Align Glycine betaine/proline/ectoine/pipecolic acid transporter OusA; Osmoprotectant uptake system A (characterized)
to candidate PP_3666 PP_3666 Metabolite MFS transporter, MHS family
Query= SwissProt::Q47421 (501 letters) >FitnessBrowser__Putida:PP_3666 Length = 444 Score = 335 bits (859), Expect = 2e-96 Identities = 170/429 (39%), Positives = 263/429 (61%), Gaps = 12/429 (2%) Query: 24 LRKAITAAALGNAMEWFDFGVYGFVAYALGQVFFPGADPGVQMIAALATFSVPFLIRPLG 83 LRKA A+ +GN +EWFD+ YG++A + FFP D ++A A F++ FL+RPLG Sbjct: 23 LRKAARASFMGNFVEWFDYAAYGYLATIIAATFFPQTDKTTGLLATFAVFALSFLVRPLG 82 Query: 84 GVFFGALGDKYGRQKILAITIIIMSISTFCIGLIPSYERIGIWAPILLLLAKMAQGFSVG 143 G+ +G GD++GR+ L+ +I+IMS+STFCIGL+P Y +IG+WAP LLLL ++ QGFS Sbjct: 83 GIVWGHFGDRHGRRNALSWSILIMSVSTFCIGLLPGYAQIGLWAPALLLLIRLVQGFSAS 142 Query: 144 GEYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTLIGEQAFLAWGWRL 203 GEY GA+ F+AEY+P +RG S + + AG + GA V ++ L+ +A WGWRL Sbjct: 143 GEYAGAAAFLAEYAPPGRRGLYTSIVPASTAAGLLFGAAFVAVLHELLSSEALHEWGWRL 202 Query: 204 PFFLALPLGLIGLYLRHALEETPAFRQHVEKLEQNDRDGLKAGPGVSFREIATHHWKSLL 263 PF LA P GL+G Y+R +L++TP F + ++LE + G+ P RE+ H +SL Sbjct: 203 PFLLAAPFGLVGRYIRMSLQDTPKFLEMEQRLE--TKAGMATTP---LRELLGQHRRSLA 257 Query: 264 VCIGLVIATNVTYYMLLTYMPSYLSHSLHYSENHGVL---IIIAIMIGMLFVQPVMGLLS 320 + +G+ V +Y+LL+YMP+YLS + SE + + +A IG++F +MG LS Sbjct: 258 IGMGVTCLNAVAFYLLLSYMPTYLSSEMGMSERDSFIASTVSLATYIGLIF---LMGRLS 314 Query: 321 DRFGRKPFVVIGSVAMFFLAVPSFMLINSDIIGLIFLGLLMLAVILNAFTGVMASTLPAL 380 D+FGRK +V+ S+ L VP F L++ + +I ++ +L G + L + Sbjct: 315 DQFGRKTMLVVASLLFLGLTVPLFRLLDGQPLLVILAIQILFGAMLAMNDGTLPCLLAEI 374 Query: 381 FPTHIRYSALASAFNI-SVLIAGLTPTVAAWLVESSQNLYMPAYYLMVIAVIGLLTGLFM 439 FPT +R+S A +FN+ + L G P +A WL++ + + PA YL+ A++ L+ L Sbjct: 375 FPTRVRFSGFALSFNVANALFGGTAPFIATWLIQVTGSKLAPAGYLLAAALVALVAMLMC 434 Query: 440 KETANKPLK 448 +ETA+ L+ Sbjct: 435 RETAHAALE 443 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: 579 Number of extensions: 34 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: 444 Length adjustment: 33 Effective length of query: 468 Effective length of database: 411 Effective search space: 192348 Effective search space used: 192348 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