Align ABC transporter for L-asparagine and L-glutamate, permease component 1 (characterized)
to candidate GFF18 Psest_0018 ectoine/hydroxyectoine ABC transporter, permease protein EhuC
Query= reanno::pseudo1_N1B4:Pf1N1B4_772 (248 letters) >FitnessBrowser__psRCH2:GFF18 Length = 219 Score = 98.6 bits (244), Expect = 9e-26 Identities = 69/213 (32%), Positives = 109/213 (51%), Gaps = 11/213 (5%) Query: 26 LSGLGWTIAIAVAAWIIALLLGSILGVMRTVPNRIVSGIATCYVELFRNVPLLVQLFIWY 85 L G T+ + ++A+ I + R P + +A Y+E+FR LLVQLF Y Sbjct: 9 LQGAWVTVKVTFFGSLLAIACALIAALARLSPVAPLRWLAITYIEVFRGSSLLVQLFWLY 68 Query: 86 FLVPDLLPADIQEWYKQDLNPTTSAFLSVVVCLGLFTTARVCEQVRTGIQALPRGQEAAA 145 F++P + P +I+ SAF VV LGL A E +R I+++ RGQ A Sbjct: 69 FVLP-MPPFNIE----------MSAFAVAVVGLGLNIGAYGAEVLRGAIRSVHRGQHEAC 117 Query: 146 RAMGFKLPQIYWNVLLPQAYRIIIPPLTSEFLNVFKNSSVASLIGLMELLAQTKQTAEFS 205 +A+ ++LPQA IPP T+ + + KN+S+ SLI L +L + +Q + + Sbjct: 118 QALNMTPLTRMRRIILPQALLAAIPPGTNLLIELLKNTSLVSLITLSDLAFRARQLDQAT 177 Query: 206 ANLFEAFTLATLIYFTLNMSLMLLMRSVEKKVA 238 E F LA +IYF L ++ MR +E+++A Sbjct: 178 LMTMEIFGLALVIYFVLAQTINFGMRQLERRLA 210 Lambda K H 0.326 0.140 0.433 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: 119 Number of extensions: 5 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: 248 Length of database: 219 Length adjustment: 23 Effective length of query: 225 Effective length of database: 196 Effective search space: 44100 Effective search space used: 44100 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 (21.7 bits) S2: 46 (22.3 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