Align Glycine betaine/proline/ectoine/pipecolic acid transporter OusA; Osmoprotectant uptake system A (characterized)
to candidate GFF1418 PS417_07205 LysR family transcriptional regulator
Query= SwissProt::Q47421 (501 letters) >FitnessBrowser__WCS417:GFF1418 Length = 439 Score = 248 bits (632), Expect = 4e-70 Identities = 140/413 (33%), Positives = 222/413 (53%), Gaps = 7/413 (1%) Query: 25 RKAITAAALGNAMEWFDFGVYGFVA-YALGQVFFPGADPGVQMIAALATFSVPFLIRPLG 83 R+A AA +G +EW+DF +Y A GQ+FFP D +AA TF+V F RPLG Sbjct: 10 RRAAAAAFIGTMIEWYDFYIYATAAALVFGQLFFPSDDKLFSTMAAFGTFAVGFFARPLG 69 Query: 84 GVFFGALGDKYGRQKILAITIIIMSISTFCIGLIPSYERIGIWAPILLLLAKMAQGFSVG 143 G+ FG +GD+ GR+K L IT+++M + T CIGL+P+Y +IG AP+LL+L ++ QG +VG Sbjct: 70 GIVFGHIGDRIGRKKSLVITLVMMGVVTVCIGLLPTYAQIGAAAPVLLVLLRVVQGIAVG 129 Query: 144 GEYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTLIGEQAFLAWGWRL 203 GE+ GA + E++P +R F S+ GS AG +L + T + E L+WGWR+ Sbjct: 130 GEWGGAVLMAGEHAPKGRRNFFASFAQLGSPAGLILSL-LAFSAVTRLPEDELLSWGWRV 188 Query: 204 PFFLALPLGLIGLYLRHALEETPAFRQHVEKLEQNDRDGLKAGPGVSFREIATHHWKSLL 263 PF + L ++GL +R + E+P F + E+ P + E+ W+ LL Sbjct: 189 PFLASALLLVVGLAIRLGVNESPEFLEDKALAEKARAIKKDQAPVI---EVLRTAWRPLL 245 Query: 264 VCIGLVIATNVTYYMLLTYMPSYLSHSLHYSENHGVLIIIAIMIGMLFVQPVMGLLSDRF 323 +CIG Y T+M +Y + L + + + + I VQP+ ++++ Sbjct: 246 LCIGANTLGIAGVYFTNTFMIAYSTQQLGLPRSLILECLFFVAIIQFCVQPLAAWVAEKV 305 Query: 324 GRKPFVVIGSVAMFFLAVPSFMLINSDIIGLIFLGLLMLAVILNAFTGVMASTLPALFPT 383 G F+ +V P F+L++S LI LG+ + V + +F V+A + LF T Sbjct: 306 GATRFLCAMTVLAMASPYPMFVLVSSGQAPLIILGIALAVVCMASFYAVIAGFVSGLFET 365 Query: 384 HIRYSALASAFNI-SVLIAGLTPTVAAWLVESSQNLYMP-AYYLMVIAVIGLL 434 +RY+A++ A+ + L GLTP + WL Q + P A + +IA + L+ Sbjct: 366 RVRYTAISLAYQVCGALAGGLTPLIGTWLAHEYQGQWWPMAVFYSLIAAVSLV 418 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: 483 Number of extensions: 29 Number of successful extensions: 6 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: 439 Length adjustment: 33 Effective length of query: 468 Effective length of database: 406 Effective search space: 190008 Effective search space used: 190008 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