GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Polaromonas naphthalenivorans CJ2

Best path

AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, ocd, put1, putA

Rules

Overview: Citrulline can be catabolized via ornithine carbamoyltransferase in reverse (PMID:3129535). Genetic evidence suggests that some bacteria use a putative citrullinase (EC 3.5.1.20) to consume citrulline.

51 steps (32 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
AO353_03055 ABC transporter for L-Citrulline, periplasmic substrate-binding component
AO353_03050 ABC transporter for L-Citrulline, permease component 1 PNAP_RS05125 PNAP_RS10320
AO353_03045 ABC transporter for L-Citrulline, permease component 2 PNAP_RS20255 PNAP_RS05125
AO353_03040 ABC transporter for L-Citrulline, ATPase component PNAP_RS10325 PNAP_RS05130
arcB ornithine carbamoyltransferase PNAP_RS15065 PNAP_RS16710
arcC carbamate kinase
ocd ornithine cyclodeaminase PNAP_RS18850
put1 proline dehydrogenase PNAP_RS20290
putA L-glutamate 5-semialdeyde dehydrogenase PNAP_RS20290 PNAP_RS07980
Alternative steps:
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astC succinylornithine transaminase PNAP_RS15060 PNAP_RS13135
astD succinylglutamate semialdehyde dehydrogenase PNAP_RS07980 PNAP_RS13310
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase PNAP_RS05805 PNAP_RS00315
citrullinase putative citrullinase
davD glutarate semialdehyde dehydrogenase PNAP_RS13165 PNAP_RS07980
davT 5-aminovalerate aminotransferase PNAP_RS13135 PNAP_RS15060
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase PNAP_RS16825 PNAP_RS10675
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase PNAP_RS17360 PNAP_RS10710
gabD succinate semialdehyde dehydrogenase PNAP_RS00780 PNAP_RS13165
gabT gamma-aminobutyrate transaminase PNAP_RS13135 PNAP_RS14300
gcdG succinyl-CoA:glutarate CoA-transferase PNAP_RS01095 PNAP_RS19030
gcdH glutaryl-CoA dehydrogenase PNAP_RS10685 PNAP_RS05675
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
odc L-ornithine decarboxylase PNAP_RS10125
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) PNAP_RS14300 PNAP_RS20130
patD gamma-aminobutyraldehyde dehydrogenase PNAP_RS15070 PNAP_RS13165
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 PNAP_RS01615
PS417_17590 ABC transporter for L-Citrulline, periplasmic substrate-binding component PNAP_RS10395
PS417_17595 ABC transporter for L-Citrulline, permease component 1 PNAP_RS10320 PNAP_RS07455
PS417_17600 ABC transporter for L-Citrulline, permease component 2 PNAP_RS10410 PNAP_RS10320
PS417_17605 ABC transporter for L-Citrulline, ATPase component PNAP_RS10325 PNAP_RS20250
puo putrescine oxidase
puuA glutamate-putrescine ligase PNAP_RS14305
puuB gamma-glutamylputrescine oxidase PNAP_RS05135
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PNAP_RS15070 PNAP_RS08450
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase PNAP_RS14310 PNAP_RS19740
rocA 1-pyrroline-5-carboxylate dehydrogenase PNAP_RS20290 PNAP_RS07980
rocD ornithine aminotransferase PNAP_RS13135 PNAP_RS15060

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