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.
Or see definitions of steps
| Step | Description | Best candidate | 2nd candidate |
|---|---|---|---|
| ans | asparaginase | BIBO1_RS16335 | BIBO1_RS14115 |
| aapJ | ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ | BIBO1_RS07165 | BIBO1_RS18960 |
| aapQ | ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) | BIBO1_RS07170 | BIBO1_RS19985 |
| aapM | ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) | BIBO1_RS07175 | BIBO1_RS19985 |
| aapP | ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP | BIBO1_RS07180 | BIBO1_RS20000 |
| Alternative steps: | |||
| aatJ | aspartate/asparagine ABC transporter, substrate-binding component AatJ | ||
| aatM | aspartate/asparagine ABC transporter, permease component 2 (AatM) | BIBO1_RS19985 | BIBO1_RS07175 |
| aatP | aspartate/asparagine ABC transporter, ATPase component | BIBO1_RS20000 | BIBO1_RS07180 |
| aatQ | aspartate/asparagine ABC transporter, permease component 1 (AatQ) | BIBO1_RS19985 | BIBO1_RS14880 |
| acaP | aspartate permease AcaP | ||
| agcS | Probable asparagine:Na+ symporter AgcS | BIBO1_RS17340 | |
| AGP1 | L-asparagine permease AGP1 | BIBO1_RS14845 | |
| ansP | L-asparagine permease AnsP | BIBO1_RS14845 | |
| bgtA | aspartate ABC transporter, ATPase component BgtA | BIBO1_RS07180 | BIBO1_RS20000 |
| bgtB' | aspartate ABC transporter, permease component 1 (BgtB) | BIBO1_RS07170 | |
| BPHYT_RS17540 | aspartate:H+ (or asparagine) symporter | ||
| bztA | aspartate/asparagine ABC transporter, substrate-binding component BztA | BIBO1_RS07165 | BIBO1_RS18960 |
| bztB | aspartate/asparagine ABC transporter, permease component 1 (BztB) | BIBO1_RS07170 | BIBO1_RS19985 |
| bztC | aspartate/asparagine ABC transporter, permease component 2 (BztC) | BIBO1_RS07175 | |
| bztD | aspartate/asparagine ABC transporter, ATPase component (BztD) | BIBO1_RS07180 | BIBO1_RS20000 |
| 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 | BIBO1_RS07180 | BIBO1_RS20000 |
| glt | aspartate:proton symporter Glt | ||
| natF | aspartate ABC transporter, substrate-binding component NatF | BIBO1_RS18960 | BIBO1_RS07165 |
| natG | aspartate ABC transporter, permease component 1 (NatG) | BIBO1_RS19985 | BIBO1_RS17105 |
| natH | aspartate ABC transporter, permease component 2 (NatH) | BIBO1_RS07175 | BIBO1_RS19985 |
| peb1A | aspartate ABC transporter, perisplasmic substrate-binding component Peb1A | BIBO1_RS16855 | |
| peb1B | aspartate ABC transporter, permease component 1 (Peb1B) | BIBO1_RS19985 | BIBO1_RS17105 |
| peb1C | aspartate ABC transporter, ATPase component Peb1C | BIBO1_RS07180 | BIBO1_RS20000 |
| peb1D | aspartate ABC transporter, permease component 2 (Peb1D) | BIBO1_RS17105 | BIBO1_RS19985 |
| 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.
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:
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