GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Dinoroseobacter shibae DFL-12

Best path

artJ, artM, artP, artQ, arcA, arcB, arcC, ocd, 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 (43 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
artJ L-arginine ABC transporter, periplasmic substrate-binding component ArtJ/HisJ/ArtI/AotJ/ArgT Dshi_2222
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) Dshi_2224 Dshi_0320
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA Dshi_2221 Dshi_0321
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) Dshi_2223 Dshi_2224
arcA arginine deiminase Dshi_0432
arcB ornithine carbamoyltransferase Dshi_0433 Dshi_0796
arcC carbamate kinase Dshi_0434
ocd ornithine cyclodeaminase Dshi_2310 Dshi_0890
put1 proline dehydrogenase Dshi_2311
putA L-glutamate 5-semialdeyde dehydrogenase Dshi_2311 Dshi_0577
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA)
aguA agmatine deiminase
aguB N-carbamoylputrescine hydrolase
arg-monooxygenase arginine 2-monooxygenase
aroD L-arginine oxidase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH L-arginine:pyruvate transaminase Dshi_0762 Dshi_1168
aruI 2-ketoarginine decarboxylase Dshi_3840
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase Dshi_0798 Dshi_1446
astD succinylglutamate semialdehyde dehydrogenase Dshi_1425 Dshi_0577
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase Dshi_3066 Dshi_3331
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) Dshi_3725 Dshi_0861
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) Dshi_0379
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) Dshi_0375 Dshi_3727
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) Dshi_0381 Dshi_1400
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase Dshi_2887 Dshi_0577
davT 5-aminovalerate aminotransferase Dshi_1446 Dshi_0798
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Dshi_3370 Dshi_0835
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Dshi_3826 Dshi_0835
gabD succinate semialdehyde dehydrogenase Dshi_2887 Dshi_1430
gabT gamma-aminobutyrate transaminase Dshi_1366 Dshi_2042
gbamidase guanidinobutyramidase Dshi_3506
gbuA guanidinobutyrase Dshi_1735
gcdG succinyl-CoA:glutarate CoA-transferase Dshi_3269 Dshi_1057
gcdH glutaryl-CoA dehydrogenase Dshi_2357 Dshi_1297
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase Dshi_3017 Dshi_1095
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
odc L-ornithine decarboxylase Dshi_1375
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 Dshi_2298
ortA 2-amino-4-oxopentanoate thiolase, alpha subunit
ortB 2-amino-4-oxopentanoate thiolase, beta subunit
patA putrescine aminotransferase (PatA/SpuC) Dshi_1366 Dshi_2042
patD gamma-aminobutyraldehyde dehydrogenase Dshi_1095 Dshi_3017
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 Dshi_2645
puo putrescine oxidase
puuA glutamate-putrescine ligase Dshi_2226 Dshi_1839
puuB gamma-glutamylputrescine oxidase Dshi_2227
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase Dshi_1430 Dshi_3017
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase Dshi_1229 Dshi_3925
rocA 1-pyrroline-5-carboxylate dehydrogenase Dshi_2311 Dshi_0577
rocD ornithine aminotransferase Dshi_2042 Dshi_1366
rocE L-arginine permease
rocF arginase Dshi_2309
speB agmatinase Dshi_1735

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