GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Pontibacillus litoralis JSM 072002

Best path

rocE, rocF, rocD, PRO3, put1, putA

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 (35 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rocE L-arginine permease
rocF arginase N784_RS15520 N784_RS09645
rocD ornithine aminotransferase N784_RS05620 N784_RS03985
PRO3 pyrroline-5-carboxylate reductase N784_RS07295
put1 proline dehydrogenase N784_RS14090
putA L-glutamate 5-semialdeyde dehydrogenase N784_RS14095 N784_RS08305
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) N784_RS00060 N784_RS12385
aguA agmatine deiminase
aguB N-carbamoylputrescine hydrolase
arcA arginine deiminase
arcB ornithine carbamoyltransferase N784_RS06990 N784_RS03120
arcC carbamate kinase
arg-monooxygenase arginine 2-monooxygenase
aroD L-arginine oxidase
artJ L-arginine ABC transporter, periplasmic substrate-binding component ArtJ/HisJ/ArtI/AotJ/ArgT
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) N784_RS11720
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA N784_RS07340 N784_RS11605
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) N784_RS11720
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH L-arginine:pyruvate transaminase N784_RS04610 N784_RS08200
aruI 2-ketoarginine decarboxylase
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase N784_RS05620 N784_RS03985
astD succinylglutamate semialdehyde dehydrogenase N784_RS11405 N784_RS01660
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase N784_RS09620 N784_RS09270
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
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) N784_RS05545
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE)
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) N784_RS05555
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) N784_RS05550 N784_RS08100
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase N784_RS14395 N784_RS08305
davT 5-aminovalerate aminotransferase N784_RS03985 N784_RS05620
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase N784_RS08160 N784_RS16575
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase N784_RS11655 N784_RS09615
gabD succinate semialdehyde dehydrogenase N784_RS14395 N784_RS08305
gabT gamma-aminobutyrate transaminase N784_RS03985 N784_RS05620
gbamidase guanidinobutyramidase
gbuA guanidinobutyrase N784_RS09645
gcdG succinyl-CoA:glutarate CoA-transferase N784_RS08290 N784_RS11190
gcdH glutaryl-CoA dehydrogenase N784_RS09610 N784_RS08285
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD) N784_RS03970
kauB 4-guanidinobutyraldehyde dehydrogenase N784_RS05800 N784_RS14940
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) N784_RS03965
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase
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) N784_RS05620 N784_RS03985
patD gamma-aminobutyraldehyde dehydrogenase N784_RS08150 N784_RS14940
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase
puo putrescine oxidase
puuA glutamate-putrescine ligase N784_RS11240
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase N784_RS05800 N784_RS14940
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase N784_RS14095 N784_RS08305
speB agmatinase N784_RS09645

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