GapMind for catabolism of small carbon sources


L-arginine catabolism in Chromobacterium vaccinii MWU205

Best path

artJ, artM, artP, artQ, astA, astB, astC, astD, astE


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 (50 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
artJ L-arginine ABC transporter, periplasmic substrate-binding component ArtJ/HisJ/ArtI/AotJ/ArgT VL52_RS06115 VL52_RS17825
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) VL52_RS06125 VL52_RS17815
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA VL52_RS06130 VL52_RS19750
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) VL52_RS06120 VL52_RS17820
astA arginine N-succinyltransferase VL52_RS15520 VL52_RS15515
astB N-succinylarginine dihydrolase VL52_RS15505
astC succinylornithine transaminase VL52_RS15525 VL52_RS16645
astD succinylglutamate semialdehyde dehydrogenase VL52_RS15510 VL52_RS21455
astE succinylglutamate desuccinylase VL52_RS21985
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) VL52_RS21980 VL52_RS21315
aguA agmatine deiminase VL52_RS19625 VL52_RS10900
aguB N-carbamoylputrescine hydrolase
arcA arginine deiminase VL52_RS02440
arcB ornithine carbamoyltransferase VL52_RS02435 VL52_RS21320
arcC carbamate kinase VL52_RS02430
arg-monooxygenase arginine 2-monooxygenase
aroD L-arginine oxidase VL52_RS15120
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) VL52_RS15520 VL52_RS15515
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) VL52_RS15515 VL52_RS15520
aruH L-arginine:pyruvate transaminase VL52_RS16045
aruI 2-ketoarginine decarboxylase VL52_RS18265
atoB acetyl-CoA C-acetyltransferase VL52_RS14225 VL52_RS21005
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 VL52_RS18885 VL52_RS09675
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) VL52_RS15500
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) VL52_RS15495
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) VL52_RS15490 VL52_RS08010
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) VL52_RS15485 VL52_RS03360
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1 VL52_RS03530
davD glutarate semialdehyde dehydrogenase VL52_RS20940 VL52_RS07105
davT 5-aminovalerate aminotransferase VL52_RS20935 VL52_RS15525
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase VL52_RS18865 VL52_RS21030
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase VL52_RS10360 VL52_RS21015
gabD succinate semialdehyde dehydrogenase VL52_RS20535 VL52_RS20940
gabT gamma-aminobutyrate transaminase VL52_RS20935 VL52_RS07075
gbamidase guanidinobutyramidase
gbuA guanidinobutyrase
gcdG succinyl-CoA:glutarate CoA-transferase VL52_RS20890
gcdH glutaryl-CoA dehydrogenase VL52_RS20895 VL52_RS19965
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase VL52_RS07105 VL52_RS21455
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) VL52_RS05540
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase VL52_RS08800 VL52_RS21315
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) VL52_RS07075 VL52_RS18210
patD gamma-aminobutyraldehyde dehydrogenase VL52_RS07105 VL52_RS21455
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase VL52_RS09515
PRO3 pyrroline-5-carboxylate reductase VL52_RS05330
puo putrescine oxidase
put1 proline dehydrogenase VL52_RS18890
putA L-glutamate 5-semialdeyde dehydrogenase VL52_RS18890 VL52_RS20940
puuA glutamate-putrescine ligase VL52_RS07080 VL52_RS11885
puuB gamma-glutamylputrescine oxidase VL52_RS11115
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase VL52_RS07105 VL52_RS21455
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase VL52_RS07085
rocA 1-pyrroline-5-carboxylate dehydrogenase VL52_RS18890 VL52_RS20940
rocD ornithine aminotransferase VL52_RS15525 VL52_RS20935
rocE L-arginine permease VL52_RS10410 VL52_RS13800
rocF arginase
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