Finding step cycA for L-alanine catabolism in Dethiosulfovibrio salsuginis USBA 82
No candidates for cycA: L-alanine symporter CycA
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 cycA
- Curated sequence P0AAE0: D-serine/D-alanine/glycine transporter. D-Serine/D-alanine/glycine/D-cycloserine:H+ symporter. D-serine/alanine/glycine/:H+symporter. D-serine/alanine/glycine/:H+symporter
- Curated sequence F2HQ24: Serine transporter, SerP2 or YdgB, of 459 aas and 12 TMSs (Trip et al. 2013). Transports L-alanine (Km = 20 μM), D-alanine (Km = 38 μM), L-serine, D-serine (Km = 356 μM) and glycine (Noens and Lolkema 2015). The encoding gene is adjacent to the one encoding SerP1 (TC# 2.A.3.1.21)
- Curated sequence M1IW84: D-serine/L-alanine/D-alanine/glycine/D-cycloserine uptake porter of 556 aas, CycA
- Curated sequence Q2VQZ4: Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids)
- Curated sequence GFF1065: L-alanine and D-alanine permease
- Curated sequence AO353_16120: D-alanine and L-alanine transporter
- Curated sequence AO356_17670: L-alanine and D-alanine permease
- Ignore hits to A0A0H2VDI7 when looking for 'other' hits (D-serine/D-alanine/glycine transporter)
- Curated sequence A2RI86: DL-alanine permease SerP2
- Curated sequence P19145: general amino-acid permease GAP1. General amino-acid permease GAP1. General amino acid permease (all L-amino acids and some D-amino acids as well as β-alanine, polyamines and GABA)
- Curated sequence A0A1D8PK89: General amino-acid permease GAP2. General amino and permease and transceptor, GAP2. Transports all amino acids including citruline and eight tested toxic amino acid derivatives
- Comment: A sequence nearly identical to E. coli K-12's cycA (CYCA_ECOL6 / A0A0H2VDI7) is annotated as a D-alanine transporter only, ignore. And add DL-alanine permease SERP2_LACLM / A2RI86. And add general amino-acid permease GAP1_YEAST / P19145, GAP2_CANAL / A0A1D8PK89.
Or cluster all characterized cycA 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