi_2204
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 Echvi_0675
aruI 2-ketoarginine decarboxylase Echvi_2056
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase Echvi_3848 Echvi_0577
astD succinylglutamate semialdehyde dehydrogenase Echvi_0481
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase Echvi_3705 Echvi_1071
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) Echvi_1333
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) Echvi_1333 Echvi_2909
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase Echvi_0481 Echvi_3822
davT 5-aminovalerate aminotransferase Echvi_2919 Echvi_3848
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Echvi_4069 Echvi_0069
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Echvi_1069 Echvi_3304
gabD succinate semialdehyde dehydrogenase Echvi_3822 Echvi_0481
gabT gamma-aminobutyrate transaminase Echvi_2919 Echvi_2790
gbamidase guanidinobutyramidase
gbuA guanidinobutyrase Echvi_3131
gcdG succinyl-CoA:glutarate CoA-transferase Echvi_1686 Echvi_1687
gcdH glutaryl-CoA dehydrogenase Echvi_2990 Echvi_0738
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase Echvi_0481 Echvi_3822
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) Echvi_3348
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 Echvi_2799
ortA 2-amino-4-oxopentanoate thiolase, alpha subunit
ortB 2-amino-4-oxopentanoate thiolase, beta subunit
patA putrescine aminotransferase (PatA/SpuC) Echvi_2919 Echvi_0577
patD gamma-aminobutyraldehyde dehydrogenase Echvi_0481 Echvi_3822
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase Echvi_3951
puo putrescine oxidase
puuA glutamate-putrescine ligase
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase Echvi_0481 Echvi_3822
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase Echvi_1300 Echvi_0481
speB agmatinase Echvi_3131

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