Align Tyrosine permease (characterized)
to candidate 17769 b3709 tryptophan transporter of low affinity (NCBI)
Query= TCDB::P0AAD4 (403 letters) >FitnessBrowser__Keio:17769 Length = 415 Score = 217 bits (553), Expect = 4e-61 Identities = 133/408 (32%), Positives = 211/408 (51%), Gaps = 6/408 (1%) Query: 2 KNRTLGSVFIVAGTTIGAGMLAMPLAAAGVGFSVTLILLIGLWALMCYTALLLLEVYQHV 61 K+ V ++AGT IG GM A+P+ AG F +LI W M ++ LLLLE + Sbjct: 8 KHSAFWGVMVIAGTVIGGGMFALPVDLAGAWFFWGAFILIIAWFSMLHSGLLLLEANLNY 67 Query: 62 PADTGLGTLAKRYLGRYGQWLTGFSMMFLMYALTAAYISGAGELLASSISDWTGISMSAT 121 P + T+ K +G ++G ++ F++Y LT AYIS G +++ +IS G + Sbjct: 68 PVGSSFNTITKDLIGNTWNIISGITVAFVLYILTYAYISANGAIISETISMNLGYHANPR 127 Query: 122 -AGVLLFTFVAGGVVCVGTSLVDLFNRFLFSAKIIFLVVMLVLLLPHIHKVNLLTLPLQQ 180 G+ FVA + + + + FL I F++V + + Sbjct: 128 IVGICTAIFVASVLWLSSLAASRITSLFLGLKIISFVIVFGSFFFQVDYSILRDATSSTA 187 Query: 181 GLA-----LSAIPVIFTSFGFHGSVPSIVSYMDGNIRKLRWVFIIGSAIPLVAYIFWQVA 235 G + A+PV SFGFHG++PS++ KL + GS + LV Y+FW Sbjct: 188 GTSYFPYIFMALPVCLASFGFHGNIPSLIICYGKRKDKLIKSVVFGSLLALVIYLFWLYC 247 Query: 236 TLGSIDSTTFMGLLANHAGLNGLLQALREMVASPHVELAVHLFADLALATSFLGVALGLF 295 T+G+I +F ++++ ++ L+++ +E + +F++LA+A+SF GV LGLF Sbjct: 248 TMGNIPRESFKAIISSGGNVDSLVKSFLGTKQHGIIEFCLLVFSNLAVASSFFGVTLGLF 307 Query: 296 DYLADLFQRSNTVGGRLQTGAITFLPPLAFALFYPRGFVMALGYAGVALAVLALIIPSLL 355 DYLADLF+ N+ GGR +T +TFLPP L +P GF+ +G AG+ + A+IIP++L Sbjct: 308 DYLADLFKIDNSHGGRFKTVLLTFLPPALLYLIFPNGFIYGIGGAGLCATIWAVIIPAVL 367 Query: 356 TWQSRKHNPQAGYRVKGGRPALVVVFLCGIAVIGVQFLIAAGLLPEVG 403 ++RK P + V GG +V L GI VI F +LP+ G Sbjct: 368 AIKARKKFPNQMFTVWGGNLIPAIVILFGITVILCWFGNVFNVLPKFG 415 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: 436 Number of extensions: 21 Number of successful extensions: 1 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: 415 Length adjustment: 31 Effective length of query: 372 Effective length of database: 384 Effective search space: 142848 Effective search space used: 142848 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