GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Ochrobactrum thiophenivorans DSM 7216

Best path

braC, braD, braE, braF, braG, 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 (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 CEV31_RS03660 CEV31_RS03655
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) CEV31_RS03685 CEV31_RS13110
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) CEV31_RS03680 CEV31_RS13105
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) CEV31_RS03675 CEV31_RS14825
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) CEV31_RS03670 CEV31_RS14820
rocF arginase CEV31_RS02455 CEV31_RS10165
ocd ornithine cyclodeaminase CEV31_RS02450
put1 proline dehydrogenase CEV31_RS15250 CEV31_RS01735
putA L-glutamate 5-semialdeyde dehydrogenase CEV31_RS15250 CEV31_RS01730
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA)
aguA agmatine deiminase
aguB N-carbamoylputrescine hydrolase
arcA arginine deiminase
arcB ornithine carbamoyltransferase CEV31_RS07280 CEV31_RS16395
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 CEV31_RS11200 CEV31_RS14695
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) CEV31_RS20080 CEV31_RS11190
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA CEV31_RS19205 CEV31_RS18525
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) CEV31_RS11195 CEV31_RS20085
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH L-arginine:pyruvate transaminase CEV31_RS01885 CEV31_RS17370
aruI 2-ketoarginine decarboxylase
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase CEV31_RS07275 CEV31_RS17075
astD succinylglutamate semialdehyde dehydrogenase CEV31_RS17495 CEV31_RS18595
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase CEV31_RS03605 CEV31_RS02650
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 CEV31_RS02995 CEV31_RS17495
davT 5-aminovalerate aminotransferase CEV31_RS07275 CEV31_RS17075
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase CEV31_RS05620 CEV31_RS09090
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase CEV31_RS15760 CEV31_RS04315
gabD succinate semialdehyde dehydrogenase CEV31_RS02995 CEV31_RS17935
gabT gamma-aminobutyrate transaminase CEV31_RS17470 CEV31_RS19110
gbamidase guanidinobutyramidase CEV31_RS04230
gbuA guanidinobutyrase CEV31_RS10165
gcdG succinyl-CoA:glutarate CoA-transferase CEV31_RS11730 CEV31_RS09080
gcdH glutaryl-CoA dehydrogenase CEV31_RS11735 CEV31_RS05790
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase CEV31_RS06610 CEV31_RS16975
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) CEV31_RS17795 CEV31_RS18945
odc L-ornithine decarboxylase CEV31_RS13805
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) CEV31_RS19110 CEV31_RS17470
patD gamma-aminobutyraldehyde dehydrogenase CEV31_RS19025 CEV31_RS08350
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase CEV31_RS03690
PRO3 pyrroline-5-carboxylate reductase CEV31_RS15700
puo putrescine oxidase
puuA glutamate-putrescine ligase CEV31_RS15610 CEV31_RS09105
puuB gamma-glutamylputrescine oxidase CEV31_RS15615 CEV31_RS19040
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase CEV31_RS06610 CEV31_RS16975
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase CEV31_RS02805
rocA 1-pyrroline-5-carboxylate dehydrogenase CEV31_RS15250 CEV31_RS01730
rocD ornithine aminotransferase CEV31_RS17075 CEV31_RS17470
rocE L-arginine permease CEV31_RS18290 CEV31_RS20665
speB agmatinase CEV31_RS10165

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