GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Methylocystis bryophila S285

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 (31 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rocE L-arginine permease
rocF arginase
rocD ornithine aminotransferase B1812_RS09075 B1812_RS21480
PRO3 pyrroline-5-carboxylate reductase B1812_RS21170
put1 proline dehydrogenase B1812_RS02885
putA L-glutamate 5-semialdeyde dehydrogenase B1812_RS02885 B1812_RS01610
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) B1812_RS12020
aguA agmatine deiminase
aguB N-carbamoylputrescine hydrolase
arcA arginine deiminase
arcB ornithine carbamoyltransferase B1812_RS12410 B1812_RS05295
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 B1812_RS01090
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM)
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA B1812_RS07310 B1812_RS18275
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ)
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH L-arginine:pyruvate transaminase B1812_RS18690 B1812_RS20525
aruI 2-ketoarginine decarboxylase B1812_RS19855 B1812_RS19550
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase B1812_RS12405 B1812_RS09075
astD succinylglutamate semialdehyde dehydrogenase B1812_RS13395 B1812_RS02885
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase B1812_RS02620 B1812_RS16320
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) B1812_RS04370
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) B1812_RS04380 B1812_RS12645
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) B1812_RS04360 B1812_RS12645
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1 B1812_RS04230 B1812_RS03615
davD glutarate semialdehyde dehydrogenase B1812_RS10880 B1812_RS13395
davT 5-aminovalerate aminotransferase B1812_RS21480 B1812_RS12405
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase B1812_RS05255 B1812_RS13170
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase B1812_RS19300 B1812_RS13170
gabD succinate semialdehyde dehydrogenase B1812_RS10880 B1812_RS13395
gabT gamma-aminobutyrate transaminase B1812_RS09075 B1812_RS21480
gbamidase guanidinobutyramidase
gbuA guanidinobutyrase
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase B1812_RS16285 B1812_RS14765
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase B1812_RS13395 B1812_RS07050
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) B1812_RS08345 B1812_RS21390
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase B1812_RS12020 B1812_RS06935
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) B1812_RS19660 B1812_RS09075
patD gamma-aminobutyraldehyde dehydrogenase B1812_RS13395 B1812_RS07050
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
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase B1812_RS13395 B1812_RS07050
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase B1812_RS02885 B1812_RS01610
speB agmatinase

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