Finding step lysP for L-lysine catabolism in Aquimarina macrocephali JAMB N27
No candidates for lysP: L-lysine:H+ symporter LysP
GapMind classifies a step as low confidence even if it does not find any candidates. You can still try to find candidates by using Curated BLAST (which searches the 6-frame translation) or by text search of the annotations (which may indicate weak homology, under 30% identity or 50% coverage, that GapMind does not consider). See the links below.
Definition of step lysP
- Curated sequence CH_003129: lysine-specific permease. Lysine:H+ symporter. Forms a stable complex with CadC to allow lysine-dependent adaptation to acidic stress (Rauschmeier et al. 2013). The Salmonella orthologue is 95% identical to the E. coli protein and is highly specific for Lysine. Residues involved in lysine binding have been identified. lysine:H+ symporter. lysine:H+ symporter
- Curated sequence CH_091040: lysine-specific permease. Lysine-specific permease. Lysine permease of 611 aas and 13 putative TMSs, Lyp1
- Curated sequence CH_091257: S-adenosylmethionine permease SAM3. S-adenosylmethionine permease SAM3; S-adenosylmethionine metabolism protein 3. S-adenosylmethionine uptake permease, SAM3 (also takes up polyamines, glutamate, lysine and the toxic S-adenosylmethionine analogue sinefungin)
- Curated sequence CH_091412: uncharacterized amino-acid permease C869.11. The basic amino acid (canavanine sensitivity) transporter, Cat1
- Curated sequence A0A1D8PPG4: Probable lysine/arginine permease CAN3; Basic amino acids permease CAN3
- Curated sequence A0A1D8PPI5: Lysine/arginine permease CAN1; Basic amino acids permease CAN1
- Curated sequence A2RNZ6: Lysine permease LysP
- Curated sequence Q59WU0: Probable lysine/arginine permease CAN2; Basic amino acids permease CAN2
- Curated sequence K7VV21: The lysine specific transporter, LysP of 488 aas and 12 TMSs
- Curated sequence P43059: The high affinity basic amino acid (Arg, Lys, His) transporter, Can1
Or cluster all characterized lysP proteins
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:
- ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
- HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.
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:
- ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
- ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
- HMMer finds a hit (regardless of coverage or other bits).
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:
- our ignorance of proteins' functions,
- omissions in the gene models,
- frame-shift errors in the genome sequence, or
- the organism lacks the pathway.
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