GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Flavobacterium ummariense DS-12

Best path

rocE, rocF, rocD, rocA

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 (26 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rocE L-arginine permease BM253_RS06410
rocF arginase
rocD ornithine aminotransferase BM253_RS04065 BM253_RS04610
rocA 1-pyrroline-5-carboxylate dehydrogenase BM253_RS09455 BM253_RS15450
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 BM253_RS14640
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 BM253_RS02520 BM253_RS12820
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 BM253_RS07965
aruI 2-ketoarginine decarboxylase
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase BM253_RS04065 BM253_RS04610
astD succinylglutamate semialdehyde dehydrogenase BM253_RS02660 BM253_RS15450
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase BM253_RS12775 BM253_RS15640
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)
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) BM253_RS06735
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1 BM253_RS05795
davD glutarate semialdehyde dehydrogenase BM253_RS15450 BM253_RS02725
davT 5-aminovalerate aminotransferase BM253_RS04610 BM253_RS04065
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BM253_RS01100 BM253_RS15650
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BM253_RS15650 BM253_RS03300
gabD succinate semialdehyde dehydrogenase BM253_RS02725 BM253_RS15450
gabT gamma-aminobutyrate transaminase BM253_RS04610 BM253_RS08990
gbamidase guanidinobutyramidase
gbuA guanidinobutyrase
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase BM253_RS00785 BM253_RS12625
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase BM253_RS15450
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 BM253_RS00405
ortA 2-amino-4-oxopentanoate thiolase, alpha subunit
ortB 2-amino-4-oxopentanoate thiolase, beta subunit
patA putrescine aminotransferase (PatA/SpuC) BM253_RS04610 BM253_RS04065
patD gamma-aminobutyraldehyde dehydrogenase BM253_RS15450 BM253_RS02660
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
puo putrescine oxidase
put1 proline dehydrogenase BM253_RS14675
putA L-glutamate 5-semialdeyde dehydrogenase BM253_RS09455 BM253_RS15450
puuA glutamate-putrescine ligase
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase BM253_RS15450
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
speB agmatinase BM253_RS14275

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