Align Tyrosine permease (characterized)
to candidate 5210760 Shew_3188 aromatic amino acid permease (RefSeq)
Query= TCDB::P0AAD4 (403 letters) >FitnessBrowser__PV4:5210760 Length = 395 Score = 295 bits (754), Expect = 2e-84 Identities = 166/398 (41%), Positives = 237/398 (59%), Gaps = 13/398 (3%) Query: 6 LGSVFIVAGTTIGAGMLAMPLAAAGVGFSVTLILLIGLWALMCYTALLLLEVYQHVPADT 65 LGS+ IVAGT IG GMLA+PLA A +G L+LL+ +W + YT+LL+LE+ Sbjct: 2 LGSIAIVAGTAIGGGMLALPLATASLGTIPALLLLVAIWGVSIYTSLLMLEINLRAGVGL 61 Query: 66 GLGTLAKRYLGRYGQWLTGFSMMFLMYALTAAYISGAGELLASSISDWTGISMSATAGVL 125 + + + LG+ GQ + G S + L++ALT Y+ G LL S GI ++ A VL Sbjct: 62 NVHAITGKTLGKVGQLIQGGSFLSLLFALTMVYLMGGSSLLESRFEP-LGIKVNHEAAVL 120 Query: 126 LFTFVAGGVVCVGTSLVDLFNRFLFSAKIIFLVVMLVLLLPHIHKVNLL----TLPLQQG 181 +FT V GG + +G S +D +R LFSA + V++++ LLP + +L T + +G Sbjct: 121 IFTLVFGGFIAIGVSWIDKVSRVLFSAMVALFVIVVLFLLPEVSPSYILRESATELVSKG 180 Query: 182 ----LALSAIPVIFTSFGFHGSVPSIVSYMDGNIRKLRWVFIIGSAIPLVAYIFWQVATL 237 L L+AIPV+FTSFGFH + +IV Y+DG+ LR V +IGS IPLV YI W + TL Sbjct: 181 ELGNLWLAAIPVVFTSFGFHVCIATIVRYLDGDAMSLRKVLMIGSTIPLVCYILWLMVTL 240 Query: 238 GSIDSTTFMGLLANHAGLNGLLQALREMVASPHVELAVHLFADLALATSFLGVALGLFDY 297 G++ T G L L+ AL+ + S + + LFA+LAL TSFLGV + LFDY Sbjct: 241 GTVGGATVYGF---EGSLPKLVSALQGIAHSDILRQCIDLFANLALITSFLGVTMSLFDY 297 Query: 298 LADLFQRSNTVGGRLQTGAITFLPPLAFALFYPRGFVMALGYAGVALAVLALIIPSLLTW 357 +A+L + + + GRLQT ITF+PPL AL+YP GF+ LG+A + L V+ + +P + Sbjct: 298 IAELTRARDNLLGRLQTWLITFVPPLLCALYYPDGFIKVLGFAALPLVVMIIFLPIAMAL 357 Query: 358 QSRKHNPQAGYRVKGGRPALVVVFLCGIAVIGVQFLIA 395 RK N GY+V GG+ AL L G+ +I Q +A Sbjct: 358 GQRKQN-LGGYQVSGGQFALAASALVGLVIIAAQLWVA 394 Lambda K H 0.329 0.143 0.432 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: 450 Number of extensions: 21 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: 403 Length of database: 395 Length adjustment: 31 Effective length of query: 372 Effective length of database: 364 Effective search space: 135408 Effective search space used: 135408 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 (21.8 bits) S2: 50 (23.9 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