GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Halomonas titanicae BH1

Best path

artJ, artM, artP, artQ, adiA, aguA, aguB, puuA, puuB, puuC, puuD, gabT, gabD

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 (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 HALTITAN_RS15235 HALTITAN_RS11445
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) HALTITAN_RS15240 HALTITAN_RS11435
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA HALTITAN_RS15250 HALTITAN_RS11450
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) HALTITAN_RS15245 HALTITAN_RS11440
adiA arginine decarboxylase (AdiA/SpeA) HALTITAN_RS23450
aguA agmatine deiminase HALTITAN_RS00720 HALTITAN_RS04665
aguB N-carbamoylputrescine hydrolase HALTITAN_RS04660 HALTITAN_RS00275
puuA glutamate-putrescine ligase HALTITAN_RS00675 HALTITAN_RS19480
puuB gamma-glutamylputrescine oxidase HALTITAN_RS00680 HALTITAN_RS01005
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase HALTITAN_RS00660 HALTITAN_RS00740
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase HALTITAN_RS00670 HALTITAN_RS11255
gabT gamma-aminobutyrate transaminase HALTITAN_RS00665 HALTITAN_RS00620
gabD succinate semialdehyde dehydrogenase HALTITAN_RS06075 HALTITAN_RS00625
Alternative steps:
AAP3 L-arginine transporter AAP3
arcA arginine deiminase HALTITAN_RS20140
arcB ornithine carbamoyltransferase HALTITAN_RS20135 HALTITAN_RS18565
arcC carbamate kinase HALTITAN_RS20130
arg-monooxygenase arginine 2-monooxygenase
aroD L-arginine oxidase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) HALTITAN_RS20110 HALTITAN_RS20115
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) HALTITAN_RS20115 HALTITAN_RS20110
aruH L-arginine:pyruvate transaminase HALTITAN_RS11460 HALTITAN_RS18070
aruI 2-ketoarginine decarboxylase HALTITAN_RS13895
astA arginine N-succinyltransferase HALTITAN_RS20115 HALTITAN_RS20110
astB N-succinylarginine dihydrolase HALTITAN_RS20125
astC succinylornithine transaminase HALTITAN_RS20105 HALTITAN_RS07740
astD succinylglutamate semialdehyde dehydrogenase HALTITAN_RS20120 HALTITAN_RS00740
astE succinylglutamate desuccinylase HALTITAN_RS15255
atoB acetyl-CoA C-acetyltransferase HALTITAN_RS18010 HALTITAN_RS18730
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) HALTITAN_RS02320 HALTITAN_RS05180
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE)
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) HALTITAN_RS02310 HALTITAN_RS22540
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) HALTITAN_RS02305 HALTITAN_RS22535
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase HALTITAN_RS06075 HALTITAN_RS00625
davT 5-aminovalerate aminotransferase HALTITAN_RS00620 HALTITAN_RS07740
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase HALTITAN_RS11900 HALTITAN_RS16865
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase HALTITAN_RS23950 HALTITAN_RS11895
gbamidase guanidinobutyramidase HALTITAN_RS04660 HALTITAN_RS17720
gbuA guanidinobutyrase HALTITAN_RS13885 HALTITAN_RS01450
gcdG succinyl-CoA:glutarate CoA-transferase HALTITAN_RS07755 HALTITAN_RS23045
gcdH glutaryl-CoA dehydrogenase HALTITAN_RS07760 HALTITAN_RS05155
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase HALTITAN_RS00660 HALTITAN_RS00740
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
ocd ornithine cyclodeaminase HALTITAN_RS07445
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) HALTITAN_RS00665 HALTITAN_RS12685
patD gamma-aminobutyraldehyde dehydrogenase HALTITAN_RS00660 HALTITAN_RS00740
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase HALTITAN_RS08850 HALTITAN_RS20345
PRO3 pyrroline-5-carboxylate reductase HALTITAN_RS18100
puo putrescine oxidase
put1 proline dehydrogenase HALTITAN_RS10685 HALTITAN_RS10675
putA L-glutamate 5-semialdeyde dehydrogenase HALTITAN_RS10685 HALTITAN_RS10675
rocA 1-pyrroline-5-carboxylate dehydrogenase HALTITAN_RS10685 HALTITAN_RS10675
rocD ornithine aminotransferase HALTITAN_RS01040 HALTITAN_RS07740
rocE L-arginine permease HALTITAN_RS15020
rocF arginase HALTITAN_RS01450 HALTITAN_RS13885
speB agmatinase HALTITAN_RS01450 HALTITAN_RS13885

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