GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Algoriphagus aquaeductus T4

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 CLV31_RS07770 CLV31_RS01090
citrullinase putative citrullinase CLV31_RS04585 CLV31_RS12815
rocD ornithine aminotransferase CLV31_RS08060 CLV31_RS06615
PRO3 pyrroline-5-carboxylate reductase CLV31_RS15425
put1 proline dehydrogenase CLV31_RS17960
putA L-glutamate 5-semialdeyde dehydrogenase CLV31_RS07880 CLV31_RS07110
Alternative steps:
arcB ornithine carbamoyltransferase CLV31_RS04660 CLV31_RS11435
arcC carbamate kinase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astC succinylornithine transaminase CLV31_RS08060 CLV31_RS11440
astD succinylglutamate semialdehyde dehydrogenase
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase CLV31_RS09120 CLV31_RS03395
davD glutarate semialdehyde dehydrogenase CLV31_RS07110
davT 5-aminovalerate aminotransferase CLV31_RS11440 CLV31_RS13960
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase CLV31_RS05805 CLV31_RS13180
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase CLV31_RS03385 CLV31_RS11275
gabD succinate semialdehyde dehydrogenase CLV31_RS07110 CLV31_RS02335
gabT gamma-aminobutyrate transaminase CLV31_RS11440 CLV31_RS13960
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase CLV31_RS15640 CLV31_RS21080
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) CLV31_RS15940
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 CLV31_RS07595
ortA 2-amino-4-oxopentanoate thiolase, alpha subunit
ortB 2-amino-4-oxopentanoate thiolase, beta subunit
patA putrescine aminotransferase (PatA/SpuC) CLV31_RS13960 CLV31_RS11440
patD gamma-aminobutyraldehyde dehydrogenase CLV31_RS07110
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase CLV31_RS15185
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 CLV31_RS07770 CLV31_RS09345
puo putrescine oxidase CLV31_RS13120
puuA glutamate-putrescine ligase
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase CLV31_RS07110
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase CLV31_RS07880 CLV31_RS07110

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