Align Glycine betaine/proline/ectoine/pipecolic acid transporter OusA; Osmoprotectant uptake system A (characterized)
to candidate GFF1381 HP15_1348 major facilitator family transporter
Query= SwissProt::Q47421 (501 letters) >FitnessBrowser__Marino:GFF1381 Length = 414 Score = 247 bits (630), Expect = 6e-70 Identities = 130/423 (30%), Positives = 230/423 (54%), Gaps = 14/423 (3%) Query: 30 AAALGNAMEWFDFGVYGFVAYALGQVFFPGADPGVQMIAALATFSVPFLIRPLGGVFFGA 89 A +GN +EW+DF VYG++A + VFF A+P +I F+ F++RPLG FG Sbjct: 2 AGFIGNVVEWYDFAVYGYLAGVIAPVFFSSANPTAALIGTYGIFAAGFIMRPLGAAVFGW 61 Query: 90 LGDKYGRQKILAITIIIMSISTFCIGLIPSYERIGIWAPILLLLAKMAQGFSVGGEYTGA 149 GD+YGR + + I++++M++ T +G++PSY++ G+ AP+LL+L ++ QG SVGGE++ + Sbjct: 62 FGDRYGRARTMQISVMLMALPTLLLGMLPSYQQAGLLAPVLLVLIRLLQGLSVGGEFSSS 121 Query: 150 SIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTLIGEQAFLAWGWRLPFFLAL 209 + ++ E +PD KRG GSW + GS+ G +LG L++ + EQ WGWRLPF Sbjct: 122 ATYLVETAPDGKRGLTGSWANIGSMTGSLLGVAAAALVTNTLDEQTLSDWGWRLPFLGGA 181 Query: 210 PLGLIGLYLRHALEETPAFRQHVEKLEQNDRDGLKAGPGVSFREIATHHWKSLLVCIGLV 269 LG+ + +R L + F QH E ++ + T + + L+ + Sbjct: 182 ILGIAAIAIRRNLHNSERFSQHHENRDETS----------PLLQAFTTNRRETLLALAFA 231 Query: 270 IATNVTYYMLLTYMPSYLSHSLHYSENHGVLIIIAIMIGMLFVQPVMGLLSDRF-GRKPF 328 + YY++ Y+P +LS S +LI +M+ ++ P+ ++ DR+ R+ + Sbjct: 232 SSYGTCYYIVFVYLPEWLSAQELLSRGTALLINTGMMLLVIPAMPLFAIVGDRWLRRRSW 291 Query: 329 VVIGSVAMFFLAVP--SFMLINSDIIGLIFLGLLMLAVILNAFTGVMASTLPALFPTHIR 386 + I + +A P ++ML + + ++ L ++ ++L G + +FP R Sbjct: 292 IAISLFLLTVVAWPLHAWMLSSGGSLYVVVLAHALVFLLLAIPLGSAPALFVEMFPESDR 351 Query: 387 YSALASAFNISV-LIAGLTPTVAAWLVESSQNLYMPAYYLMVIAVIGLLTGLFMKETANK 445 S + AFN+ + + GLTP +A L+ ++ + PA YL V A I +L + M + + + Sbjct: 352 LSGYSVAFNLGLGVFGGLTPMIATSLIATTGVVTAPAMYLAVTAFIAVLALIAMPDRSRE 411 Query: 446 PLK 448 PL+ Sbjct: 412 PLR 414 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: 530 Number of extensions: 29 Number of successful extensions: 4 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: 414 Length adjustment: 33 Effective length of query: 468 Effective length of database: 381 Effective search space: 178308 Effective search space used: 178308 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