GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Aquimarina macrocephali JAMB N27

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 (28 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rocE L-arginine permease
rocF arginase Z054_RS0115645 Z054_RS0114900
rocD ornithine aminotransferase Z054_RS0124165 Z054_RS0116790
PRO3 pyrroline-5-carboxylate reductase Z054_RS0117460
put1 proline dehydrogenase Z054_RS0106545
putA L-glutamate 5-semialdeyde dehydrogenase Z054_RS0125405 Z054_RS0121915
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 Z054_RS0106805 Z054_RS0117470
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 Z054_RS0118835 Z054_RS0104180
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 Z054_RS0124040 Z054_RS0115610
aruI 2-ketoarginine decarboxylase Z054_RS0121920 Z054_RS0117425
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase Z054_RS0124165 Z054_RS0117465
astD succinylglutamate semialdehyde dehydrogenase Z054_RS0105015 Z054_RS0121915
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase Z054_RS0106210 Z054_RS0115825
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) Z054_RS0104130 Z054_RS0104180
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase Z054_RS0121915 Z054_RS0121900
davT 5-aminovalerate aminotransferase Z054_RS0124165 Z054_RS0107025
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Z054_RS0106865 Z054_RS0108580
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Z054_RS0115830 Z054_RS0112885
gabD succinate semialdehyde dehydrogenase Z054_RS0121900 Z054_RS0121915
gabT gamma-aminobutyrate transaminase Z054_RS0124165 Z054_RS0107025
gbamidase guanidinobutyramidase
gbuA guanidinobutyrase Z054_RS0115645
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase Z054_RS0123520 Z054_RS0121070
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase Z054_RS0121900 Z054_RS0110935
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) Z054_RS0117465 Z054_RS0116790
patD gamma-aminobutyraldehyde dehydrogenase Z054_RS0121900 Z054_RS0110935
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase Z054_RS0123730 Z054_RS0121525
puo putrescine oxidase
puuA glutamate-putrescine ligase
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase Z054_RS0121900 Z054_RS0110935
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase Z054_RS0125405 Z054_RS0121915
speB agmatinase Z054_RS0115645

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