Align The SnatA carrier. Transports glycine, L-alanine, L-serine, L-threonine and a variety of neutral L-amino acids (characterized)
to candidate WP_008485442.1 B3C1_RS13330 YchE family NAAT transporter
Query= TCDB::Q8J305 (216 letters) >NCBI__GCF_000299915.1:WP_008485442.1 Length = 210 Score = 138 bits (348), Expect = 7e-38 Identities = 76/197 (38%), Positives = 113/197 (57%), Gaps = 4/197 (2%) Query: 18 LFAITNPVGAVPVFLSVTHDLSWRERREIASKTAISVVATLVVFALLGQWIFKFFGSSTD 77 + AI NP G +PVF+ +T ERR A A + L V LLG+ + KFF S Sbjct: 13 MLAIVNPFGLLPVFMGLTSHQDQAERRRTAMMAAFASAVILWVVLLLGEDLLKFFSISVA 72 Query: 78 AFAIAGGILLFRMALDMLSGKLSSVKISNEETEEFSEEVVTLEEVAIIPLAIPLISGPGA 137 +F +AGG+LL AL ML GKL + + EE E +E V ++PLA+PLI+GP A Sbjct: 73 SFQVAGGVLLSFTALSMLQGKLGETRRTTEE----GREAARMESVTLVPLALPLIAGPAA 128 Query: 138 ITTVMLYMAKSTTNLQRLAVILTIILIGITVWFVLCSANRIKARLGRVGIKVMTRMMGLI 197 ITTV+++ + + + A+ L I ++ + W V A + LG GI ++TR+MGLI Sbjct: 129 ITTVIVFTQAHHSLVDKGALGLAIGILALVTWGVFLCAPMLARWLGTTGINLITRVMGLI 188 Query: 198 LTSMAVQMIINGIKGAF 214 + ++AV+ + G+KG F Sbjct: 189 MMALAVEFMAKGVKGLF 205 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: 119 Number of extensions: 4 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: 210 Length adjustment: 22 Effective length of query: 194 Effective length of database: 188 Effective search space: 36472 Effective search space used: 36472 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 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