Align Tyrosine permease (characterized)
to candidate 6938836 Sama_2939 tyrosine-specific transport protein, putative (RefSeq)
Query= TCDB::P0AAD4 (403 letters) >FitnessBrowser__SB2B:6938836 Length = 395 Score = 308 bits (788), Expect = 2e-88 Identities = 171/401 (42%), Positives = 244/401 (60%), Gaps = 13/401 (3%) Query: 1 MKNRTLGSVFIVAGTTIGAGMLAMPLAAAGVGFSVTLILLIGLWALMCYTALLLLEVYQH 60 M +TLGS+ IVAGT IGAGMLA+PLA A +G L+LL+ +WA+ YT+LL+LE+ Sbjct: 1 MNLKTLGSIAIVAGTAIGAGMLALPLATAALGVIPALLLLLVVWAISAYTSLLMLEINLR 60 Query: 61 VPADTGLGTLAKRYLGRYGQWLTGFSMMFLMYALTAAYISGAGELLASSISDWTGISMSA 120 + + + LG+ GQ + G S + L+YALTAAY++G LL + I++ Sbjct: 61 SGVGDNVHAITGKTLGKKGQLIQGASFLSLLYALTAAYLTGGSSLLVHRMESVFSINLDG 120 Query: 121 TAGVLLFTFVAGGVVCVGTSLVDLFNRFLFSAKIIFLVVMLVLLLPHIHKVNLLTLPLQQ 180 VLLFT V G V +G S VD +R LFS ++ LV+++ LLP I + ++ Sbjct: 121 QLAVLLFTLVLGSVAALGVSWVDKLSRLLFSLMVVLLVLVVGFLLPEIRPSVIAADAFEK 180 Query: 181 GLA---LSAIPVIFTSFGFHGSVPSIVSYMDGNIRKLRWVFIIGSAIPLVAYIFWQVATL 237 A ++AIPV+FTSFGFH + ++V Y+DG+ LR V +IGS IPLV YI W + TL Sbjct: 181 VSANAWMAAIPVVFTSFGFHVCIATLVRYLDGDAVNLRKVLLIGSTIPLVCYILWLLVTL 240 Query: 238 GSI---DSTTFMGLLANHAGLNGLLQALREMVASPHVELAVHLFADLALATSFLGVALGL 294 G++ + TF G L L+ AL+E+ A P V ++ +FADLAL TSFLGV + L Sbjct: 241 GTVGGDEIATFNGALPK------LISALQELAAHPVVGQSIAVFADLALVTSFLGVTMSL 294 Query: 295 FDYLADLFQRSNTVGGRLQTGAITFLPPLAFALFYPRGFVMALGYAGVALAVLALIIPSL 354 FD+LA++ + +GGRLQT ITFLPPL ALF P GFV LG+A + L + + +P Sbjct: 295 FDFLAEMTRSKGGIGGRLQTWIITFLPPLLCALFVPEGFVAVLGFAAIPLVFMIIFLPIA 354 Query: 355 LTWQSRKHNPQAGYRVKGGRPALVVVFLCGIAVIGVQFLIA 395 + R + GY+V GG+ AL ++ + G+A+I Q +A Sbjct: 355 MALNQRAQY-RDGYQVSGGKLALSLIGVAGVAIIAAQLWVA 394 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: 485 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: 395 Length adjustment: 31 Effective length of query: 372 Effective length of database: 364 Effective search space: 135408 Effective search space used: 135408 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