GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Geobacter daltonii FRC-32

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 (33 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rocE L-arginine permease
rocF arginase GEOB_RS05040
rocD ornithine aminotransferase GEOB_RS05585 GEOB_RS14935
rocA 1-pyrroline-5-carboxylate dehydrogenase GEOB_RS12935 GEOB_RS17645
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) GEOB_RS08350
aguA agmatine deiminase GEOB_RS11660
aguB N-carbamoylputrescine hydrolase GEOB_RS11655
arcA arginine deiminase
arcB ornithine carbamoyltransferase GEOB_RS05590 GEOB_RS16210
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 GEOB_RS14455 GEOB_RS02825
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
aruI 2-ketoarginine decarboxylase GEOB_RS07510
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase GEOB_RS05585 GEOB_RS14935
astD succinylglutamate semialdehyde dehydrogenase GEOB_RS12935 GEOB_RS17645
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase GEOB_RS01200 GEOB_RS00490
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) GEOB_RS13885
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) GEOB_RS13890
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) GEOB_RS13895 GEOB_RS13900
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) GEOB_RS13900 GEOB_RS11345
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase GEOB_RS17645 GEOB_RS12935
davT 5-aminovalerate aminotransferase GEOB_RS05585 GEOB_RS14935
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase GEOB_RS00800 GEOB_RS01210
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase GEOB_RS00795 GEOB_RS00835
gabD succinate semialdehyde dehydrogenase GEOB_RS17645 GEOB_RS12935
gabT gamma-aminobutyrate transaminase GEOB_RS14935 GEOB_RS02285
gbamidase guanidinobutyramidase GEOB_RS05490
gbuA guanidinobutyrase
gcdG succinyl-CoA:glutarate CoA-transferase GEOB_RS12030
gcdH glutaryl-CoA dehydrogenase GEOB_RS10880 GEOB_RS01170
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase GEOB_RS17645
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) GEOB_RS14935 GEOB_RS05585
patD gamma-aminobutyraldehyde dehydrogenase GEOB_RS17645 GEOB_RS12935
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 GEOB_RS08330
puo putrescine oxidase
put1 proline dehydrogenase GEOB_RS12935
putA L-glutamate 5-semialdeyde dehydrogenase GEOB_RS12935 GEOB_RS17645
puuA glutamate-putrescine ligase GEOB_RS14845
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase GEOB_RS17645 GEOB_RS12935
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
speB agmatinase

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