Align Glycine betaine/proline/ectoine/pipecolic acid transporter OusA; Osmoprotectant uptake system A (characterized)
to candidate PfGW456L13_3155 L-Proline/Glycine betaine transporter ProP
Query= SwissProt::Q47421 (501 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3155 Length = 429 Score = 301 bits (770), Expect = 4e-86 Identities = 158/417 (37%), Positives = 240/417 (57%), Gaps = 10/417 (2%) Query: 28 ITAAALGNAMEWFDFGVYGFVAYALGQVFFPGADPGVQMIAALATFSVPFLIRPLGGVFF 87 I AA +GN +EWFDF VYGF+A + Q FFP D ++ A F+V F RPLGG+FF Sbjct: 2 IVAAGIGNFVEWFDFAVYGFLATTIAQQFFPSGDASAALLKTFAVFAVAFAFRPLGGIFF 61 Query: 88 GALGDKYGRQKILAITIIIMSISTFCIGLIPSYERIGIWAPILLLLAKMAQGFSVGGEYT 147 G LGD+ GR++ LA+TI++M+ +T IGL+P+Y IG+ APILL L + AQGFS GGEY Sbjct: 62 GMLGDRIGRKRTLAMTILLMAGATTLIGLLPTYAAIGVMAPILLSLIRCAQGFSAGGEYA 121 Query: 148 GASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTLIGEQAFLAWGWRLPFFL 207 GA ++ E++P KR + GS++ + + F A V + + +A +WGWRLPF + Sbjct: 122 GACAYLMEHAPSDKRAWYGSFIPVSTFSAFAAAAVVAYALEASLSAEAMGSWGWRLPFLI 181 Query: 208 ALPLGLIGLYLRHALEETPAFRQHVEKLEQNDRDGLKAGPGVSFREIATHHWKSLLVCIG 267 A PLGL+GLYLR L+ETPAF+ ++ A +E +H ++ Sbjct: 182 AAPLGLVGLYLRWKLDETPAFQAVTQE---------HAVAHSPLKETLRNHGAAICCLGA 232 Query: 268 LVIATNVTYYMLLTYMPSYLSHSLHYSENHGVLIIIAIMIGMLFVQPVMGLLSDRFGRKP 327 V T +++YM TY +YL + S +L+ + ++ + P+ GL SDR GR+ Sbjct: 233 FVSLTALSFYMFTTYFATYLQVAGGLSRATALLVSLIALLFAAAICPLAGLYSDRVGRRV 292 Query: 328 FVVIGSVAMFFLAVPSFMLINSDIIGLIFLGLLMLAVILNAFTGVMASTLPALFPTHIRY 387 V+ + + PSF++ +S +G+++LA+ V A+ L FPT RY Sbjct: 293 TVMTACALLIVVVYPSFLMASSGSFAASIVGVMLLAIGAVLCGVVTAALLSETFPTRTRY 352 Query: 388 SALASAFNIS-VLIAGLTPTVAAWLVESSQNLYMPAYYLMVIAVIGLLTGLFMKETA 443 +A A +N++ L G P VA WL+ ++ + PA+YL+ IA++ L GL + ET+ Sbjct: 353 TASAITYNMAYTLFGGTAPLVATWLISTTGSNLSPAFYLIAIALLALAGGLALPETS 409 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: 506 Number of extensions: 26 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: 429 Length adjustment: 33 Effective length of query: 468 Effective length of database: 396 Effective search space: 185328 Effective search space used: 185328 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