Align ABC transporter for Xylitol, permease component 1 (characterized)
to candidate AO356_27675 AO356_27675 sugar ABC transporter permease
Query= reanno::Dino:3607126 (288 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_27675 Length = 311 Score = 121 bits (303), Expect = 2e-32 Identities = 84/279 (30%), Positives = 138/279 (49%), Gaps = 7/279 (2%) Query: 14 IGPAVIGLALVGIAPLLYALWTSLHFYNLTKLRRVEFIGLENYWTVLTDEVFWQAMGRTF 73 + P+V L L I PL ++ S+ YNL EF+GLEN+ LTD F T Sbjct: 32 VSPSVALLLLWMIVPLGMTVYFSMIRYNLLYPGENEFVGLENFTYFLTDSGFMPGATNTL 91 Query: 74 FLLGTALPLQIALGLGIALVLHQPGLTLVKTLARLSLVLPMATTYAVVGLLGQ-VMFNQK 132 L+G+ L + I LG+ I+ +L + + R+ L+ P V L+ + ++F+ Sbjct: 92 LLVGSVLLISIVLGVLISALLEASEF-FGRGIVRVLLISPFFIMPTVGALIWKNLIFHPV 150 Query: 133 FGV---VNQLLGGADINWIGDPENAFAMIIFWDVWQWTPFVALVLLAGLTMVPGEVEEAA 189 G+ V +L G ++W+ II WQW PF L+L+ + + E +EAA Sbjct: 151 SGILASVWKLFGAQPVDWLA--HYPLLSIIIIVSWQWLPFAILILMTAMQSLDQEQKEAA 208 Query: 190 RLETKSKWTVLRYVQLPFLLPGLVAVLILRTADTLKLFDMVFTLTRGGPGSSTEFISLMI 249 RL+ + ++ LP L + VL++ T L +F +FT T GGPG ++ ++ +I Sbjct: 209 RLDGAGPIAIFWHLTLPHLARPIAVVLMIETIFLLSVFAEIFTTTNGGPGYASTNLAYLI 268 Query: 250 QRVGFRGFDQGLASAQAIILLIITIVLAQIYIRVFYKEV 288 FD G+ASA +I ++I + A I +R+ K + Sbjct: 269 YNQALVQFDVGMASAGGLIAVVIANIAAIILVRMIGKNL 307 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: 271 Number of extensions: 14 Number of successful extensions: 2 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: 311 Length adjustment: 27 Effective length of query: 261 Effective length of database: 284 Effective search space: 74124 Effective search space used: 74124 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