GapMind for catabolism of small carbon sources


L-arginine catabolism in Burkholderia phytofirmans PsJN

Best path

artJ, artM, artP, artQ, astA, astB, 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 (54 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 BPHYT_RS07735 BPHYT_RS00160
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) BPHYT_RS07680 BPHYT_RS05500
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA BPHYT_RS07685 BPHYT_RS05495
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) BPHYT_RS07675 BPHYT_RS05505
astA arginine N-succinyltransferase BPHYT_RS07700 BPHYT_RS07705
astB N-succinylarginine dihydrolase BPHYT_RS07715
astC succinylornithine transaminase BPHYT_RS07695 BPHYT_RS15580
astD succinylglutamate semialdehyde dehydrogenase BPHYT_RS07710 BPHYT_RS25810
astE succinylglutamate desuccinylase BPHYT_RS07720
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) BPHYT_RS04980
aguA agmatine deiminase
aguB N-carbamoylputrescine hydrolase BPHYT_RS00250
arcA arginine deiminase BPHYT_RS27680
arcB ornithine carbamoyltransferase BPHYT_RS27685 BPHYT_RS15915
arcC carbamate kinase BPHYT_RS27690
arg-monooxygenase arginine 2-monooxygenase
aroD L-arginine oxidase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) BPHYT_RS07700 BPHYT_RS07705
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) BPHYT_RS07705 BPHYT_RS07700
aruH L-arginine:pyruvate transaminase BPHYT_RS27000 BPHYT_RS15405
aruI 2-ketoarginine decarboxylase BPHYT_RS21705
atoB acetyl-CoA C-acetyltransferase BPHYT_RS09150 BPHYT_RS09180
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 BPHYT_RS31715 BPHYT_RS19350
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) BPHYT_RS15605 BPHYT_RS31740
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) BPHYT_RS31745 BPHYT_RS15600
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) BPHYT_RS15595 BPHYT_RS31750
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) BPHYT_RS15590 BPHYT_RS31755
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1 BPHYT_RS33230 BPHYT_RS01785
davD glutarate semialdehyde dehydrogenase BPHYT_RS22430 BPHYT_RS34305
davT 5-aminovalerate aminotransferase BPHYT_RS22435 BPHYT_RS07695
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BPHYT_RS17335 BPHYT_RS28020
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BPHYT_RS13545 BPHYT_RS03225
gabD succinate semialdehyde dehydrogenase BPHYT_RS10925 BPHYT_RS34305
gabT gamma-aminobutyrate transaminase BPHYT_RS23155 BPHYT_RS22435
gbamidase guanidinobutyramidase BPHYT_RS00250
gbuA guanidinobutyrase BPHYT_RS05090 BPHYT_RS31515
gcdG succinyl-CoA:glutarate CoA-transferase BPHYT_RS13985 BPHYT_RS31850
gcdH glutaryl-CoA dehydrogenase BPHYT_RS03780 BPHYT_RS23260
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase BPHYT_RS23175 BPHYT_RS29875
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) BPHYT_RS28480 BPHYT_RS01855
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase BPHYT_RS04980 BPHYT_RS00645
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) BPHYT_RS23155 BPHYT_RS30220
patD gamma-aminobutyraldehyde dehydrogenase BPHYT_RS23175 BPHYT_RS25160
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase BPHYT_RS28265 BPHYT_RS22640
PRO3 pyrroline-5-carboxylate reductase BPHYT_RS03490
puo putrescine oxidase BPHYT_RS09910
put1 proline dehydrogenase BPHYT_RS19355 BPHYT_RS29290
putA L-glutamate 5-semialdeyde dehydrogenase BPHYT_RS19355 BPHYT_RS28770
puuA glutamate-putrescine ligase BPHYT_RS23160 BPHYT_RS09955
puuB gamma-glutamylputrescine oxidase BPHYT_RS23125 BPHYT_RS23120
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase BPHYT_RS23175 BPHYT_RS29875
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase BPHYT_RS23165 BPHYT_RS15045
rocA 1-pyrroline-5-carboxylate dehydrogenase BPHYT_RS19355 BPHYT_RS28770
rocD ornithine aminotransferase BPHYT_RS22435 BPHYT_RS10155
rocE L-arginine permease BPHYT_RS15500 BPHYT_RS21680
rocF arginase BPHYT_RS05090 BPHYT_RS31515
speB agmatinase BPHYT_RS26640 BPHYT_RS05090

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:

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