GapMind for catabolism of small carbon sources

 

L-asparagine catabolism in Marinomonas arctica 328

Best path

ans, glt

Rules

Overview: Asparagine catabolism in GapMind is based on asparaginase, which forms ammonia and aspartate. The asparaginase may be secreted or cytoplasmic. Asparatate can be transaminated to oxaloacetate, which is an intermediate in central metabolism.

34 steps (23 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ans asparaginase DK187_RS19560 DK187_RS10065
glt aspartate:proton symporter Glt DK187_RS16790
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ DK187_RS03070 DK187_RS01945
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) DK187_RS03060 DK187_RS01935
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP DK187_RS03055 DK187_RS01930
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) DK187_RS03065 DK187_RS01940
aatJ aspartate/asparagine ABC transporter, substrate-binding component AatJ
aatM aspartate/asparagine ABC transporter, permease component 2 (AatM) DK187_RS16320 DK187_RS03060
aatP aspartate/asparagine ABC transporter, ATPase component DK187_RS03055 DK187_RS01930
aatQ aspartate/asparagine ABC transporter, permease component 1 (AatQ) DK187_RS16320 DK187_RS07190
acaP aspartate permease AcaP
agcS Probable asparagine:Na+ symporter AgcS DK187_RS02255 DK187_RS10075
AGP1 L-asparagine permease AGP1
ansP L-asparagine permease AnsP
bgtA aspartate ABC transporter, ATPase component BgtA DK187_RS03055 DK187_RS16315
bgtB' aspartate ABC transporter, permease component 1 (BgtB) DK187_RS03065 DK187_RS01940
BPHYT_RS17540 aspartate:H+ (or asparagine) symporter
bztA aspartate/asparagine ABC transporter, substrate-binding component BztA DK187_RS03070 DK187_RS01945
bztB aspartate/asparagine ABC transporter, permease component 1 (BztB) DK187_RS03065 DK187_RS01940
bztC aspartate/asparagine ABC transporter, permease component 2 (BztC) DK187_RS01935 DK187_RS03060
bztD aspartate/asparagine ABC transporter, ATPase component (BztD) DK187_RS03055 DK187_RS01930
dauA dicarboxylic acid transporter DauA
glnP L-asparagine ABC transporter, fused permease and substrate-binding components GlnP
glnQ L-asparagine ABC transporter, ATPase component GlnQ DK187_RS16315 DK187_RS03055
natF aspartate ABC transporter, substrate-binding component NatF DK187_RS03070 DK187_RS01945
natG aspartate ABC transporter, permease component 1 (NatG) DK187_RS03065 DK187_RS16320
natH aspartate ABC transporter, permease component 2 (NatH) DK187_RS01935 DK187_RS03060
peb1A aspartate ABC transporter, perisplasmic substrate-binding component Peb1A
peb1B aspartate ABC transporter, permease component 1 (Peb1B) DK187_RS16320 DK187_RS20500
peb1C aspartate ABC transporter, ATPase component Peb1C DK187_RS03055 DK187_RS16315
peb1D aspartate ABC transporter, permease component 2 (Peb1D) DK187_RS01935 DK187_RS20500
SLC7A13 sodium-independent aspartate transporter
yhiT probable L-asparagine transporter YhiT
yveA aspartate:proton symporter YveA

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