Align Glycine betaine/proline/ectoine/pipecolic acid transporter OusA; Osmoprotectant uptake system A (characterized)
to candidate WP_004687208.1 BMI_RS13345 MHS family MFS transporter
Query= SwissProt::Q47421 (501 letters) >NCBI__GCF_000022745.1:WP_004687208.1 Length = 426 Score = 239 bits (610), Expect = 1e-67 Identities = 134/424 (31%), Positives = 234/424 (55%), Gaps = 25/424 (5%) Query: 24 LRKAITAAALGNAMEWFDFGVYGFVAYAL-GQVFFPGADPGVQMIAALATFSVPFLIRPL 82 +R+ +TA+ +G +E+FDF +Y A + +FFP +D ++ + ATF++ F RP+ Sbjct: 14 VRRVLTASMIGTTIEFFDFYIYATAAVIVFPHLFFPASDGNSALLQSFATFAIAFFARPV 73 Query: 83 GGVFFGALGDKYGRQKILAITIIIMSISTFCIGLIPSYERIGIWAPILLLLAKMAQGFSV 142 G FG GDK GR+ L ++ M +ST IG +P+Y IG+ AP+LL L ++ QG + Sbjct: 74 GAAIFGHFGDKIGRKATLVAALMTMGLSTVAIGFLPTYASIGVAAPLLLALCRLGQGLGL 133 Query: 143 GGEYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTLIGEQAFLAWGWR 202 GGE+ GA + E +P+ KR + G + G+ AGF+L G+ +L++ + E+ F A+GWR Sbjct: 134 GGEWGGAVLLATENAPEGKRTWYGMFPQLGAPAGFILATGIFLLLAETMTEEQFFAYGWR 193 Query: 203 LPFFLALPLGLIGLYLRHALEETPAFRQHVEKLEQNDRDGLKAGPGVSFREIATHHWKSL 262 +PF + L +GL++R + ETP F++ ++K E+ V ++ HH +L Sbjct: 194 VPFIASAILVAVGLFIRLRIAETPEFQKAIDKAER---------VAVPAAQLFRHHKMNL 244 Query: 263 LVCIGLVIATNVTYYMLLTYMPSYLSHSLHYSENHGVLIIIAIMIGMLF---VQPVMGLL 319 + +AT V +Y++ + + + +L YS ++ MIG++F P+ LL Sbjct: 245 FLGTIGTMATFVLFYLMTVFSLGWGTRALGYSREE---FLVLQMIGVIFFGLTIPLSALL 301 Query: 320 SDRFGRKPFVVIGSVAM---FFLAVPSFMLINSDIIGLIFLGLLMLAVILNAFTGVMAST 376 SDR+G + +VI +V + F+ P F + ++G + +G ++ + V+A Sbjct: 302 SDRYGMRTIMVIVTVLIGLYGFIMAPLFAAGTAGVLGFLIIGFGLMGMTYGPIGAVLAEP 361 Query: 377 LPALFPTHIRYSALASAFNIS-VLIAGLTPTVAAWLVESSQNLYMPAYYLMVIAVIGLLT 435 FPT +RY+ + AFN++ +L A L P +A WL Y+ YY++ A+I L+ Sbjct: 362 ----FPTSVRYTGASLAFNLAGILGASLAPYIATWLATDYGFAYV-GYYMVAAAIISLIG 416 Query: 436 GLFM 439 +F+ Sbjct: 417 FVFI 420 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: 529 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: 426 Length adjustment: 33 Effective length of query: 468 Effective length of database: 393 Effective search space: 183924 Effective search space used: 183924 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 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