GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Xanthobacter autotrophicus Py2

Best path

braC, braD, braE, braF, braG, adiA, speB, 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 (43 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 XAUT_RS19760 XAUT_RS07820
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) XAUT_RS19735 XAUT_RS03235
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) XAUT_RS19740 XAUT_RS20495
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) XAUT_RS19745 XAUT_RS25540
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) XAUT_RS19750 XAUT_RS03220
adiA arginine decarboxylase (AdiA/SpeA) XAUT_RS03215
speB agmatinase XAUT_RS17610
patA putrescine aminotransferase (PatA/SpuC) XAUT_RS13720 XAUT_RS11560
patD gamma-aminobutyraldehyde dehydrogenase XAUT_RS13710 XAUT_RS01855
gabT gamma-aminobutyrate transaminase XAUT_RS21405 XAUT_RS13720
gabD succinate semialdehyde dehydrogenase XAUT_RS16460 XAUT_RS13655
Alternative steps:
AAP3 L-arginine transporter AAP3
aguA agmatine deiminase
aguB N-carbamoylputrescine hydrolase
arcA arginine deiminase
arcB ornithine carbamoyltransferase XAUT_RS06115 XAUT_RS19830
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 XAUT_RS11985
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) XAUT_RS10435 XAUT_RS12260
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA XAUT_RS08010 XAUT_RS10445
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) XAUT_RS08015 XAUT_RS10440
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH L-arginine:pyruvate transaminase XAUT_RS02030 XAUT_RS13770
aruI 2-ketoarginine decarboxylase XAUT_RS14070
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase XAUT_RS06110 XAUT_RS21405
astD succinylglutamate semialdehyde dehydrogenase XAUT_RS16460 XAUT_RS06795
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase XAUT_RS23630 XAUT_RS15615
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 XAUT_RS16460 XAUT_RS13655
davT 5-aminovalerate aminotransferase XAUT_RS21405 XAUT_RS06110
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase XAUT_RS16635 XAUT_RS04570
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase XAUT_RS04535 XAUT_RS04610
gbamidase guanidinobutyramidase XAUT_RS15515
gbuA guanidinobutyrase XAUT_RS17610
gcdG succinyl-CoA:glutarate CoA-transferase XAUT_RS23885 XAUT_RS06250
gcdH glutaryl-CoA dehydrogenase XAUT_RS23880 XAUT_RS21625
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase XAUT_RS13710 XAUT_RS01855
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) XAUT_RS14090
ocd ornithine cyclodeaminase XAUT_RS17685
odc L-ornithine decarboxylase XAUT_RS03215 XAUT_RS13750
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 XAUT_RS12780
puo putrescine oxidase
put1 proline dehydrogenase XAUT_RS17390 XAUT_RS04350
putA L-glutamate 5-semialdeyde dehydrogenase XAUT_RS17390 XAUT_RS13655
puuA glutamate-putrescine ligase XAUT_RS09760 XAUT_RS11750
puuB gamma-glutamylputrescine oxidase XAUT_RS09765 XAUT_RS12125
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase XAUT_RS13710 XAUT_RS01855
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase XAUT_RS28200
rocA 1-pyrroline-5-carboxylate dehydrogenase XAUT_RS17390 XAUT_RS13655
rocD ornithine aminotransferase XAUT_RS05230 XAUT_RS21405
rocE L-arginine permease
rocF arginase XAUT_RS17610

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 Apr 09 2024. 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