Align Glycine betaine/proline/ectoine/pipecolic acid transporter OusA; Osmoprotectant uptake system A (characterized)
to candidate PfGW456L13_2328 L-Proline/Glycine betaine transporter ProP
Query= SwissProt::Q47421 (501 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2328 Length = 459 Score = 255 bits (652), Expect = 2e-72 Identities = 141/426 (33%), Positives = 241/426 (56%), Gaps = 11/426 (2%) Query: 24 LRKAITAAALGNAMEWFDFGVYGFV-AYALGQVFFPGADPGVQMIAALATFSVPFLIRPL 82 ++K A+ +G +EW+D V+ A +VFFP P + + A TF+ +L R + Sbjct: 20 MKKVAVASVIGTTVEWYDLFVFATASALVFNKVFFPDFVPLIGTLLAFGTFASAYLARIV 79 Query: 83 GGVFFGALGDKYGRQKILAITIIIMSISTFCIGLIPSYERIGIWAPILLLLAKMAQGFSV 142 G FG GD+ GR+ +L I+++ M +TF IGL+P + IGIWAPILLLL ++ QG ++ Sbjct: 80 GAALFGHFGDRLGRKSMLLISLLTMGAATFAIGLLPDFATIGIWAPILLLLLRVVQGLAL 139 Query: 143 GGEYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTLIGEQAFLAWGWR 202 GGE+ GA + E++P KRG GSW+ G AG ++ +LI+ + + LAWGWR Sbjct: 140 GGEWGGAVLMAVEHAPANKRGLYGSWVQIGVPAGTMIANLAFLLIAAWLSPEDLLAWGWR 199 Query: 203 LPFFLALPLGLIGLYLRHALEETPAFRQHVEKLEQNDRDGLKAGPGVSFREIATHHWKSL 262 +PF ++ L +GLY+R + ETPAF + V++ E + + E+ +WK + Sbjct: 200 IPFLASVLLIAVGLYIRLNISETPAFNK-VKEAEVQVK--------MPLAEVFRKYWKQV 250 Query: 263 LVCIGLVIATNVTYYMLLTYMPSYLSHSLHYSENHGVLIIIAIMIGMLFVQPVMGLLSDR 322 L+ ++T ++ +++ + +Y + +L +S + + +++ + + PV G LSDR Sbjct: 251 LLGGIATMSTGASFNIIVAFGLTYGTQNLGFSRSVMLGVVLLSCAWCIVMLPVFGALSDR 310 Query: 323 FGRKPFVVIGSVAMFFLAVPSFMLINSDIIGLIFLGLLMLAVILNAFTGVMASTLPALFP 382 FGRKP +V G +A +A P F L+++ + ++ G L+L A G +A+ L LF Sbjct: 311 FGRKPIIVGGIIAEALVAFPMFWLMDTKELSMVVFGYLLLMTAFAANYGPIATFLAELFG 370 Query: 383 THIRYSALASAFNISVLI-AGLTPTVAAWLVESSQNLYMPAYYLMVIAVIGLLTGLFMKE 441 T +RYS L+ ++ +S L+ + TP V L+ ++ A+Y++ A+I L+ L + E Sbjct: 371 TRVRYSGLSISYMLSGLLGSAATPIVTTALLAATGKGSSVAWYMIGAALISLVALLLLTE 430 Query: 442 TANKPL 447 T K + Sbjct: 431 TFKKDI 436 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: 587 Number of extensions: 32 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: 459 Length adjustment: 34 Effective length of query: 467 Effective length of database: 425 Effective search space: 198475 Effective search space used: 198475 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