GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Pseudomonas baetica a390

Best path

artJ, artM, artP, artQ, arcA, arcB, arcC, aruF, aruG, astC, astD, astE

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 (52 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 C0J26_RS10590 C0J26_RS01690
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) C0J26_RS10600 C0J26_RS01680
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA C0J26_RS10610 C0J26_RS01695
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) C0J26_RS10595 C0J26_RS01685
arcA arginine deiminase C0J26_RS20820
arcB ornithine carbamoyltransferase C0J26_RS20830 C0J26_RS21570
arcC carbamate kinase C0J26_RS20835
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) C0J26_RS10635 C0J26_RS16245
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) C0J26_RS10640 C0J26_RS16250
astC succinylornithine transaminase C0J26_RS10630 C0J26_RS22150
astD succinylglutamate semialdehyde dehydrogenase C0J26_RS10645 C0J26_RS15895
astE succinylglutamate desuccinylase C0J26_RS10660
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) C0J26_RS03830 C0J26_RS12010
aguA agmatine deiminase C0J26_RS01545 C0J26_RS11815
aguB N-carbamoylputrescine hydrolase C0J26_RS22475 C0J26_RS02700
arg-monooxygenase arginine 2-monooxygenase C0J26_RS02705
aroD L-arginine oxidase
aruH L-arginine:pyruvate transaminase C0J26_RS15065 C0J26_RS21910
aruI 2-ketoarginine decarboxylase C0J26_RS21290
astA arginine N-succinyltransferase C0J26_RS10640 C0J26_RS16250
astB N-succinylarginine dihydrolase C0J26_RS10650
atoB acetyl-CoA C-acetyltransferase C0J26_RS15230 C0J26_RS16155
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 C0J26_RS09040
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) C0J26_RS09035
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) C0J26_RS09030
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) C0J26_RS09025 C0J26_RS03610
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) C0J26_RS09020 C0J26_RS03600
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase C0J26_RS01025 C0J26_RS12950
davT 5-aminovalerate aminotransferase C0J26_RS01030 C0J26_RS25540
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase C0J26_RS15240 C0J26_RS25285
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase C0J26_RS25285 C0J26_RS22935
gabD succinate semialdehyde dehydrogenase C0J26_RS01025 C0J26_RS12640
gabT gamma-aminobutyrate transaminase C0J26_RS29440 C0J26_RS01030
gbamidase guanidinobutyramidase C0J26_RS02700 C0J26_RS21695
gbuA guanidinobutyrase C0J26_RS10240
gcdG succinyl-CoA:glutarate CoA-transferase C0J26_RS00750 C0J26_RS06235
gcdH glutaryl-CoA dehydrogenase C0J26_RS00745 C0J26_RS16985
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase C0J26_RS30270 C0J26_RS15895
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase C0J26_RS04915 C0J26_RS12010
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) C0J26_RS29440 C0J26_RS04130
patD gamma-aminobutyraldehyde dehydrogenase C0J26_RS30270 C0J26_RS15895
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 C0J26_RS29000
puo putrescine oxidase
put1 proline dehydrogenase C0J26_RS02535
putA L-glutamate 5-semialdeyde dehydrogenase C0J26_RS02535 C0J26_RS05085
puuA glutamate-putrescine ligase C0J26_RS29450 C0J26_RS15900
puuB gamma-glutamylputrescine oxidase C0J26_RS18685 C0J26_RS15890
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase C0J26_RS30270 C0J26_RS15895
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase C0J26_RS15905
rocA 1-pyrroline-5-carboxylate dehydrogenase C0J26_RS02535 C0J26_RS05085
rocD ornithine aminotransferase C0J26_RS22150 C0J26_RS01030
rocE L-arginine permease C0J26_RS21710 C0J26_RS01700
rocF arginase C0J26_RS10240
speB agmatinase C0J26_RS10240

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 24 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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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:

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