Align Tyrosine permease (characterized)
to candidate 7023682 Shewana3_0912 aromatic amino acid permease (RefSeq)
Query= TCDB::P0AAD4 (403 letters) >FitnessBrowser__ANA3:7023682 Length = 391 Score = 305 bits (781), Expect = 2e-87 Identities = 161/393 (40%), Positives = 240/393 (61%), Gaps = 7/393 (1%) Query: 6 LGSVFIVAGTTIGAGMLAMPLAAAGVGFSVTLILLIGLWALMCYTALLLLEVYQHVPADT 65 LGS+ IVAGT IGAGMLA+PLA A +G ++L++ +W L YT+LL+LE+ Sbjct: 2 LGSIAIVAGTAIGAGMLALPLATAALGMVPAILLMVVIWGLSAYTSLLMLEINLRSGVGD 61 Query: 66 GLGTLAKRYLGRYGQWLTGFSMMFLMYALTAAYISGAGELLASSISDWTGISMSATAGVL 125 + + + LG+ GQ + G S + L++ALTAAY++G LL + + + V+ Sbjct: 62 NVHAITGKLLGKKGQMVQGASFLSLLFALTAAYLTGGSSLLVLKAKNMFDLVLDNQLAVV 121 Query: 126 LFTFVAGGVVCVGTSLVDLFNRFLFSAKIIFLVVMLVLLLPHIHKVNLLTLPLQQGLA-- 183 LFT V GG +G + VD +RFLFS I+ L+V+++ LLP + ++ T + + + Sbjct: 122 LFTLVLGGFAALGVAWVDKASRFLFSLMILLLIVVVLFLLPEVSISSMATSAVAESMTSS 181 Query: 184 -LSAIPVIFTSFGFHGSVPSIVSYMDGNIRKLRWVFIIGSAIPLVAYIFWQVATLGSIDS 242 ++AIPV+FTSFGFH + ++V Y+DG+ LR V +IGS IPL YIFW + TLG++ Sbjct: 182 WMAAIPVVFTSFGFHVCIATLVRYLDGDAVSLRKVLLIGSTIPLACYIFWLLVTLGTVGG 241 Query: 243 TTFMGLLANHAGLNGLLQALREMVASPHVELAVHLFADLALATSFLGVALGLFDYLADLF 302 T + L L+ AL+E+ +P + + LFADLAL TSFLGV L L+D++A+L Sbjct: 242 TEISSF---NGSLPALISALQEIAHTPWISKCISLFADLALITSFLGVTLSLYDFVAELT 298 Query: 303 QRSNTVGGRLQTGAITFLPPLAFALFYPRGFVMALGYAGVALAVLALIIPSLLTWQSRKH 362 + T GR QT +TF+PPL AL+ P GFV LG+A V L V+ + +P ++ + R+ Sbjct: 299 RAKKTFLGRAQTWLLTFVPPLLCALYVPEGFVAVLGFAAVPLVVMIIFLPIVMALRQRQA 358 Query: 363 NPQAGYRVKGGRPALVVVFLCGIAVIGVQFLIA 395 PQ GY+V GG +L + L G +IG Q +A Sbjct: 359 TPQ-GYQVSGGTFSLGIAGLLGAVIIGAQLFVA 390 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: 465 Number of extensions: 21 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: 391 Length adjustment: 31 Effective length of query: 372 Effective length of database: 360 Effective search space: 133920 Effective search space used: 133920 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