Align The lysine specific transporter, LysP of 488 aas and 12 TMSs (characterized)
to candidate BPHYT_RS15500 BPHYT_RS15500 aromatic amino acid transporter
Query= TCDB::K7VV21 (488 letters) >FitnessBrowser__BFirm:BPHYT_RS15500 Length = 461 Score = 297 bits (760), Expect = 6e-85 Identities = 170/470 (36%), Positives = 264/470 (56%), Gaps = 41/470 (8%) Query: 13 VKRGLKSRHVSMIALGGTIGTGLFLTSGDVIHTAGPFGALTAYVLIGAMVYFLMTSLGEM 72 +KRGLK+RH+ +IALGG IGTGLFL S V+ AGP + Y + G + + +M LGEM Sbjct: 10 LKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGP-SMILGYAIGGIIAFMIMRQLGEM 68 Query: 73 ATYLPTSGSFSDYGTRYVDPAFGFALGWNYWLNWAITVAVDLTAVALCIKFWLPDVPSWI 132 P +GSFS + +Y GF GWNYW+ + + +LTAV I +W P VP+W+ Sbjct: 69 VAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYIHYWWPGVPTWV 128 Query: 133 FSLIALIIVFSINALSVKTFGETEYWLSAIKITVVVLFLII-GFLSIFGIMGGHIDVAKN 191 +L+ ++ +IN +VK +GETE+W + IK+ V+ ++ G+L I G G + Sbjct: 129 SALVCFALINAINLANVKAYGETEFWFAIIKVVAVIGMIVFGGYLLISGHGGPQASITNL 188 Query: 192 LSVGN---HGFVGGLGSFTTGGGILGVLLVAGFSFQGTELLGITAGEAENPEKSIPKAMN 248 S G HGF G+ +L V FSF G EL+GITA EA+ P+KSIPKA+N Sbjct: 189 WSHGGFFPHGF----------HGLFMMLAVIMFSFGGLELIGITAAEADQPQKSIPKAVN 238 Query: 249 SIFWRILVFYILSIFVMAAIIPFTDPHLVGGNSAAQSPFTIVFERVGFSIAASIMNAVVL 308 + +RIL+FYI S+ V+ ++ P+ + +A SPF ++F ++G ++ A+++N VVL Sbjct: 239 QVIYRILIFYICSLTVLLSLYPWNEV------AAGGSPFVMIFSQIGSTLTANVLNVVVL 292 Query: 309 TSVVSAANSGMYASTRMLYSLAKDGGAPTIFSKTSKNGIPFIAL----LATTAVALLTFL 364 T+ +S NSG+YA++RMLY LA+ G AP K + G+P++A+ LAT ++ +L Sbjct: 293 TAALSVYNSGVYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYL 352 Query: 365 TSIYGVSFFTFLVSASGLTGFIAWIGIAISHFRFRRAYVAQGKDVKKLPYHAKLFPFGP- 423 + LV A+ + + W I+++H + R+A VA G + L + + FP Sbjct: 353 IPAEALGLLMALVVAALV---LNWALISLTHLKSRKAMVAAG---ETLVFKSFWFPVSNW 406 Query: 424 -ILALIMTVLVTLGQDPMLLFGKTWVQGVVMYAAIPLFFILYLGYKFKNK 472 LA + +LV L P L V ++ +++ GY FK + Sbjct: 407 ICLAFMALILVILAMTPGL--------SVSVWLVPAWLVVMWAGYVFKRR 448 Lambda K H 0.326 0.141 0.425 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: 567 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: 488 Length of database: 461 Length adjustment: 33 Effective length of query: 455 Effective length of database: 428 Effective search space: 194740 Effective search space used: 194740 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 (21.6 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