Align ABC transporter for Xylitol, permease component 1 (characterized)
to candidate Synpcc7942_0949 Synpcc7942_0949 permease protein of sugar ABC transporter
Query= reanno::Dino:3607126 (288 letters) >FitnessBrowser__SynE:Synpcc7942_0949 Length = 292 Score = 157 bits (397), Expect = 3e-43 Identities = 102/264 (38%), Positives = 141/264 (53%), Gaps = 11/264 (4%) Query: 16 PAVIGLALVGIAPLLYALWTSLHFYNLTKLRRVEFIGLENYWTVLTDEVFWQAMGRTFFL 75 PA++ + V PLL A W SL NL + FIGL NY + D FW + T Sbjct: 11 PALLTITGVFAYPLLRAAWLSLQALNLNTQLQPVFIGLANYQRLWGDSRFWGDLFNTTVF 70 Query: 76 LGTALPLQIALGLGIALVLHQPGLTL--VKTLARLSLVLPMATTYAVVGLLGQVMFNQKF 133 T++ L++ LGL IAL+LHQP ++T+A L VLP A V+ L +FN + Sbjct: 71 TVTSVSLELVLGLAIALLLHQPSRWRGPLRTIALLPWVLPTA----VMALGWAWIFNDPY 126 Query: 134 GVVN---QLLG--GADINWIGDPENAFAMIIFWDVWQWTPFVALVLLAGLTMVPGEVEEA 188 GV N Q LG A INW+G+P A+ ++ DVW+ TPFVA++LLAG +P ++ EA Sbjct: 127 GVWNDWLQQLGWIAAPINWLGNPRWAWLTLVAADVWKTTPFVAILLLAGRQAIPEDLYEA 186 Query: 189 ARLETKSKWTVLRYVQLPFLLPGLVAVLILRTADTLKLFDMVFTLTRGGPGSSTEFISLM 248 LE + W + LP L P L L+ R+A LFD+V +T GGP +STE ++L Sbjct: 187 HCLEGATAWQSFWQITLPLLRPQLAIALLFRSAQAFGLFDLVKVMTGGGPANSTETLALY 246 Query: 249 IQRVGFRGFDQGLASAQAIILLII 272 R D G + AI+ I Sbjct: 247 AYTTALRYLDFGYGATLAIVTAAI 270 Lambda K H 0.329 0.144 0.440 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: 261 Number of extensions: 15 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: 288 Length of database: 292 Length adjustment: 26 Effective length of query: 262 Effective length of database: 266 Effective search space: 69692 Effective search space used: 69692 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: 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