GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Photobacterium jeanii R-40508

Best path

artJ, artM, artP, artQ, astA, astB, 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 (41 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 A3K86_RS01795 A3K86_RS13005
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) A3K86_RS01785 A3K86_RS13015
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA A3K86_RS13000 A3K86_RS01800
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) A3K86_RS13010 A3K86_RS01790
astA arginine N-succinyltransferase A3K86_RS09060
astB N-succinylarginine dihydrolase A3K86_RS19400
astC succinylornithine transaminase A3K86_RS09055 A3K86_RS14790
astD succinylglutamate semialdehyde dehydrogenase A3K86_RS09065 A3K86_RS19720
astE succinylglutamate desuccinylase A3K86_RS04085
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) A3K86_RS05720
aguA agmatine deiminase A3K86_RS18230
aguB N-carbamoylputrescine hydrolase
arcA arginine deiminase A3K86_RS01400
arcB ornithine carbamoyltransferase A3K86_RS01390 A3K86_RS18210
arcC carbamate kinase A3K86_RS18220 A3K86_RS01395
arg-monooxygenase arginine 2-monooxygenase
aroD L-arginine oxidase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) A3K86_RS09060
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) A3K86_RS09060
aruH L-arginine:pyruvate transaminase
aruI 2-ketoarginine decarboxylase A3K86_RS01190
atoB acetyl-CoA C-acetyltransferase A3K86_RS19875 A3K86_RS15935
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)
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) A3K86_RS19745
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) A3K86_RS04635 A3K86_RS13000
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase A3K86_RS14375 A3K86_RS19720
davT 5-aminovalerate aminotransferase A3K86_RS09055 A3K86_RS14790
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase A3K86_RS15920 A3K86_RS17390
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase A3K86_RS17390 A3K86_RS06710
gabD succinate semialdehyde dehydrogenase A3K86_RS14375 A3K86_RS19720
gabT gamma-aminobutyrate transaminase A3K86_RS09055 A3K86_RS14790
gbamidase guanidinobutyramidase
gbuA guanidinobutyrase A3K86_RS05725
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase A3K86_RS15945 A3K86_RS15925
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase A3K86_RS19720 A3K86_RS14375
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
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 A3K86_RS13045
ortA 2-amino-4-oxopentanoate thiolase, alpha subunit
ortB 2-amino-4-oxopentanoate thiolase, beta subunit
patA putrescine aminotransferase (PatA/SpuC) A3K86_RS09055 A3K86_RS14790
patD gamma-aminobutyraldehyde dehydrogenase A3K86_RS19720 A3K86_RS14375
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 A3K86_RS00145
puo putrescine oxidase
put1 proline dehydrogenase A3K86_RS18285
putA L-glutamate 5-semialdeyde dehydrogenase A3K86_RS18285 A3K86_RS19720
puuA glutamate-putrescine ligase A3K86_RS00765
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase A3K86_RS19720 A3K86_RS14375
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase A3K86_RS18285 A3K86_RS19720
rocD ornithine aminotransferase A3K86_RS14790 A3K86_RS04565
rocE L-arginine permease
rocF arginase A3K86_RS05725
speB agmatinase A3K86_RS05725

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