Align Tyrosine permease (characterized)
to candidate 203671 SO4601 tryptophan-specific transport protein (NCBI ptt file)
Query= TCDB::P0AAD4 (403 letters) >FitnessBrowser__MR1:203671 Length = 414 Score = 268 bits (686), Expect = 2e-76 Identities = 148/400 (37%), Positives = 230/400 (57%), Gaps = 5/400 (1%) Query: 6 LGSVFIVAGTTIGAGMLAMPLAAAGVGFSVTLILLIGLWALMCYTALLLLEVYQHVPADT 65 LG I+AGTT+GAGM ++P+ +G+ F ++++L+G+W M + LLLLE H Sbjct: 14 LGGAMIIAGTTVGAGMFSLPVVGSGMWFGYSILMLLGIWFCMLMSGLLLLETNLHFEPGA 73 Query: 66 GLGTLAKRYLGRYGQWLTGFSMMFLMYALTAAYISGAGELLASSISDWTGISMSATAGVL 125 TL K LG++ + + G S+ F++Y LT AYISG G ++ S+ GI + + L Sbjct: 74 SFDTLTKETLGQFWRIVNGVSIAFVLYILTYAYISGGGSIVNHSLQGM-GIELPQSVAGL 132 Query: 126 LFTFVAGGVVCVGTSLVDLFNRFLFSAKIIFLVVMLVLLLPHIHKVNLLTLPLQQGLA-- 183 +FT V +V + T VD + II + + LL I LL Q Sbjct: 133 VFTVVLACIVLISTKAVDRITTIMLGGMIITFFLAIGNLLIEIDVTKLLEPDGNQRFIPY 192 Query: 184 -LSAIPVIFTSFGFHGSVPSIVSYMDGNIRKLRWVFIIGSAIPLVAYIFWQVATLGSIDS 242 A+P SFG+HG+VPS+V Y + + +G+ I L+ Y+ W VAT+G+I Sbjct: 193 LWVALPFGLASFGYHGNVPSLVKYYGKDSSTIIKAIFVGTFIALIIYVCWLVATMGNIPR 252 Query: 243 TTFMGLLANHAGLNGLLQALREMVASPHVELAVHLFADLALATSFLGVALGLFDYLADLF 302 + F ++A + L+ AL +++ S + + LFA+LA+A+SFLGV LGLFDYLADLF Sbjct: 253 SQFSEIIAQGGNMGVLVGALSKVMESSWLNSMLTLFANLAVASSFLGVTLGLFDYLADLF 312 Query: 303 QRSNTVGGRLQTGAITFLPPLAFALFYPRGFVMALGYAGVALAVLALIIPSLLTWQSRKH 362 ++ GR++T +TF+PP F L +P GF++A+G+A +A V A+I+P+L+ ++SR+ Sbjct: 313 GFDDSRSGRMKTAIVTFVPPTVFGLLFPDGFLIAIGFAALAATVWAVIVPALMAYKSRQL 372 Query: 363 NP-QAGYRVKGGRPALVVVFLCGIAVIGVQFLIAAGLLPE 401 P G+RV GG P +++V L G+ L A LLP+ Sbjct: 373 FPNHQGFRVFGGTPLIILVVLFGVVTGACHLLAMANLLPQ 412 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: 388 Number of extensions: 13 Number of successful extensions: 4 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: 414 Length adjustment: 31 Effective length of query: 372 Effective length of database: 383 Effective search space: 142476 Effective search space used: 142476 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