Align ABC transporter for L-Fucose, permease component 1 (characterized)
to candidate Synpcc7942_0949 Synpcc7942_0949 permease protein of sugar ABC transporter
Query= reanno::Smeli:SM_b21104 (298 letters) >FitnessBrowser__SynE:Synpcc7942_0949 Length = 292 Score = 144 bits (364), Expect = 2e-39 Identities = 90/268 (33%), Positives = 136/268 (50%), Gaps = 3/268 (1%) Query: 9 PTLLLLPAFIVLAVFIVLPLIFSLYSSFTPFRLTKPDSLWVFIGFRNYVNVLTNAEFWVA 68 P L +PA + + PL+ + + S L VFIG NY + ++ FW Sbjct: 5 PRWLTIPALLTITGVFAYPLLRAAWLSLQALNLNTQLQP-VFIGLANYQRLWGDSRFWGD 63 Query: 69 FGRTVLLLTVALNAEMFLGLGLALLVNKATYGQRALRTAMMFPMMFSPVLVGFQFKFLFN 128 T + +++ E+ LGL +ALL+++ + + LRT + P + ++ + ++FN Sbjct: 64 LFNTTVFTVTSVSLELVLGLAIALLLHQPSRWRGPLRTIALLPWVLPTAVMALGWAWIFN 123 Query: 129 DNIGFVNNALQSLGLTDRAIPWLIDGNLALFSIIVAEVWSSTAVFAILILAGLLAMPKDP 188 D G N+ LQ LG I WL + A +++ A+VW +T AIL+LAG A+P+D Sbjct: 124 DPYGVWNDWLQQLGWIAAPINWLGNPRWAWLTLVAADVWKTTPFVAILLLAGRQAIPEDL 183 Query: 189 VEAAHVDGCTPWQTFRYVTWPYLMPFAFIAMTIRSLDVARAYDIVKIMTDGGPAKRTELL 248 EA ++G T WQ+F +T P L P IA+ RS +D+VK+MT GGPA TE L Sbjct: 184 YEAHCLEGATAWQSFWQITLPLLRPQLAIALLFRSAQAFGLFDLVKVMTGGGPANSTETL 243 Query: 249 WTLIGRTA--YGDARMGMANAMAYVAIL 274 TA Y D G A+ AIL Sbjct: 244 ALYAYTTALRYLDFGYGATLAIVTAAIL 271 Lambda K H 0.331 0.142 0.441 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: 282 Number of extensions: 13 Number of successful extensions: 1 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: 298 Length of database: 292 Length adjustment: 26 Effective length of query: 272 Effective length of database: 266 Effective search space: 72352 Effective search space used: 72352 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 48 (23.1 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