GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Azohydromonas australica DSM 1124

Best path

rocE, 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 (39 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rocE L-arginine permease
rocF arginase H537_RS0107490
ocd ornithine cyclodeaminase H537_RS0133445
put1 proline dehydrogenase H537_RS0124445 H537_RS44845
putA L-glutamate 5-semialdeyde dehydrogenase H537_RS0124445 H537_RS44845
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) H537_RS0110665
aguA agmatine deiminase
aguB N-carbamoylputrescine hydrolase
arcA arginine deiminase
arcB ornithine carbamoyltransferase H537_RS0120485 H537_RS0100960
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 H537_RS0108525
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) H537_RS0108530 H537_RS0104890
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA H537_RS0107725 H537_RS0128690
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) H537_RS0108530 H537_RS0107735
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH L-arginine:pyruvate transaminase H537_RS0108750 H537_RS0111980
aruI 2-ketoarginine decarboxylase H537_RS0111925 H537_RS0133840
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase H537_RS0137245 H537_RS0120480
astD succinylglutamate semialdehyde dehydrogenase H537_RS0110805 H537_RS0121615
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase H537_RS0122115 H537_RS0129600
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 H537_RS0112015 H537_RS0135945
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) H537_RS0121280 H537_RS0108425
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) H537_RS0121275 H537_RS0124590
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) H537_RS0124590 H537_RS0108415
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) H537_RS0121265 H537_RS0108410
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase H537_RS0138620 H537_RS0120085
davT 5-aminovalerate aminotransferase H537_RS0120050 H537_RS0137245
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase H537_RS0100790 H537_RS0111045
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase H537_RS0132195 H537_RS0116855
gabD succinate semialdehyde dehydrogenase H537_RS0101950 H537_RS0138620
gabT gamma-aminobutyrate transaminase H537_RS0136115 H537_RS0120050
gbamidase guanidinobutyramidase
gbuA guanidinobutyrase
gcdG succinyl-CoA:glutarate CoA-transferase H537_RS0123940 H537_RS44370
gcdH glutaryl-CoA dehydrogenase H537_RS0120055 H537_RS0115055
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase H537_RS0122420 H537_RS0136110
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) H537_RS0114715
odc L-ornithine decarboxylase H537_RS0110665
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) H537_RS0136115 H537_RS0136130
patD gamma-aminobutyraldehyde dehydrogenase H537_RS0136110 H537_RS0122420
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 H537_RS0134655
puo putrescine oxidase
puuA glutamate-putrescine ligase H537_RS0136120 H537_RS0125925
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase H537_RS0122420 H537_RS0136110
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase H537_RS0136125 H537_RS0129405
rocA 1-pyrroline-5-carboxylate dehydrogenase H537_RS0124445 H537_RS44845
rocD ornithine aminotransferase H537_RS0120050 H537_RS0137245
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