GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Dokdonella koreensis DS-123

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 (33 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rocE L-arginine permease
rocF arginase I596_RS13740
rocD ornithine aminotransferase I596_RS12880 I596_RS03965
PRO3 pyrroline-5-carboxylate reductase I596_RS03265
put1 proline dehydrogenase I596_RS14475
putA L-glutamate 5-semialdeyde dehydrogenase I596_RS14475 I596_RS04140
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) I596_RS16195
aguA agmatine deiminase I596_RS09405
aguB N-carbamoylputrescine hydrolase I596_RS08295
arcA arginine deiminase
arcB ornithine carbamoyltransferase I596_RS10160 I596_RS03730
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)
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA I596_RS09325 I596_RS10410
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 I596_RS06770 I596_RS17735
aruI 2-ketoarginine decarboxylase
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase I596_RS03960 I596_RS12880
astD succinylglutamate semialdehyde dehydrogenase I596_RS02225 I596_RS04570
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase I596_RS05370 I596_RS06325
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)
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) I596_RS06835
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) I596_RS07805 I596_RS14770
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1 I596_RS08865 I596_RS16250
davD glutarate semialdehyde dehydrogenase I596_RS02225 I596_RS04140
davT 5-aminovalerate aminotransferase I596_RS03960 I596_RS12880
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase I596_RS12940 I596_RS02240
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase I596_RS06330 I596_RS02240
gabD succinate semialdehyde dehydrogenase I596_RS04570 I596_RS02225
gabT gamma-aminobutyrate transaminase I596_RS12880 I596_RS03960
gbamidase guanidinobutyramidase I596_RS09485
gbuA guanidinobutyrase
gcdG succinyl-CoA:glutarate CoA-transferase I596_RS10325
gcdH glutaryl-CoA dehydrogenase I596_RS15145 I596_RS15670
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase I596_RS04570 I596_RS02225
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase
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) I596_RS12880 I596_RS03960
patD gamma-aminobutyraldehyde dehydrogenase I596_RS04570 I596_RS02225
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 I596_RS17215
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase I596_RS04570 I596_RS02225
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase I596_RS03770
rocA 1-pyrroline-5-carboxylate dehydrogenase I596_RS14475 I596_RS04140
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 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