GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Cupriavidus basilensis 4G11

Best path

artJ, artM, artP, artQ, rocF, ocd, 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 (46 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 RR42_RS29645 RR42_RS34315
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) RR42_RS29655 RR42_RS16450
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA RR42_RS29660 RR42_RS07815
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) RR42_RS29650 RR42_RS04400
rocF arginase RR42_RS02455 RR42_RS14625
ocd ornithine cyclodeaminase RR42_RS03960 RR42_RS29670
put1 proline dehydrogenase RR42_RS20125
putA L-glutamate 5-semialdeyde dehydrogenase RR42_RS20125 RR42_RS27350
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) RR42_RS15940 RR42_RS19905
aguA agmatine deiminase
aguB N-carbamoylputrescine hydrolase
arcA arginine deiminase
arcB ornithine carbamoyltransferase RR42_RS17175 RR42_RS15860
arcC carbamate kinase
arg-monooxygenase arginine 2-monooxygenase
aroD L-arginine oxidase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH L-arginine:pyruvate transaminase RR42_RS35305 RR42_RS15580
aruI 2-ketoarginine decarboxylase RR42_RS29140 RR42_RS26245
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase RR42_RS16955 RR42_RS26240
astD succinylglutamate semialdehyde dehydrogenase RR42_RS26255 RR42_RS21375
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase RR42_RS07610 RR42_RS25455
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 RR42_RS16980 RR42_RS14425
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) RR42_RS14420 RR42_RS16975
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) RR42_RS14415 RR42_RS16970
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) RR42_RS14410 RR42_RS29450
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) RR42_RS14405 RR42_RS16960
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1 RR42_RS01585
davD glutarate semialdehyde dehydrogenase RR42_RS21760 RR42_RS24555
davT 5-aminovalerate aminotransferase RR42_RS26160 RR42_RS26240
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase RR42_RS18250 RR42_RS23710
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase RR42_RS02510 RR42_RS36415
gabD succinate semialdehyde dehydrogenase RR42_RS26155 RR42_RS21760
gabT gamma-aminobutyrate transaminase RR42_RS26160 RR42_RS26240
gbamidase guanidinobutyramidase RR42_RS26020
gbuA guanidinobutyrase RR42_RS02455
gcdG succinyl-CoA:glutarate CoA-transferase RR42_RS15155 RR42_RS36540
gcdH glutaryl-CoA dehydrogenase RR42_RS15400 RR42_RS28565
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase RR42_RS21485 RR42_RS26255
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) RR42_RS06495
odc L-ornithine decarboxylase RR42_RS15940
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) RR42_RS27405 RR42_RS01575
patD gamma-aminobutyraldehyde dehydrogenase RR42_RS26255 RR42_RS21485
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase RR42_RS36345
PRO3 pyrroline-5-carboxylate reductase RR42_RS17360
puo putrescine oxidase RR42_RS24640 RR42_RS24620
puuA glutamate-putrescine ligase RR42_RS12995
puuB gamma-glutamylputrescine oxidase RR42_RS34300 RR42_RS07820
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase RR42_RS21485 RR42_RS26255
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase RR42_RS20125 RR42_RS27350
rocD ornithine aminotransferase RR42_RS26240 RR42_RS21370
rocE L-arginine permease RR42_RS11100 RR42_RS28305
speB agmatinase RR42_RS02455

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 Aug 02 2021. The underlying query database was built on Aug 02 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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