GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Granulicella mallensis MP5ACTX8

Best path

AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, 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 (27 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 ACIX8_RS02065 ACIX8_RS18020
arcB ornithine carbamoyltransferase ACIX8_RS10410 ACIX8_RS02750
arcC carbamate kinase
rocD ornithine aminotransferase ACIX8_RS09780 ACIX8_RS09750
PRO3 pyrroline-5-carboxylate reductase ACIX8_RS13325
put1 proline dehydrogenase ACIX8_RS20890 ACIX8_RS07595
putA L-glutamate 5-semialdeyde dehydrogenase ACIX8_RS07595 ACIX8_RS06770
Alternative steps:
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astC succinylornithine transaminase ACIX8_RS10415 ACIX8_RS09780
astD succinylglutamate semialdehyde dehydrogenase ACIX8_RS07595 ACIX8_RS16850
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase ACIX8_RS05900
citrullinase putative citrullinase ACIX8_RS06345
davD glutarate semialdehyde dehydrogenase ACIX8_RS16850 ACIX8_RS07595
davT 5-aminovalerate aminotransferase ACIX8_RS09750 ACIX8_RS10415
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase ACIX8_RS02780 ACIX8_RS18945
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase ACIX8_RS10250 ACIX8_RS18095
gabD succinate semialdehyde dehydrogenase ACIX8_RS16850 ACIX8_RS07595
gabT gamma-aminobutyrate transaminase ACIX8_RS09750 ACIX8_RS13335
gcdG succinyl-CoA:glutarate CoA-transferase ACIX8_RS15465
gcdH glutaryl-CoA dehydrogenase ACIX8_RS10450 ACIX8_RS18780
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase ACIX8_RS09230
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) ACIX8_RS13335 ACIX8_RS10415
patD gamma-aminobutyraldehyde dehydrogenase ACIX8_RS16850 ACIX8_RS07595
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase ACIX8_RS23540
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 ACIX8_RS07680 ACIX8_RS17850
puo putrescine oxidase
puuA glutamate-putrescine ligase ACIX8_RS06360
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase ACIX8_RS16850 ACIX8_RS07595
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase ACIX8_RS24210
rocA 1-pyrroline-5-carboxylate dehydrogenase ACIX8_RS07595 ACIX8_RS06770

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