GapMind for catabolism of small carbon sources

 

L-asparagine catabolism in Chromobacterium vaccinii MWU205

Best path

ans, aatJ, aatQ, aatM, aatP

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 (26 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ans asparaginase VL52_RS19285 VL52_RS13000
aatJ aspartate/asparagine ABC transporter, substrate-binding component AatJ VL52_RS19735
aatQ aspartate/asparagine ABC transporter, permease component 1 (AatQ) VL52_RS19740 VL52_RS12150
aatM aspartate/asparagine ABC transporter, permease component 2 (AatM) VL52_RS19745 VL52_RS08850
aatP aspartate/asparagine ABC transporter, ATPase component VL52_RS19750 VL52_RS06130
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) VL52_RS08850 VL52_RS19745
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP VL52_RS19750 VL52_RS06130
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) VL52_RS19740 VL52_RS19745
acaP aspartate permease AcaP
agcS Probable asparagine:Na+ symporter AgcS VL52_RS12720 VL52_RS04010
AGP1 L-asparagine permease AGP1 VL52_RS10410
ansP L-asparagine permease AnsP VL52_RS13800 VL52_RS00285
bgtA aspartate ABC transporter, ATPase component BgtA VL52_RS19750 VL52_RS06130
bgtB' aspartate ABC transporter, permease component 1 (BgtB) VL52_RS08005 VL52_RS12155
BPHYT_RS17540 aspartate:H+ (or asparagine) symporter VL52_RS21090
bztA aspartate/asparagine ABC transporter, substrate-binding component BztA
bztB aspartate/asparagine ABC transporter, permease component 1 (BztB) VL52_RS19740
bztC aspartate/asparagine ABC transporter, permease component 2 (BztC) VL52_RS08850 VL52_RS19745
bztD aspartate/asparagine ABC transporter, ATPase component (BztD) VL52_RS19750 VL52_RS06130
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 VL52_RS19750 VL52_RS06130
glt aspartate:proton symporter Glt VL52_RS12325 VL52_RS02095
natF aspartate ABC transporter, substrate-binding component NatF
natG aspartate ABC transporter, permease component 1 (NatG) VL52_RS19740 VL52_RS12150
natH aspartate ABC transporter, permease component 2 (NatH) VL52_RS19745 VL52_RS08850
peb1A aspartate ABC transporter, perisplasmic substrate-binding component Peb1A
peb1B aspartate ABC transporter, permease component 1 (Peb1B) VL52_RS19740 VL52_RS08850
peb1C aspartate ABC transporter, ATPase component Peb1C VL52_RS19750 VL52_RS06130
peb1D aspartate ABC transporter, permease component 2 (Peb1D) VL52_RS19745 VL52_RS08005
SLC7A13 sodium-independent aspartate transporter
yhiT probable L-asparagine transporter YhiT VL52_RS12780 VL52_RS03165
yveA aspartate:proton symporter YveA VL52_RS21090

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