Align Tyrosine permease (characterized)
to candidate 6939387 Sama_3479 aromatic amino acid transport protein (RefSeq)
Query= TCDB::P0AAD4 (403 letters) >FitnessBrowser__SB2B:6939387 Length = 418 Score = 264 bits (674), Expect = 4e-75 Identities = 148/399 (37%), Positives = 224/399 (56%), Gaps = 5/399 (1%) Query: 6 LGSVFIVAGTTIGAGMLAMPLAAAGVGFSVTLILLIGLWALMCYTALLLLEVYQHVPADT 65 LG I+AGTT+GAGM ++P+ AG+ F +L+L++ +W M + LLLLE Sbjct: 18 LGGAMIIAGTTVGAGMFSLPVVGAGMWFGYSLLLMVAIWLCMLLSGLLLLETNLRFEPGA 77 Query: 66 GLGTLAKRYLGRYGQWLTGFSMMFLMYALTAAYISGAGELLASSISDWTGISMSATAGVL 125 TL + LGR+G+ + G S+ F++Y LT AYISG G ++ S+S GIS+ + L Sbjct: 78 SFDTLTRDSLGRFGRIVNGLSIAFVLYILTYAYISGGGSIVNHSLSGM-GISLPQSVAGL 136 Query: 126 LFTFVAGGVVCVGTSLVDLFNRFLFSAKIIFLVVMLVLLLPHIHKVNLLTLPLQQGLA-- 183 +F V +V + T VD + I+ + + LL + NL + + A Sbjct: 137 VFAAVLAAIVMISTKAVDRITTIMLGGMIMTFFLAVGNLLIEVQPSNLFSPDGEARFAPF 196 Query: 184 -LSAIPVIFTSFGFHGSVPSIVSYMDGNIRKLRWVFIIGSAIPLVAYIFWQVATLGSIDS 242 +AIP SFG+HG+VPS+V Y N + IG+ I LV Y+ W +A +G++ Sbjct: 197 LWAAIPFGLASFGYHGNVPSLVKYYGKNPSVIIKAICIGTFIALVIYVCWLLAAMGNLPR 256 Query: 243 TTFMGLLANHAGLNGLLQALREMVASPHVELAVHLFADLALATSFLGVALGLFDYLADLF 302 + F ++A + L+ AL E++A+ + + LFA+LA+A+SFLGV LGLFDYLADLF Sbjct: 257 SQFSDIIAQGGNMGVLVSALSEVMANDWLGKMLTLFANLAVASSFLGVTLGLFDYLADLF 316 Query: 303 QRSNTVGGRLQTGAITFLPPLAFALFYPRGFVMALGYAGVALAVLALIIPSLLTWQSRKH 362 ++ GR +T A+TFLPP L +P GF++A+G+A +A V L++P ++ + RK Sbjct: 317 GFADDAKGRFKTAAVTFLPPTLLGLLFPDGFLVAIGFAALAATVWTLLVPGVMALKLRKQ 376 Query: 363 NPQ-AGYRVKGGRPALVVVFLCGIAVIGVQFLIAAGLLP 400 P G+RV GG + +V GI L A LLP Sbjct: 377 QPDYPGFRVPGGAGVIYLVISFGILTAACHLLAMAELLP 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: 414 Number of extensions: 20 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: 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 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