GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Xenophilus azovorans DSM 13620

Best path

braC, braD, braE, braF, braG, rocF, ocd, 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 (39 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC Q392_RS28895 Q392_RS05395
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) Q392_RS11645 Q392_RS07410
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) Q392_RS11640 Q392_RS28475
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) Q392_RS23140 Q392_RS27095
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) Q392_RS11630 Q392_RS09840
rocF arginase Q392_RS04710
ocd ornithine cyclodeaminase Q392_RS24765
put1 proline dehydrogenase Q392_RS22165
putA L-glutamate 5-semialdeyde dehydrogenase Q392_RS22165 Q392_RS10485
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) Q392_RS28855 Q392_RS00925
aguA agmatine deiminase
aguB N-carbamoylputrescine hydrolase
arcA arginine deiminase
arcB ornithine carbamoyltransferase Q392_RS30560
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) Q392_RS15965 Q392_RS27605
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA Q392_RS21800 Q392_RS15975
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) Q392_RS21815 Q392_RS21810
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH L-arginine:pyruvate transaminase Q392_RS28935 Q392_RS30785
aruI 2-ketoarginine decarboxylase Q392_RS25480 Q392_RS08980
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase Q392_RS30555 Q392_RS30065
astD succinylglutamate semialdehyde dehydrogenase Q392_RS10485 Q392_RS28505
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase Q392_RS11095 Q392_RS22590
bgtB L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase Q392_RS13135 Q392_RS25500
davT 5-aminovalerate aminotransferase Q392_RS30555 Q392_RS21065
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Q392_RS17990 Q392_RS02545
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Q392_RS25280 Q392_RS25070
gabD succinate semialdehyde dehydrogenase Q392_RS24795 Q392_RS13135
gabT gamma-aminobutyrate transaminase Q392_RS31975 Q392_RS06435
gbamidase guanidinobutyramidase Q392_RS04995
gbuA guanidinobutyrase
gcdG succinyl-CoA:glutarate CoA-transferase Q392_RS20245 Q392_RS22810
gcdH glutaryl-CoA dehydrogenase Q392_RS20240 Q392_RS27255
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase Q392_RS19250 Q392_RS25600
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) Q392_RS16755
odc L-ornithine decarboxylase Q392_RS28855
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) Q392_RS31975 Q392_RS06435
patD gamma-aminobutyraldehyde dehydrogenase Q392_RS19250 Q392_RS19065
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 Q392_RS04500
puo putrescine oxidase
puuA glutamate-putrescine ligase Q392_RS21365
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase Q392_RS19250 Q392_RS25600
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase Q392_RS11100
rocA 1-pyrroline-5-carboxylate dehydrogenase Q392_RS22165 Q392_RS10485
rocD ornithine aminotransferase Q392_RS30065 Q392_RS30555
rocE L-arginine permease
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 Apr 09 2024. 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