Align The SnatA carrier. Transports glycine, L-alanine, L-serine, L-threonine and a variety of neutral L-amino acids (characterized)
to candidate 15362 b1242 predicted inner membrane protein (NCBI)
Query= TCDB::Q8J305 (216 letters) >FitnessBrowser__Keio:15362 Length = 215 Score = 130 bits (328), Expect = 1e-35 Identities = 71/198 (35%), Positives = 113/198 (57%), Gaps = 4/198 (2%) Query: 17 GLFAITNPVGAVPVFLSVTHDLSWRERREIASKTAISVVATLVVFALLGQWIFKFFGSST 76 GLFA+ NPVG +PVF+S+T + R + +SV L + LG I + FG S Sbjct: 17 GLFALVNPVGIIPVFISMTSYQTAAARNKTNLTANLSVAIILWISLFLGDTILQLFGISI 76 Query: 77 DAFAIAGGILLFRMALDMLSGKLSSVKISNEETEEFSEEVVTLEEVAIIPLAIPLISGPG 136 D+F IAGGIL+ +A+ M+SGKL K + +E E E + ++PLA+PL++GPG Sbjct: 77 DSFRIAGGILVVTIAMSMISGKLGEDKQNKQE----KSETAVRESIGVVPLALPLMAGPG 132 Query: 137 AITTVMLYMAKSTTNLQRLAVILTIILIGITVWFVLCSANRIKARLGRVGIKVMTRMMGL 196 AI++ +++ + + + I L + W + A + L + GI V+TR+MGL Sbjct: 133 AISSTIVWGTRYHSISYLFGFFVAIALFALCCWGLFRMAPWLVRVLRQTGINVITRIMGL 192 Query: 197 ILTSMAVQMIINGIKGAF 214 +L ++ ++ I+ GIKG F Sbjct: 193 LLMALGIEFIVTGIKGIF 210 Lambda K H 0.327 0.141 0.396 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: 137 Number of extensions: 5 Number of successful extensions: 2 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: 216 Length of database: 215 Length adjustment: 22 Effective length of query: 194 Effective length of database: 193 Effective search space: 37442 Effective search space used: 37442 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 45 (21.9 bits)
This GapMind analysis is from Sep 17 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