Align Glycine betaine/proline/ectoine/pipecolic acid transporter OusA; Osmoprotectant uptake system A (characterized)
to candidate PP_2411 PP_2411 Major facilitator family transporter
Query= SwissProt::Q47421 (501 letters) >FitnessBrowser__Putida:PP_2411 Length = 445 Score = 309 bits (791), Expect = 2e-88 Identities = 162/426 (38%), Positives = 248/426 (58%), Gaps = 9/426 (2%) Query: 19 IDDGRLRKAITAAALGNAMEWFDFGVYGFVAYALGQVFFPGADPGVQMIAALATFSVPFL 78 + LR+ I A+A+GN +EWFDF VYGF+A + FF D V ++ A F+V F Sbjct: 7 VSPATLRRVIAASAIGNFVEWFDFAVYGFLATLIASQFFASEDASVALLKTFAVFAVAFA 66 Query: 79 IRPLGGVFFGALGDKYGRQKILAITIIIMSISTFCIGLIPSYERIGIWAPILLLLAKMAQ 138 +RPLGG+ FGALGD+ GR++IL++TI++M+ ST IGL+P+Y IG+ AP LL LA+ Q Sbjct: 67 LRPLGGIVFGALGDRLGRKRILSLTILLMAGSTTLIGLLPTYASIGLAAPALLTLARCLQ 126 Query: 139 GFSVGGEYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTLIGEQAFLA 198 GFS GGEY GA ++ E++PD KR F GS++ + + F A + + + +A A Sbjct: 127 GFSAGGEYAGACAYLMEHAPDDKRAFYGSFVPVSTFSAFACAAVIAYGLEASLSTEAMNA 186 Query: 199 WGWRLPFFLALPLGLIGLYLRHALEETPAFRQHVEKLEQNDRDGLKAGPGVSFREIATHH 258 WGWR+PF +A PLGL+GLYLR +EETPAFR+ V + ++++ LK E HH Sbjct: 187 WGWRIPFLIAAPLGLVGLYLRWRMEETPAFREAVAQGKEHEHSPLK--------ETLRHH 238 Query: 259 WKSLLVCIGLVIATNVTYYMLLTYMPSYLSHSLHYSENHGVLIIIAIMIGMLFVQPVMGL 318 + + + T +++YM TY +YL + + +L+ ++ P+ G Sbjct: 239 GRVIRNLGAFISLTALSFYMFTTYFATYLQLVGNLTRAQSLLVTTVALLFAAVGCPLAGA 298 Query: 319 LSDRFGRKPFVVIGSVAMFFLAVPSFMLINSDIIGLIFLGLLMLAVILNAFTGVMASTLP 378 SDR GR+ + + + P++ L +S + LG+++LAV V A+ L Sbjct: 299 FSDRVGRRKTIGFTCLWVMLCVFPAYWLASSGSMSGALLGVILLAVGALCSGVVTAALLS 358 Query: 379 ALFPTHIRYSALASAFNIS-VLIAGLTPTVAAWLVESSQNLYMPAYYLMVIAVIGLLTGL 437 FPT RY+A A +N++ L G P VA WL+ + + PA+YL+VIA++ L+ GL Sbjct: 359 ESFPTRTRYTASAITYNVAYTLFGGTAPLVATWLIAQTGSSLAPAFYLVVIALVALVGGL 418 Query: 438 FMKETA 443 + ET+ Sbjct: 419 ALPETS 424 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: 535 Number of extensions: 30 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: 445 Length adjustment: 33 Effective length of query: 468 Effective length of database: 412 Effective search space: 192816 Effective search space used: 192816 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