Align The SnatA carrier. Transports glycine, L-alanine, L-serine, L-threonine and a variety of neutral L-amino acids (characterized)
to candidate SMc01232 SMc01232 hypothetical protein
Query= TCDB::Q8J305 (216 letters) >FitnessBrowser__Smeli:SMc01232 Length = 209 Score = 125 bits (313), Expect = 8e-34 Identities = 72/200 (36%), Positives = 115/200 (57%), Gaps = 9/200 (4%) Query: 18 LFAITNPVGAVPVFLSVTHDLSWRERREIASKTAISVVATLVVFALLGQWIFKFFGSSTD 77 L +P G P+FLS+T LS ++R ++A++ ++ L FAL G I G S Sbjct: 14 LLVTLDPPGLAPIFLSLTVGLSRQQRFQVATRGSLIAFFILAAFALFGDGILGLLGISIG 73 Query: 78 AFAIAGGILLFRMALDMLSGKLSSVKISNEETEEFSEEVVT---LEEVAIIPLAIPLISG 134 AF IAGG+LLF +A +M+ K E E+ E +T L +A+ PLA+PLI+G Sbjct: 74 AFRIAGGMLLFWIAFEMIFEK------RQERKEKAGETAITKDHLHNIAVFPLALPLIAG 127 Query: 135 PGAITTVMLYMAKSTTNLQRLAVILTIILIGITVWFVLCSANRIKARLGRVGIKVMTRMM 194 PGAI+ +L + + L+R+ +I+ I ++ L A RI LG G ++TR++ Sbjct: 128 PGAISATILLGSSFPSALERVQLIVVIAASMAILFLALVIAERIDRFLGVTGRAILTRLL 187 Query: 195 GLILTSMAVQMIINGIKGAF 214 G+IL ++AVQ +++G++ AF Sbjct: 188 GVILAALAVQFVVDGVRSAF 207 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: 114 Number of extensions: 7 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: 209 Length adjustment: 21 Effective length of query: 195 Effective length of database: 188 Effective search space: 36660 Effective search space used: 36660 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