Align Glycine betaine/proline/ectoine/pipecolic acid transporter OusA; Osmoprotectant uptake system A (characterized)
to candidate Ga0059261_3091 Ga0059261_3091 Sugar (and other) transporter
Query= SwissProt::Q47421 (501 letters) >FitnessBrowser__Korea:Ga0059261_3091 Length = 430 Score = 210 bits (534), Expect = 9e-59 Identities = 128/421 (30%), Positives = 205/421 (48%), Gaps = 18/421 (4%) Query: 26 KAITAAALGNAMEWFDFGVYGFVAYALGQVFFPGADPGVQMIAALATFSVPFLIRPLGGV 85 K+I + GN +EW+D+ Y FFP D Q++ A F+V FL+RP+GG Sbjct: 15 KSILGGSAGNLVEWYDWYAYAAFTLYFAPHFFPKGDQTTQLLNTAAVFAVGFLMRPIGGW 74 Query: 86 FFGALGDKYGRQKILAITIIIMSISTFCIGLIPSYERIGIWAPILLLLAKMAQGFSVGGE 145 G DKYGR+ L +++ +M + I + P YE IG AP LL+ A++ QG S+GGE Sbjct: 75 LMGVYADKYGRKAGLTLSVSLMCAGSLLIAVTPGYETIGALAPALLVFARLMQGLSIGGE 134 Query: 146 YTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTLIGEQAFLAWGWRLPF 205 Y ++ +++E + ++RGF S+ I+G ++ GV++++ + E A +WGWR+PF Sbjct: 135 YGASATYLSEMAGRKRRGFFSSFQYVTLISGQLIALGVLLILQASMSEAALESWGWRIPF 194 Query: 206 FLALPLGLIGLYLRHALEETPAFRQHVEKLEQNDRDGLKAGPGVSFREIATHHWKSLLVC 265 F+ L +I +LR L ET +F E +G K G RE H L+ Sbjct: 195 FIGGALAVIVFWLRRGLSETQSF-------ENAKAEGRKTGALALLRE----HPGEFLLV 243 Query: 266 IGLVIATNVTYYMLLTYMPSYLSHSLHYSENHGVLIIIAIMIGMLFVQPVMGLLSDRFGR 325 + L + +Y Y+ +L ++ + I A + + +QP+ G LSDR GR Sbjct: 244 MALTAGGTLAFYAYSIYLQKFLVNTSGFDRETASEINAAALFVFMCIQPLAGALSDRIGR 303 Query: 326 KPFVVIGSVAMFFLAVPSFMLINSDIIGLIFLGLLMLA-VILNAFTGVMASTLPALFPTH 384 KP ++ V P F + GL++ A VI+ +T + A LFP H Sbjct: 304 KPLMIGFGVLGVLCTYPIFTALEQVSSAWAAFGLMLGALVIVTGYTSINAVVKAELFPAH 363 Query: 385 IRYSALASAFNI-SVLIAGLTPTVAAWLVESSQNLYMPAYYLMVIAVIG--LLTGLFMKE 441 IR +A + + + + G VA W + +Y V +IG L+ L M++ Sbjct: 364 IRTLGVALPYALANAIFGGTAEYVALWFKDQGME---RGFYWYVTGMIGISLIVYLRMRD 420 Query: 442 T 442 T Sbjct: 421 T 421 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: 522 Number of extensions: 21 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: 430 Length adjustment: 33 Effective length of query: 468 Effective length of database: 397 Effective search space: 185796 Effective search space used: 185796 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