Align The SnatA carrier. Transports glycine, L-alanine, L-serine, L-threonine and a variety of neutral L-amino acids (characterized)
to candidate AZOBR_RS31980 AZOBR_RS31980 membrane protein
Query= TCDB::Q8J305 (216 letters) >FitnessBrowser__azobra:AZOBR_RS31980 Length = 221 Score = 92.4 bits (228), Expect = 6e-24 Identities = 59/209 (28%), Positives = 102/209 (48%), Gaps = 6/209 (2%) Query: 12 ILLYGGLFAITNPVGAVPVFLSVTHDLSWRERREIASKTAISVVATLVVFALLGQWIFKF 71 +L + LF+I NP+ +F VT + S +ER ++A++ A+ ++ G ++ F Sbjct: 6 LLAFTALFSIVNPIAMALIFSQVTAERSPKERVQLAARVAVYSAIVMLAALWAGSYVLNF 65 Query: 72 FGSSTDAFAIAGGILLFRMALDMLSGKLSSVKISNEETEEFSEEVVT-LEEVAIIPLAIP 130 FG S A IAGG ++ A +LS + ++ E + + E A PL IP Sbjct: 66 FGISLAALRIAGGFVVAERAWALLSAPEAHEARKQKQAAPAEEAGDSDVGESAFFPLTIP 125 Query: 131 LISGPGAITTVMLYMA---KSTTNLQR--LAVILTIILIGITVWFVLCSANRIKARLGRV 185 +GPG I+ + A + T L + V + I + +W SA+R+ A LG Sbjct: 126 FTTGPGTISVAIALGATRPRGTEGLTEFFIGVSAAALAIALLIWLSYRSADRLVALLGHT 185 Query: 186 GIKVMTRMMGLILTSMAVQMIINGIKGAF 214 +V+TR+ +L + VQ+++ G+ AF Sbjct: 186 RARVLTRLFAFLLFCVGVQILLTGLLDAF 214 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: 86 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: 221 Length adjustment: 22 Effective length of query: 194 Effective length of database: 199 Effective search space: 38606 Effective search space used: 38606 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