GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Pseudomonas simiae WCS417

Best path

artJ, artM, artP, artQ, arcA, arcB, arcC, aruF, aruG, 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 (53 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 PS417_21745 PS417_01495
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) PS417_21735 PS417_01485
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA PS417_21725 PS417_01500
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) PS417_21740 PS417_01490
arcA arginine deiminase PS417_22330
arcB ornithine carbamoyltransferase PS417_22335 PS417_05595
arcC carbamate kinase PS417_22340
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) PS417_21705 PS417_21700
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) PS417_21700 PS417_21705
astC succinylornithine transaminase PS417_21710 PS417_08025
astD succinylglutamate semialdehyde dehydrogenase PS417_21695 PS417_04200
astE succinylglutamate desuccinylase PS417_21680
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) PS417_03005 PS417_12240
aguA agmatine deiminase PS417_01340
aguB N-carbamoylputrescine hydrolase PS417_10630 PS417_25915
arg-monooxygenase arginine 2-monooxygenase PS417_25910
aroD L-arginine oxidase
aruH L-arginine:pyruvate transaminase PS417_13545 PS417_19025
aruI 2-ketoarginine decarboxylase PS417_10695 PS417_07295
astA arginine N-succinyltransferase PS417_21700 PS417_21705
astB N-succinylarginine dihydrolase PS417_21690
atoB acetyl-CoA C-acetyltransferase PS417_10515 PS417_13855
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 PS417_02655 PS417_06615
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) PS417_02660 PS417_06610
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) PS417_06605 PS417_02665
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) PS417_02670 PS417_06600
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) PS417_02675 PS417_06595
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase PS417_00895 PS417_17840
davT 5-aminovalerate aminotransferase PS417_00900 PS417_23355
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase PS417_13845 PS417_07575
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase PS417_07575 PS417_21215
gabD succinate semialdehyde dehydrogenase PS417_00895 PS417_18705
gabT gamma-aminobutyrate transaminase PS417_27130 PS417_00900
gbamidase guanidinobutyramidase PS417_25915 PS417_10630
gbuA guanidinobutyrase PS417_20180
gcdG succinyl-CoA:glutarate CoA-transferase PS417_00585 PS417_14920
gcdH glutaryl-CoA dehydrogenase PS417_00580 PS417_17015
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase PS417_27745 PS417_26340
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
ocd ornithine cyclodeaminase PS417_17585
odc L-ornithine decarboxylase PS417_04005 PS417_12240
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) PS417_27130 PS417_11165
patD gamma-aminobutyraldehyde dehydrogenase PS417_05920 PS417_05945
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase PS417_14305
PRO3 pyrroline-5-carboxylate reductase PS417_26730
puo putrescine oxidase
put1 proline dehydrogenase PS417_02175
putA L-glutamate 5-semialdeyde dehydrogenase PS417_02175 PS417_04200
puuA glutamate-putrescine ligase PS417_27140 PS417_27135
puuB gamma-glutamylputrescine oxidase PS417_18505 PS417_27720
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PS417_27745 PS417_26340
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase PS417_02175 PS417_04200
rocD ornithine aminotransferase PS417_08025 PS417_00900
rocE L-arginine permease PS417_05405 PS417_23645
rocF arginase PS417_20180
speB agmatinase PS417_20180

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