GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Brucella inopinata BO1

Best path

braC, braD, braE, braF, braG, rocF, ocd, 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 (44 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC BIBO1_RS12225 BIBO1_RS12220
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) BIBO1_RS12250 BIBO1_RS14975
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) BIBO1_RS12245
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) BIBO1_RS12240 BIBO1_RS19765
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) BIBO1_RS12235 BIBO1_RS14990
rocF arginase BIBO1_RS18720 BIBO1_RS07375
ocd ornithine cyclodeaminase BIBO1_RS18715
put1 proline dehydrogenase BIBO1_RS16940 BIBO1_RS12740
putA L-glutamate 5-semialdeyde dehydrogenase BIBO1_RS16940 BIBO1_RS10860
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA)
aguA agmatine deiminase
aguB N-carbamoylputrescine hydrolase
arcA arginine deiminase
arcB ornithine carbamoyltransferase BIBO1_RS13060 BIBO1_RS17780
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 BIBO1_RS07950 BIBO1_RS09035
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) BIBO1_RS07940 BIBO1_RS17105
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA BIBO1_RS07180 BIBO1_RS20000
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) BIBO1_RS07945 BIBO1_RS14880
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH L-arginine:pyruvate transaminase BIBO1_RS11000
aruI 2-ketoarginine decarboxylase BIBO1_RS18945
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase BIBO1_RS13055 BIBO1_RS18510
astD succinylglutamate semialdehyde dehydrogenase BIBO1_RS17145 BIBO1_RS10860
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase BIBO1_RS17190 BIBO1_RS16830
bgtB L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase BIBO1_RS11605 BIBO1_RS17145
davT 5-aminovalerate aminotransferase BIBO1_RS13055 BIBO1_RS18510
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BIBO1_RS06755 BIBO1_RS15870
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BIBO1_RS18180 BIBO1_RS05845
gabD succinate semialdehyde dehydrogenase BIBO1_RS11605 BIBO1_RS15485
gabT gamma-aminobutyrate transaminase BIBO1_RS10785 BIBO1_RS15460
gbamidase guanidinobutyramidase BIBO1_RS12585
gbuA guanidinobutyrase BIBO1_RS07375
gcdG succinyl-CoA:glutarate CoA-transferase BIBO1_RS15880 BIBO1_RS08425
gcdH glutaryl-CoA dehydrogenase BIBO1_RS08430 BIBO1_RS17185
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase BIBO1_RS15485 BIBO1_RS10835
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) BIBO1_RS19215
odc L-ornithine decarboxylase BIBO1_RS15590
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) BIBO1_RS10785 BIBO1_RS15460
patD gamma-aminobutyraldehyde dehydrogenase BIBO1_RS20005 BIBO1_RS14100
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase BIBO1_RS12255 BIBO1_RS13215
PRO3 pyrroline-5-carboxylate reductase BIBO1_RS18120 BIBO1_RS18355
puo putrescine oxidase
puuA glutamate-putrescine ligase BIBO1_RS18050 BIBO1_RS16895
puuB gamma-glutamylputrescine oxidase BIBO1_RS18060 BIBO1_RS19990
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase BIBO1_RS15485 BIBO1_RS10835
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase BIBO1_RS19105
rocA 1-pyrroline-5-carboxylate dehydrogenase BIBO1_RS16940 BIBO1_RS10860
rocD ornithine aminotransferase BIBO1_RS13055 BIBO1_RS10785
rocE L-arginine permease BIBO1_RS14845
speB agmatinase BIBO1_RS07375

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