GapMind for catabolism of small carbon sources

 

L-asparagine catabolism in Belnapia rosea CPCC 100156

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 (22 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ans asparaginase BLR02_RS20795 BLR02_RS19120
glt aspartate:proton symporter Glt BLR02_RS19285 BLR02_RS06920
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ BLR02_RS24970 BLR02_RS21740
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) BLR02_RS24960
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP BLR02_RS24955 BLR02_RS10420
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) BLR02_RS24965
aatJ aspartate/asparagine ABC transporter, substrate-binding component AatJ
aatM aspartate/asparagine ABC transporter, permease component 2 (AatM) BLR02_RS24960 BLR02_RS10410
aatP aspartate/asparagine ABC transporter, ATPase component BLR02_RS24955 BLR02_RS10420
aatQ aspartate/asparagine ABC transporter, permease component 1 (AatQ) BLR02_RS19475 BLR02_RS10415
acaP aspartate permease AcaP
agcS Probable asparagine:Na+ symporter AgcS
AGP1 L-asparagine permease AGP1
ansP L-asparagine permease AnsP
bgtA aspartate ABC transporter, ATPase component BgtA BLR02_RS24955 BLR02_RS10420
bgtB' aspartate ABC transporter, permease component 1 (BgtB) BLR02_RS24965 BLR02_RS02410
BPHYT_RS17540 aspartate:H+ (or asparagine) symporter
bztA aspartate/asparagine ABC transporter, substrate-binding component BztA BLR02_RS24970 BLR02_RS08020
bztB aspartate/asparagine ABC transporter, permease component 1 (BztB) BLR02_RS24965
bztC aspartate/asparagine ABC transporter, permease component 2 (BztC) BLR02_RS24960
bztD aspartate/asparagine ABC transporter, ATPase component (BztD) BLR02_RS24955 BLR02_RS10420
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 BLR02_RS10420 BLR02_RS24955
natF aspartate ABC transporter, substrate-binding component NatF BLR02_RS24970 BLR02_RS21740
natG aspartate ABC transporter, permease component 1 (NatG) BLR02_RS24965 BLR02_RS10410
natH aspartate ABC transporter, permease component 2 (NatH) BLR02_RS24960 BLR02_RS02405
peb1A aspartate ABC transporter, perisplasmic substrate-binding component Peb1A
peb1B aspartate ABC transporter, permease component 1 (Peb1B) BLR02_RS02405 BLR02_RS10410
peb1C aspartate ABC transporter, ATPase component Peb1C BLR02_RS24955 BLR02_RS10420
peb1D aspartate ABC transporter, permease component 2 (Peb1D) BLR02_RS19470 BLR02_RS24965
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