GapMind for catabolism of small carbon sources

 

L-asparagine catabolism in Rhizorhabdus wittichii RW1

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 SWIT_RS14155 SWIT_RS10740
glt aspartate:proton symporter Glt SWIT_RS06135 SWIT_RS13355
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ SWIT_RS13335
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) SWIT_RS13325 SWIT_RS13330
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP SWIT_RS13320 SWIT_RS04010
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) SWIT_RS13330 SWIT_RS13325
aatJ aspartate/asparagine ABC transporter, substrate-binding component AatJ
aatM aspartate/asparagine ABC transporter, permease component 2 (AatM) SWIT_RS13325
aatP aspartate/asparagine ABC transporter, ATPase component SWIT_RS13320 SWIT_RS04010
aatQ aspartate/asparagine ABC transporter, permease component 1 (AatQ) SWIT_RS13325 SWIT_RS13330
acaP aspartate permease AcaP
agcS Probable asparagine:Na+ symporter AgcS SWIT_RS22370
AGP1 L-asparagine permease AGP1
ansP L-asparagine permease AnsP SWIT_RS03485
bgtA aspartate ABC transporter, ATPase component BgtA SWIT_RS13320 SWIT_RS10855
bgtB' aspartate ABC transporter, permease component 1 (BgtB) SWIT_RS13330 SWIT_RS13325
BPHYT_RS17540 aspartate:H+ (or asparagine) symporter
bztA aspartate/asparagine ABC transporter, substrate-binding component BztA SWIT_RS13335
bztB aspartate/asparagine ABC transporter, permease component 1 (BztB) SWIT_RS13330
bztC aspartate/asparagine ABC transporter, permease component 2 (BztC) SWIT_RS13325
bztD aspartate/asparagine ABC transporter, ATPase component (BztD) SWIT_RS13320 SWIT_RS04010
dauA dicarboxylic acid transporter DauA SWIT_RS03260 SWIT_RS25015
glnP L-asparagine ABC transporter, fused permease and substrate-binding components GlnP
glnQ L-asparagine ABC transporter, ATPase component GlnQ SWIT_RS13320 SWIT_RS00070
natF aspartate ABC transporter, substrate-binding component NatF SWIT_RS13335
natG aspartate ABC transporter, permease component 1 (NatG) SWIT_RS13330
natH aspartate ABC transporter, permease component 2 (NatH) SWIT_RS13325
peb1A aspartate ABC transporter, perisplasmic substrate-binding component Peb1A
peb1B aspartate ABC transporter, permease component 1 (Peb1B) SWIT_RS13325
peb1C aspartate ABC transporter, ATPase component Peb1C SWIT_RS13320 SWIT_RS04010
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 Apr 09 2024. 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