GapMind for catabolism of small carbon sources

 

L-asparagine catabolism in Algoriphagus machipongonensis PR1

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 (9 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ans asparaginase ALPR1_RS05195 ALPR1_RS06820
glt aspartate:proton symporter Glt ALPR1_RS02635
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)
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP ALPR1_RS13410 ALPR1_RS08010
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)
aatJ aspartate/asparagine ABC transporter, substrate-binding component AatJ
aatM aspartate/asparagine ABC transporter, permease component 2 (AatM)
aatP aspartate/asparagine ABC transporter, ATPase component ALPR1_RS13410 ALPR1_RS06390
aatQ aspartate/asparagine ABC transporter, permease component 1 (AatQ)
acaP aspartate permease AcaP
agcS Probable asparagine:Na+ symporter AgcS ALPR1_RS10620 ALPR1_RS13780
AGP1 L-asparagine permease AGP1
ansP L-asparagine permease AnsP
bgtA aspartate ABC transporter, ATPase component BgtA ALPR1_RS08255 ALPR1_RS13410
bgtB' aspartate ABC transporter, permease component 1 (BgtB)
BPHYT_RS17540 aspartate:H+ (or asparagine) symporter
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) ALPR1_RS13410 ALPR1_RS08255
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 ALPR1_RS04965 ALPR1_RS13410
natF aspartate ABC transporter, substrate-binding component NatF
natG aspartate ABC transporter, permease component 1 (NatG)
natH aspartate ABC transporter, permease component 2 (NatH)
peb1A aspartate ABC transporter, perisplasmic substrate-binding component Peb1A
peb1B aspartate ABC transporter, permease component 1 (Peb1B)
peb1C aspartate ABC transporter, ATPase component Peb1C ALPR1_RS06390 ALPR1_RS13410
peb1D aspartate ABC transporter, permease component 2 (Peb1D)
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