GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Collimonas arenae Ter10

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 (37 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rocE L-arginine permease
rocF arginase CAter10_RS21275
rocD ornithine aminotransferase CAter10_RS21330 CAter10_RS16755
PRO3 pyrroline-5-carboxylate reductase CAter10_RS03415
put1 proline dehydrogenase CAter10_RS21485
putA L-glutamate 5-semialdeyde dehydrogenase CAter10_RS21485 CAter10_RS08205
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) CAter10_RS05405
aguA agmatine deiminase
aguB N-carbamoylputrescine hydrolase
arcA arginine deiminase
arcB ornithine carbamoyltransferase CAter10_RS05530 CAter10_RS21470
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 CAter10_RS04100 CAter10_RS14910
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) CAter10_RS14915 CAter10_RS00190
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA CAter10_RS10285 CAter10_RS00185
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) CAter10_RS14915 CAter10_RS00190
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH L-arginine:pyruvate transaminase CAter10_RS13335 CAter10_RS19715
aruI 2-ketoarginine decarboxylase
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase CAter10_RS16755 CAter10_RS21330
astD succinylglutamate semialdehyde dehydrogenase CAter10_RS18190 CAter10_RS00205
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase CAter10_RS02100 CAter10_RS21010
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 CAter10_RS04200 CAter10_RS04195
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) CAter10_RS15145 CAter10_RS06915
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) CAter10_RS15140 CAter10_RS12280
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) CAter10_RS06905 CAter10_RS12280
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) CAter10_RS06900 CAter10_RS12275
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase CAter10_RS21305 CAter10_RS08205
davT 5-aminovalerate aminotransferase CAter10_RS21330 CAter10_RS16755
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase CAter10_RS03130 CAter10_RS00460
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase CAter10_RS06160 CAter10_RS15290
gabD succinate semialdehyde dehydrogenase CAter10_RS21305 CAter10_RS08205
gabT gamma-aminobutyrate transaminase CAter10_RS21330 CAter10_RS16195
gbamidase guanidinobutyramidase
gbuA guanidinobutyrase CAter10_RS21275
gcdG succinyl-CoA:glutarate CoA-transferase CAter10_RS15355 CAter10_RS15285
gcdH glutaryl-CoA dehydrogenase CAter10_RS02405 CAter10_RS15295
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase CAter10_RS08205 CAter10_RS21305
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) CAter10_RS16195 CAter10_RS00210
patD gamma-aminobutyraldehyde dehydrogenase CAter10_RS21305 CAter10_RS08205
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
puuB gamma-glutamylputrescine oxidase CAter10_RS00180
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase CAter10_RS08205 CAter10_RS21305
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase CAter10_RS01390
rocA 1-pyrroline-5-carboxylate dehydrogenase CAter10_RS21485 CAter10_RS08205
speB agmatinase CAter10_RS21275

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