GapMind for catabolism of small carbon sources

 

L-asparagine catabolism in Bacillus altitudinis 41KF2b

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 (24 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ans asparaginase BA79_RS09880 BA79_RS17775
glt aspartate:proton symporter Glt BA79_RS17920 BA79_RS05320
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) BA79_RS09605 BA79_RS06425
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP BA79_RS06410 BA79_RS09600
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) BA79_RS06420
aatJ aspartate/asparagine ABC transporter, substrate-binding component AatJ BA79_RS06415
aatM aspartate/asparagine ABC transporter, permease component 2 (AatM) BA79_RS11150 BA79_RS09605
aatP aspartate/asparagine ABC transporter, ATPase component BA79_RS09600 BA79_RS06410
aatQ aspartate/asparagine ABC transporter, permease component 1 (AatQ) BA79_RS06420 BA79_RS06425
acaP aspartate permease AcaP
agcS Probable asparagine:Na+ symporter AgcS BA79_RS15075 BA79_RS12455
AGP1 L-asparagine permease AGP1 BA79_RS16590
ansP L-asparagine permease AnsP BA79_RS12105 BA79_RS16380
bgtA aspartate ABC transporter, ATPase component BgtA BA79_RS06410 BA79_RS11155
bgtB' aspartate ABC transporter, permease component 1 (BgtB)
BPHYT_RS17540 aspartate:H+ (or asparagine) symporter BA79_RS12270
bztA aspartate/asparagine ABC transporter, substrate-binding component BztA
bztB aspartate/asparagine ABC transporter, permease component 1 (BztB)
bztC aspartate/asparagine ABC transporter, permease component 2 (BztC)
bztD aspartate/asparagine ABC transporter, ATPase component (BztD) BA79_RS06410 BA79_RS08720
dauA dicarboxylic acid transporter DauA BA79_RS05740
glnP L-asparagine ABC transporter, fused permease and substrate-binding components GlnP
glnQ L-asparagine ABC transporter, ATPase component GlnQ BA79_RS09600 BA79_RS11155
natF aspartate ABC transporter, substrate-binding component NatF
natG aspartate ABC transporter, permease component 1 (NatG) BA79_RS06425 BA79_RS06420
natH aspartate ABC transporter, permease component 2 (NatH) BA79_RS06425 BA79_RS09605
peb1A aspartate ABC transporter, perisplasmic substrate-binding component Peb1A BA79_RS06415
peb1B aspartate ABC transporter, permease component 1 (Peb1B) BA79_RS06420 BA79_RS06425
peb1C aspartate ABC transporter, ATPase component Peb1C BA79_RS06410 BA79_RS11155
peb1D aspartate ABC transporter, permease component 2 (Peb1D) BA79_RS06425 BA79_RS09605
SLC7A13 sodium-independent aspartate transporter
yhiT probable L-asparagine transporter YhiT
yveA aspartate:proton symporter YveA BA79_RS12270

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