GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Derxia gummosa DSM 723

Best path

braC, braD, braE, braF, braG, adiA, speB, puuA, puuB, puuC, puuD, gabT, gabD

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 (42 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 H566_RS0117030
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) H566_RS0102680 H566_RS0104990
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) H566_RS22525 H566_RS0104985
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) H566_RS0111715 H566_RS0102690
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) H566_RS0104975 H566_RS0102695
adiA arginine decarboxylase (AdiA/SpeA) H566_RS0101800
speB agmatinase H566_RS0109745
puuA glutamate-putrescine ligase H566_RS0106260 H566_RS0117970
puuB gamma-glutamylputrescine oxidase H566_RS0106205
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase H566_RS0113545 H566_RS0101815
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase H566_RS0106255
gabT gamma-aminobutyrate transaminase H566_RS0106265 H566_RS0108125
gabD succinate semialdehyde dehydrogenase H566_RS0108130 H566_RS0107095
Alternative steps:
AAP3 L-arginine transporter AAP3
aguA agmatine deiminase
aguB N-carbamoylputrescine hydrolase
arcA arginine deiminase
arcB ornithine carbamoyltransferase H566_RS0102950 H566_RS23155
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) H566_RS0119530 H566_RS0107445
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA H566_RS0107450 H566_RS0116820
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) H566_RS0107440 H566_RS0116810
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) H566_RS26635
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) H566_RS26635
aruH L-arginine:pyruvate transaminase H566_RS0106475 H566_RS0103260
aruI 2-ketoarginine decarboxylase
astA arginine N-succinyltransferase H566_RS26635
astB N-succinylarginine dihydrolase H566_RS0120050
astC succinylornithine transaminase H566_RS0102945 H566_RS0108125
astD succinylglutamate semialdehyde dehydrogenase H566_RS0113545 H566_RS0108110
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase H566_RS0115455 H566_RS0110200
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 H566_RS0108130 H566_RS0107095
davT 5-aminovalerate aminotransferase H566_RS0108125 H566_RS0102945
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase H566_RS0118410 H566_RS0108000
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase H566_RS0116335 H566_RS0112415
gbamidase guanidinobutyramidase
gbuA guanidinobutyrase H566_RS0109745
gcdG succinyl-CoA:glutarate CoA-transferase H566_RS0106900 H566_RS0111790
gcdH glutaryl-CoA dehydrogenase H566_RS0120480 H566_RS0116330
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase H566_RS0113545 H566_RS0101815
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase H566_RS0101800
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) H566_RS0106265 H566_RS0117810
patD gamma-aminobutyraldehyde dehydrogenase H566_RS0105030 H566_RS0113545
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 H566_RS0104400
puo putrescine oxidase
put1 proline dehydrogenase H566_RS0108110
putA L-glutamate 5-semialdeyde dehydrogenase H566_RS0108110 H566_RS0120955
rocA 1-pyrroline-5-carboxylate dehydrogenase H566_RS0108110 H566_RS0120955
rocD ornithine aminotransferase H566_RS0108125 H566_RS0117810
rocE L-arginine permease
rocF arginase H566_RS0109745

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