Align ABC transporter for L-Fucose, permease component 1 (characterized)
to candidate WP_084934373.1 HA51_RS09975 sugar ABC transporter permease
Query= reanno::Smeli:SM_b21104 (298 letters) >NCBI__GCF_002095475.1:WP_084934373.1 Length = 290 Score = 125 bits (313), Expect = 1e-33 Identities = 88/282 (31%), Positives = 139/282 (49%), Gaps = 16/282 (5%) Query: 11 LLLLPAFIVLAVFIVLPLIFSLYSSFTPFRLTKPDSLW-VFIGFRNYVNVLTNAEFWVAF 69 L LLPA +V AVF++LPL+ SL SFT + T W +F G NY+ + + FWVA Sbjct: 11 LYLLPAVLVYAVFLLLPLLASLGISFTEWDGTS----WPIFTGVSNYLRMFQDPVFWVAL 66 Query: 70 GRTVLLLTVALNAEMFLGLGLALLVNKATYGQR------ALRTAMMFPMMFSPVLVGFQF 123 G LL+ L +G+ LL+ Y R LR P + ++G + Sbjct: 67 GNNALLMLFYT----LLPIGVGLLLCSFLYDTRNNKERSVLRILFFLPYIMPMAVLGVVW 122 Query: 124 KFLFNDNIGFVNNALQSLGLTDRAIPWLIDGNLALFSIIVAEVWSSTAVFAILILAGLLA 183 ++L+N G ++ L+++GL A+ WL D AL ++ W +L +AGL Sbjct: 123 RWLYNPAFGPIDQFLRAIGLPQLALSWLGDFTWALPAVGFVATWYFFGFCLVLFMAGLQR 182 Query: 184 MPKDPVEAAHVDGCTPWQTFRYVTWPYLMPFAFIAMTIRSLDVARAYDIVKIMTDGGPAK 243 M +EAA +DG + Q F +T P L P IA+ + + +A+D+V +MT GGP Sbjct: 183 MDPSLLEAADLDGSSRRQKFMRITLPSLRPELRIALLLTVIASLKAFDLVYVMTQGGPGT 242 Query: 244 RTELLWTLIGRTAYGDARMGMANAMAYVAILLSIFF-TVYFF 284 T + + + + G A+A+A ++L+ + TV F Sbjct: 243 STMVTNIFMYKQGFDLHYFGYASAVAVFSMLIVLMINTVIHF 284 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: 264 Number of extensions: 21 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: 290 Length adjustment: 26 Effective length of query: 272 Effective length of database: 264 Effective search space: 71808 Effective search space used: 71808 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 24 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