Align Tyrosine permease (characterized)
to candidate WP_012275403.1 SHAL_RS01375 tryptophan permease
Query= TCDB::P0AAD4 (403 letters) >NCBI__GCF_000019185.1:WP_012275403.1 Length = 418 Score = 265 bits (676), Expect = 2e-75 Identities = 147/406 (36%), Positives = 225/406 (55%), Gaps = 13/406 (3%) Query: 6 LGSVFIVAGTTIGAGMLAMPLAAAGVGFSVTLILLIGLWALMCYTALLLLEVYQHVPADT 65 LG I+AGT +GAGM ++P+ AG+ F +L+++ G+W M + LLLLE H Sbjct: 18 LGGAMIIAGTAVGAGMFSLPVVGAGMWFGYSLLMMAGVWFCMLVSGLLLLETNLHFKPGD 77 Query: 66 GLGTLAKRYLGRYGQWLTGFSMMFLMYALTAAYISGAGELLASSISDWTGISMSATAGVL 125 TL + LG + + + G S+ F++Y L AYISG G ++ +++ GI + L Sbjct: 78 SFDTLTRTTLGNFWRIVNGLSIAFVLYILAYAYISGGGSIVNYNLAS-AGIELPQGIAGL 136 Query: 126 LFTFVAGGVVCVGTSLVDLFNRFLFSAKIIFLVVMLVLLLPHIHKVNLLT-------LPL 178 +F +V + T VD + +I + + LL + V L + LP Sbjct: 137 IFALGLAFIVFISTKAVDRITTIMLGGMLITFFLAVGNLLLDVESVKLFSPDGENKYLPY 196 Query: 179 QQGLALSAIPVIFTSFGFHGSVPSIVSYMDGNIRKLRWVFIIGSAIPLVAYIFWQVATLG 238 L+A+P SFG+HG+VPS+V Y + R + +IG+ I LV YI W VAT+G Sbjct: 197 M----LAALPFGLVSFGYHGNVPSLVKYYGKDHRTIIKAIVIGTGIALVIYICWLVATMG 252 Query: 239 SIDSTTFMGLLANHAGLNGLLQALREMVASPHVELAVHLFADLALATSFLGVALGLFDYL 298 +I T F+G++ + L+ AL ++ S + + LFA+LA+A+SFLGV LGLFDYL Sbjct: 253 NISRTDFIGIIEQGGNMGVLVNALSGVMTSDWLTTMLTLFANLAVASSFLGVTLGLFDYL 312 Query: 299 ADLFQRSNTVGGRLQTGAITFLPPLAFALFYPRGFVMALGYAGVALAVLALIIPSLLTWQ 358 ADLF + GR +T A+TFLPP L +P GF++A+G+A +A + A I+P+++ ++ Sbjct: 313 ADLFGFDESRSGRFKTAAVTFLPPTVLGLLFPDGFLVAIGFAALAATIWAAIVPAMMAYK 372 Query: 359 SRKHNP-QAGYRVKGGRPALVVVFLCGIAVIGVQFLIAAGLLPEVG 403 R P A Y+V GG +V+V L G+ L AG+LP G Sbjct: 373 VRVMYPDSASYKVPGGNAVIVIVILFGVITAACHLLAMAGMLPLYG 418 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: 448 Number of extensions: 27 Number of successful extensions: 3 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: 418 Length adjustment: 31 Effective length of query: 372 Effective length of database: 387 Effective search space: 143964 Effective search space used: 143964 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 24 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