Align Alpha-aminoadipate/glutamate carrier protein LysW; AAA carrier protein LysW (characterized)
to candidate WP_014026285.1 PYRFU_RS03640 sulfonate ABC transporter
Query= SwissProt::Q4JAQ0 (56 letters) >NCBI__GCF_000223395.1:WP_014026285.1 Length = 57 Score = 66.6 bits (161), Expect = 3e-17 Identities = 29/51 (56%), Positives = 36/51 (70%) Query: 6 CPICGNDVNVPDDSLPGEIVEHECGAQLEVFNSNGKLALRLAEQVGEDWGE 56 CPICG DV +PD+ + GEIVEH+CGA L V +G + L E+V EDWGE Sbjct: 7 CPICGGDVELPDNVMDGEIVEHDCGAMLVVRIRDGNVVLEQLERVEEDWGE 57 Lambda K H 0.316 0.139 0.435 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 28 Number of extensions: 1 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 56 Length of database: 57 Length adjustment: 3 Effective length of query: 53 Effective length of database: 54 Effective search space: 2862 Effective search space used: 2862 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 36 (19.2 bits) S2: 36 (18.5 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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