GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Sphingobium czechense LL01

Best path

AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, 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 (26 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 V473_RS03740 V473_RS00455
citrullinase putative citrullinase V473_RS09535
ocd ornithine cyclodeaminase
put1 proline dehydrogenase V473_RS05455
putA L-glutamate 5-semialdeyde dehydrogenase V473_RS05455 V473_RS05490
Alternative steps:
arcB ornithine carbamoyltransferase V473_RS02295 V473_RS11315
arcC carbamate kinase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) V473_RS06010
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) V473_RS06010
astC succinylornithine transaminase V473_RS02290 V473_RS20290
astD succinylglutamate semialdehyde dehydrogenase V473_RS10010 V473_RS10045
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase V473_RS07145 V473_RS00635
davD glutarate semialdehyde dehydrogenase V473_RS08475 V473_RS20300
davT 5-aminovalerate aminotransferase V473_RS02290 V473_RS18720
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase V473_RS04380 V473_RS05770
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase V473_RS00615 V473_RS18225
gabD succinate semialdehyde dehydrogenase V473_RS08475 V473_RS20730
gabT gamma-aminobutyrate transaminase V473_RS20290 V473_RS02290
gcdG succinyl-CoA:glutarate CoA-transferase V473_RS05465 V473_RS08220
gcdH glutaryl-CoA dehydrogenase V473_RS17395 V473_RS17555
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
odc L-ornithine decarboxylase V473_RS06170
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) V473_RS20290 V473_RS02290
patD gamma-aminobutyraldehyde dehydrogenase V473_RS05540 V473_RS05490
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 V473_RS11780
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 V473_RS03740 V473_RS04645
puo putrescine oxidase
puuA glutamate-putrescine ligase
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase V473_RS05540 V473_RS05490
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase V473_RS05455 V473_RS05490
rocD ornithine aminotransferase V473_RS02290

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