GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Desulfovibrio vulgaris Miyazaki F

Best path

rocE, rocF, rocD, PRO3, put1, putA

Also see fitness data for the top candidates

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 (32 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rocE L-arginine permease
rocF arginase
rocD ornithine aminotransferase DvMF_0516 DvMF_2502
PRO3 pyrroline-5-carboxylate reductase DvMF_3161
put1 proline dehydrogenase DvMF_2146
putA L-glutamate 5-semialdeyde dehydrogenase DvMF_2146
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) DvMF_1536
aguA agmatine deiminase DvMF_0652
aguB N-carbamoylputrescine hydrolase DvMF_0653
arcA arginine deiminase
arcB ornithine carbamoyltransferase DvMF_0046 DvMF_1425
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 DvMF_0860 DvMF_1571
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) DvMF_1570 DvMF_1568
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA DvMF_1920 DvMF_1342
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) DvMF_1570 DvMF_1343
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH L-arginine:pyruvate transaminase DvMF_2204 DvMF_0361
aruI 2-ketoarginine decarboxylase DvMF_1883 DvMF_0153
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase DvMF_3149 DvMF_0516
astD succinylglutamate semialdehyde dehydrogenase DvMF_2146
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase
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 DvMF_2607 DvMF_2750
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) DvMF_2608 DvMF_2751
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) DvMF_2609 DvMF_2752
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) DvMF_2610 DvMF_1481
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) DvMF_2611 DvMF_2754
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase DvMF_2146
davT 5-aminovalerate aminotransferase DvMF_1002 DvMF_3149
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase
gabD succinate semialdehyde dehydrogenase DvMF_2322 DvMF_2146
gabT gamma-aminobutyrate transaminase DvMF_0516 DvMF_1002
gbamidase guanidinobutyramidase
gbuA guanidinobutyrase
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase DvMF_2146
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) DvMF_0516 DvMF_3149
patD gamma-aminobutyraldehyde dehydrogenase DvMF_2146
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 DvMF_2099
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase DvMF_2146
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase DvMF_0015
rocA 1-pyrroline-5-carboxylate dehydrogenase DvMF_2146
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 17 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