GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Belnapia rosea CPCC 100156

Best path

braC, braD, braE, braF, braG, rocF, odc, patA, patD, gabT, gabD

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
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC BLR02_RS12505
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) BLR02_RS12525 BLR02_RS10285
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) BLR02_RS12520 BLR02_RS10290
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) BLR02_RS12515 BLR02_RS03485
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) BLR02_RS12510 BLR02_RS10300
rocF arginase BLR02_RS05475
odc L-ornithine decarboxylase BLR02_RS01030
patA putrescine aminotransferase (PatA/SpuC) BLR02_RS05825 BLR02_RS13175
patD gamma-aminobutyraldehyde dehydrogenase BLR02_RS07320 BLR02_RS18460
gabT gamma-aminobutyrate transaminase BLR02_RS05825 BLR02_RS13175
gabD succinate semialdehyde dehydrogenase BLR02_RS07320 BLR02_RS18460
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) BLR02_RS07745
aguA agmatine deiminase
aguB N-carbamoylputrescine hydrolase
arcA arginine deiminase
arcB ornithine carbamoyltransferase BLR02_RS01295 BLR02_RS05695
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) BLR02_RS10410 BLR02_RS19475
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA BLR02_RS10420 BLR02_RS24955
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) BLR02_RS19475 BLR02_RS02405
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH L-arginine:pyruvate transaminase BLR02_RS01730 BLR02_RS01735
aruI 2-ketoarginine decarboxylase BLR02_RS08675 BLR02_RS16620
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase BLR02_RS01300 BLR02_RS12085
astD succinylglutamate semialdehyde dehydrogenase BLR02_RS07320 BLR02_RS18460
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase BLR02_RS13910 BLR02_RS06650
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 BLR02_RS07320 BLR02_RS18460
davT 5-aminovalerate aminotransferase BLR02_RS01300 BLR02_RS12085
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BLR02_RS23955 BLR02_RS03400
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BLR02_RS03400 BLR02_RS23340
gbamidase guanidinobutyramidase BLR02_RS09725
gbuA guanidinobutyrase BLR02_RS05475
gcdG succinyl-CoA:glutarate CoA-transferase BLR02_RS18395 BLR02_RS04245
gcdH glutaryl-CoA dehydrogenase BLR02_RS06730 BLR02_RS03525
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase BLR02_RS07320 BLR02_RS04250
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) BLR02_RS05550
ocd ornithine cyclodeaminase
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
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 BLR02_RS07535
puo putrescine oxidase
put1 proline dehydrogenase BLR02_RS10310 BLR02_RS16755
putA L-glutamate 5-semialdeyde dehydrogenase BLR02_RS07320 BLR02_RS04250
puuA glutamate-putrescine ligase BLR02_RS09735 BLR02_RS06830
puuB gamma-glutamylputrescine oxidase BLR02_RS14590 BLR02_RS23630
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase BLR02_RS07320 BLR02_RS04250
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase BLR02_RS22265 BLR02_RS09380
rocA 1-pyrroline-5-carboxylate dehydrogenase BLR02_RS07320 BLR02_RS04250
rocD ornithine aminotransferase BLR02_RS13175 BLR02_RS05825
rocE L-arginine permease
speB agmatinase BLR02_RS05475

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