GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Algoriphagus machipongonensis PR1

Best path

AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, 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 (25 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
AO353_03045 ABC transporter for L-Citrulline, permease component 2
AO353_03040 ABC transporter for L-Citrulline, ATPase component ALPR1_RS09775 ALPR1_RS13410
citrullinase putative citrullinase ALPR1_RS16825 ALPR1_RS07465
rocD ornithine aminotransferase ALPR1_RS04740 ALPR1_RS09710
PRO3 pyrroline-5-carboxylate reductase ALPR1_RS12575
put1 proline dehydrogenase ALPR1_RS14990
putA L-glutamate 5-semialdeyde dehydrogenase ALPR1_RS17935 ALPR1_RS01205
Alternative steps:
arcB ornithine carbamoyltransferase ALPR1_RS11240
arcC carbamate kinase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astC succinylornithine transaminase ALPR1_RS03490 ALPR1_RS04740
astD succinylglutamate semialdehyde dehydrogenase ALPR1_RS01205 ALPR1_RS06860
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase ALPR1_RS13240 ALPR1_RS01085
davD glutarate semialdehyde dehydrogenase ALPR1_RS01205 ALPR1_RS06445
davT 5-aminovalerate aminotransferase ALPR1_RS03490 ALPR1_RS09710
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase ALPR1_RS16285 ALPR1_RS07745
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase ALPR1_RS01095 ALPR1_RS10470
gabD succinate semialdehyde dehydrogenase ALPR1_RS06445 ALPR1_RS01205
gabT gamma-aminobutyrate transaminase ALPR1_RS03490 ALPR1_RS09710
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase ALPR1_RS12195 ALPR1_RS19490
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) ALPR1_RS11810
ocd ornithine cyclodeaminase
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 ALPR1_RS05125
ortA 2-amino-4-oxopentanoate thiolase, alpha subunit
ortB 2-amino-4-oxopentanoate thiolase, beta subunit
patA putrescine aminotransferase (PatA/SpuC) ALPR1_RS09710 ALPR1_RS03490
patD gamma-aminobutyraldehyde dehydrogenase ALPR1_RS01205 ALPR1_RS06860
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase ALPR1_RS03510
PS417_17590 ABC transporter for L-Citrulline, periplasmic substrate-binding component
PS417_17595 ABC transporter for L-Citrulline, permease component 1
PS417_17600 ABC transporter for L-Citrulline, permease component 2
PS417_17605 ABC transporter for L-Citrulline, ATPase component ALPR1_RS06390 ALPR1_RS04965
puo putrescine oxidase
puuA glutamate-putrescine ligase
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase ALPR1_RS06860 ALPR1_RS01205
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase ALPR1_RS17935 ALPR1_RS01205

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.

Links

Downloads

Related tools

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