GapMind for catabolism of small carbon sources

 

L-asparagine catabolism in Oceanisphaera arctica V1-41

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 UN63_RS16635 UN63_RS10800
glt aspartate:proton symporter Glt UN63_RS05650 UN63_RS11200
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ UN63_RS01075
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) UN63_RS01065 UN63_RS13375
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP UN63_RS01060 UN63_RS12580
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) UN63_RS01070 UN63_RS12585
aatJ aspartate/asparagine ABC transporter, substrate-binding component AatJ
aatM aspartate/asparagine ABC transporter, permease component 2 (AatM) UN63_RS01065 UN63_RS12585
aatP aspartate/asparagine ABC transporter, ATPase component UN63_RS01060 UN63_RS12580
aatQ aspartate/asparagine ABC transporter, permease component 1 (AatQ) UN63_RS04695 UN63_RS01065
acaP aspartate permease AcaP
agcS Probable asparagine:Na+ symporter AgcS UN63_RS14780 UN63_RS11910
AGP1 L-asparagine permease AGP1
ansP L-asparagine permease AnsP
bgtA aspartate ABC transporter, ATPase component BgtA UN63_RS01060 UN63_RS12580
bgtB' aspartate ABC transporter, permease component 1 (BgtB) UN63_RS01070
BPHYT_RS17540 aspartate:H+ (or asparagine) symporter
bztA aspartate/asparagine ABC transporter, substrate-binding component BztA UN63_RS01075
bztB aspartate/asparagine ABC transporter, permease component 1 (BztB) UN63_RS01070 UN63_RS04695
bztC aspartate/asparagine ABC transporter, permease component 2 (BztC) UN63_RS01065
bztD aspartate/asparagine ABC transporter, ATPase component (BztD) UN63_RS01060 UN63_RS12580
dauA dicarboxylic acid transporter DauA UN63_RS00480
glnP L-asparagine ABC transporter, fused permease and substrate-binding components GlnP
glnQ L-asparagine ABC transporter, ATPase component GlnQ UN63_RS12580 UN63_RS03190
natF aspartate ABC transporter, substrate-binding component NatF UN63_RS01075
natG aspartate ABC transporter, permease component 1 (NatG) UN63_RS01070 UN63_RS01065
natH aspartate ABC transporter, permease component 2 (NatH) UN63_RS01065 UN63_RS13375
peb1A aspartate ABC transporter, perisplasmic substrate-binding component Peb1A
peb1B aspartate ABC transporter, permease component 1 (Peb1B) UN63_RS04695 UN63_RS01070
peb1C aspartate ABC transporter, ATPase component Peb1C UN63_RS01060 UN63_RS12580
peb1D aspartate ABC transporter, permease component 2 (Peb1D) UN63_RS03175 UN63_RS13375
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.

Links

Downloads

Related tools

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