Align ABC transporter for L-Fucose, permease component 1 (characterized)
to candidate HSERO_RS01340 HSERO_RS01340 sugar ABC transporter permease
Query= reanno::Smeli:SM_b21104 (298 letters) >FitnessBrowser__HerbieS:HSERO_RS01340 Length = 311 Score = 139 bits (350), Expect = 8e-38 Identities = 86/285 (30%), Positives = 145/285 (50%), Gaps = 20/285 (7%) Query: 13 LLPAFIVLAVFIVLPLIFSLYSSFTPFR-LTKPDSLWVFIGFRNYVNVLTNAEFWVAFGR 71 L PA ++ V+++ P+++++Y SF + +T+P F+G NYV + F+ A Sbjct: 42 LAPACVMTLVYVLYPILYTIYLSFFSWDGMTEPR----FVGLANYVELFHAPTFYTALKN 97 Query: 72 TVLLLTVALNAEMFLGLGLALLVNKATYGQRALRTAMMFPMMFSPVLVGFQFKFLFNDNI 131 VL L + L A +GL +AL +N+ G R +++ P + S V+VG + + ++ + Sbjct: 98 NVLWLLMFLLAPP-MGLAIALYLNQKVIGMRVVKSLFFAPFVLSGVVVGLMYSWFYDPSF 156 Query: 132 GFVNNALQSLGLTDRAIPWLIDGNLALFSIIVAEVWSSTAVFAILILAGLLAMPKDPVEA 191 G ++ L + +P L D A F II A +W TA IL L GL A+ D VEA Sbjct: 157 GLLSL------LFGQGVPVLGDARYATFGIIFAALWPQTAYCMILFLTGLTALNHDQVEA 210 Query: 192 AHVDGCTPWQTFRYVTWPYLMPFAFIAMTIRSLDVARAYDIVKIMTDGGPAKRTELLWTL 251 A ++G W RYV P L F+A + + R++D++ +MT GGP + + T+ Sbjct: 211 ARMEGAKGWTMLRYVILPQLRSTTFMAFVVSIIGALRSFDLISVMTSGGPYESS----TV 266 Query: 252 IGRTAYGDA----RMGMANAMAYVAILLSIFFTVYFFRKLAAARQ 292 + AY A R G + A+A + + + VY R++ A + Sbjct: 267 LAYYAYDQAIKYYRQGYSAAVAVTLFAIMLVYIVYQLRRMLRAER 311 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: 223 Number of extensions: 13 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: 298 Length of database: 311 Length adjustment: 27 Effective length of query: 271 Effective length of database: 284 Effective search space: 76964 Effective search space used: 76964 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