Align Glycine betaine/proline/ectoine/pipecolic acid transporter OusA; Osmoprotectant uptake system A (characterized)
to candidate BPHYT_RS16460 BPHYT_RS16460 major facilitator transporter
Query= SwissProt::Q47421 (501 letters) >FitnessBrowser__BFirm:BPHYT_RS16460 Length = 457 Score = 255 bits (651), Expect = 3e-72 Identities = 146/417 (35%), Positives = 229/417 (54%), Gaps = 9/417 (2%) Query: 24 LRKAITAAALGNAMEWFDFGVYGFVAYALGQVFFPGADPGVQMIAALATFSVPFLIRPLG 83 +R+ + ++++GNA+EWFDF VYG+ A + + FFP D + + A+ATF + FL+RPLG Sbjct: 25 VRRIVFSSSVGNALEWFDFLVYGYFATIIAKEFFPMKDEWLSTLLAIATFGISFLMRPLG 84 Query: 84 GVFFGALGDKYGRQKILAITIIIMSISTFCIGLIPSYERIGIWAPILLLLAKMAQGFSVG 143 V G GD+ GR+ L + I +M + TF + ++P Y IGI APIL+LLA++ QGF+VG Sbjct: 85 AVVLGIYGDRKGRKAALTLAIALMMVGTFTMAVMPPYASIGIAAPILILLARLVQGFAVG 144 Query: 144 GEYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTLIGEQAFLAWGWRL 203 GE+ A+ F+ E+S R RG+ SW + A L++ + WGWRL Sbjct: 145 GEFGSATAFMVEHSASR-RGYYASWQFASQGLAAITAAAFGSLLTAWMPPAQLNDWGWRL 203 Query: 204 PFFLALPLGLIGLYLRHALEETPAFRQHVEKLEQNDRDGLKAGPGVSFREIATHHWKSLL 263 PF L +G +G Y+R L+ETP F E E + G ++ W +LL Sbjct: 204 PFVFGLLVGPVGYYIRSHLDETPEFLALREAREAREVAGARSTASEEKDASFASQWVNLL 263 Query: 264 VCIGLVIATNVTYYMLLTYMPSYLSHSLHY--SENHGVLIIIAIMIGMLF-VQPVMGLLS 320 + +G+V + V Y+L YMP Y LH + + GV+++ G+ F + PVMG LS Sbjct: 264 LAVGIVAQSTVGVYVLQLYMPMYAVKQLHMPAAASFGVVVLNG---GLQFLLSPVMGALS 320 Query: 321 DRFGRKPFVVIGSVAMFFLAVPSFMLINS-DIIGLIFLGLLMLAVILNAFTGVMASTLPA 379 DR GR ++ S+ M L P F L+ S IG + L + A++G M + + Sbjct: 321 DRIGRIRIMLTTSILMGTLIYPMFALLQSHPTIGWLLLLQGTAGIFKAAYSGPMPALMSE 380 Query: 380 LFPTHIRYSALASAFNISVLI-AGLTPTVAAWLVESSQNLYMPAYYLMVIAVIGLLT 435 +FPT +R + L+ ++I V I G PT+ + + + P+YY+++ AV+ L+ Sbjct: 381 IFPTQVRSTGLSIGYSIGVTIFGGFAPTIVETFIHLTGDKLAPSYYVLIAAVLSGLS 437 Lambda K H 0.327 0.142 0.427 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: 546 Number of extensions: 24 Number of successful extensions: 5 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: 501 Length of database: 457 Length adjustment: 34 Effective length of query: 467 Effective length of database: 423 Effective search space: 197541 Effective search space used: 197541 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: 51 (24.3 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