GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Paraburkholderia bryophila 376MFSha3.1

Best path

artJ, artM, artP, artQ, astA, astB, astC, astD, astE

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 (50 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 H281DRAFT_06484 H281DRAFT_00224
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) H281DRAFT_06475 H281DRAFT_00222
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA H281DRAFT_06476 H281DRAFT_00221
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) H281DRAFT_06474 H281DRAFT_00223
astA arginine N-succinyltransferase H281DRAFT_06479 H281DRAFT_06480
astB N-succinylarginine dihydrolase H281DRAFT_06482
astC succinylornithine transaminase H281DRAFT_06478 H281DRAFT_04057
astD succinylglutamate semialdehyde dehydrogenase H281DRAFT_06481 H281DRAFT_00213
astE succinylglutamate desuccinylase H281DRAFT_06483
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) H281DRAFT_00160
aguA agmatine deiminase
aguB N-carbamoylputrescine hydrolase H281DRAFT_05434
arcA arginine deiminase
arcB ornithine carbamoyltransferase H281DRAFT_04119 H281DRAFT_01493
arcC carbamate kinase
arg-monooxygenase arginine 2-monooxygenase
aroD L-arginine oxidase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) H281DRAFT_06479 H281DRAFT_06480
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) H281DRAFT_06480 H281DRAFT_06479
aruH L-arginine:pyruvate transaminase H281DRAFT_02907 H281DRAFT_05564
aruI 2-ketoarginine decarboxylase H281DRAFT_03007
atoB acetyl-CoA C-acetyltransferase H281DRAFT_00852 H281DRAFT_00857
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 H281DRAFT_02405 H281DRAFT_01194
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) H281DRAFT_04062 H281DRAFT_02378
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) H281DRAFT_04061 H281DRAFT_05513
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) H281DRAFT_04060 H281DRAFT_02383
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) H281DRAFT_04059 H281DRAFT_02384
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1 H281DRAFT_02180
davD glutarate semialdehyde dehydrogenase H281DRAFT_03178 H281DRAFT_03540
davT 5-aminovalerate aminotransferase H281DRAFT_03179 H281DRAFT_06478
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase H281DRAFT_05725 H281DRAFT_02514
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase H281DRAFT_00361 H281DRAFT_04625
gabD succinate semialdehyde dehydrogenase H281DRAFT_01155 H281DRAFT_03540
gabT gamma-aminobutyrate transaminase H281DRAFT_01082 H281DRAFT_03179
gbamidase guanidinobutyramidase
gbuA guanidinobutyrase H281DRAFT_00178
gcdG succinyl-CoA:glutarate CoA-transferase H281DRAFT_04444 H281DRAFT_01169
gcdH glutaryl-CoA dehydrogenase H281DRAFT_04737 H281DRAFT_01204
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase H281DRAFT_00993 H281DRAFT_03016
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) H281DRAFT_02167
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase H281DRAFT_00160
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) H281DRAFT_01082 H281DRAFT_06342
patD gamma-aminobutyraldehyde dehydrogenase H281DRAFT_02464 H281DRAFT_00993
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase H281DRAFT_01193
PRO3 pyrroline-5-carboxylate reductase H281DRAFT_04679
puo putrescine oxidase
put1 proline dehydrogenase H281DRAFT_02404 H281DRAFT_06542
putA L-glutamate 5-semialdeyde dehydrogenase H281DRAFT_02404 H281DRAFT_03016
puuA glutamate-putrescine ligase H281DRAFT_01081 H281DRAFT_00452
puuB gamma-glutamylputrescine oxidase H281DRAFT_03219 H281DRAFT_06337
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase H281DRAFT_00993 H281DRAFT_03016
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase H281DRAFT_01080 H281DRAFT_03954
rocA 1-pyrroline-5-carboxylate dehydrogenase H281DRAFT_02404 H281DRAFT_03016
rocD ornithine aminotransferase H281DRAFT_03179 H281DRAFT_06478
rocE L-arginine permease H281DRAFT_04042 H281DRAFT_01668
rocF arginase H281DRAFT_00178
speB agmatinase H281DRAFT_00178

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, 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