GapMind for catabolism of small carbon sources


L-arginine catabolism in Pseudomonas fluorescens GW456-L13

Best path

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

Also see fitness data for the top candidates


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 PfGW456L13_1964 PfGW456L13_377
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) PfGW456L13_1966 PfGW456L13_3701
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA PfGW456L13_1967 PfGW456L13_376
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) PfGW456L13_1965 PfGW456L13_3700
arcA arginine deiminase PfGW456L13_1874
arcB ornithine carbamoyltransferase PfGW456L13_1873 PfGW456L13_1739
arcC carbamate kinase PfGW456L13_1872
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) PfGW456L13_1972 PfGW456L13_1973
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) PfGW456L13_1973 PfGW456L13_1972
astC succinylornithine transaminase PfGW456L13_1971 PfGW456L13_4910
astD succinylglutamate semialdehyde dehydrogenase PfGW456L13_1974 PfGW456L13_3205
astE succinylglutamate desuccinylase PfGW456L13_1977
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) PfGW456L13_43 PfGW456L13_3776
aguA agmatine deiminase PfGW456L13_397 PfGW456L13_3370
aguB N-carbamoylputrescine hydrolase PfGW456L13_2704 PfGW456L13_2675
arg-monooxygenase arginine 2-monooxygenase PfGW456L13_1171
aroD L-arginine oxidase
aruH L-arginine:pyruvate transaminase PfGW456L13_3206 PfGW456L13_2943
aruI 2-ketoarginine decarboxylase PfGW456L13_3207 PfGW456L13_1794
astA arginine N-succinyltransferase PfGW456L13_1973 PfGW456L13_1972
astB N-succinylarginine dihydrolase PfGW456L13_1975
atoB acetyl-CoA C-acetyltransferase PfGW456L13_2411 PfGW456L13_2982
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 PfGW456L13_124 PfGW456L13_4606
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) PfGW456L13_123 PfGW456L13_4608
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) PfGW456L13_4609 PfGW456L13_122
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) PfGW456L13_121 PfGW456L13_4610
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) PfGW456L13_120 PfGW456L13_4611
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase PfGW456L13_495 PfGW456L13_3737
davT 5-aminovalerate aminotransferase PfGW456L13_494 PfGW456L13_4982
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase PfGW456L13_2984 PfGW456L13_2434
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase PfGW456L13_4041 PfGW456L13_3873
gabD succinate semialdehyde dehydrogenase PfGW456L13_495 PfGW456L13_3880
gabT gamma-aminobutyrate transaminase PfGW456L13_927 PfGW456L13_1398
gbamidase guanidinobutyramidase PfGW456L13_1170 PfGW456L13_4783
gbuA guanidinobutyrase PfGW456L13_4435 PfGW456L13_2989
gcdG succinyl-CoA:glutarate CoA-transferase PfGW456L13_553 PfGW456L13_3635
gcdH glutaryl-CoA dehydrogenase PfGW456L13_554 PfGW456L13_2591
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase PfGW456L13_805 PfGW456L13_1397
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase PfGW456L13_5067 PfGW456L13_3336
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) PfGW456L13_927 PfGW456L13_1398
patD gamma-aminobutyraldehyde dehydrogenase PfGW456L13_4766 PfGW456L13_4760
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase PfGW456L13_3147 PfGW456L13_3583
PRO3 pyrroline-5-carboxylate reductase PfGW456L13_1010
puo putrescine oxidase PfGW456L13_2439
put1 proline dehydrogenase PfGW456L13_223
putA L-glutamate 5-semialdeyde dehydrogenase PfGW456L13_223 PfGW456L13_5044
puuA glutamate-putrescine ligase PfGW456L13_925 PfGW456L13_926
puuB gamma-glutamylputrescine oxidase PfGW456L13_3923 PfGW456L13_809
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PfGW456L13_805 PfGW456L13_1397
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase PfGW456L13_223 PfGW456L13_5044
rocD ornithine aminotransferase PfGW456L13_4910 PfGW456L13_494
rocE L-arginine permease PfGW456L13_3211 PfGW456L13_4790
rocF arginase PfGW456L13_4435 PfGW456L13_2689
speB agmatinase PfGW456L13_2989 PfGW456L13_2689

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.



Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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