Align ABC transporter for L-Fucose, permease component 1 (characterized)
to candidate WP_049989937.1 LT39_RS07855 sugar ABC transporter permease
Query= reanno::Smeli:SM_b21104 (298 letters) >NCBI__GCF_000784335.1:WP_049989937.1 Length = 308 Score = 140 bits (352), Expect = 5e-38 Identities = 85/279 (30%), Positives = 147/279 (52%), Gaps = 9/279 (3%) Query: 11 LLLLPAFIVLAVFIVLPLIFSLYSSFTPFRLTKPDSLWVFIGFRNYVNVLTNAEFWVAFG 70 L ++P +++ VFI+ P+ ++YSSF L PD F+G NY + TN + Sbjct: 26 LPIVPVMVLVGVFILYPIAQAIYSSFFDKSLLSPDEA-EFVGLANYQEIWTNPDLHQVLW 84 Query: 71 RTVLLLTVALNAEMFLGLGLA-LLVNKATYGQRALRTAMMFPMMFSPVLVGFQFKFLFND 129 T + ++V A + G L LL K Y A ++ P + V+ ++F+F Sbjct: 85 NTFVWVSVGSIAAIVFGFVLGWLLYEKFPYTSVA-SAIVLIPWVLPRVVGASIWQFMFGG 143 Query: 130 NIGFVNNALQSLGLTDRAIPWLIDGNLALFSIIVAEVWSSTAVFAILILAGLLAMPKDPV 189 + G +N L LG+ D + L G+L+L+ I+ +W +FA+L L L + + Sbjct: 144 DQGIINELLVQLGVIDEYMVMLGSGDLSLWPPIIGMIWRLAPLFALLTLTSLQGIDEHLY 203 Query: 190 EAAHVDGCTPWQTFRYVTWP---YLMPFAFIAMTIRSLDVARAYDIVKIMTDGGPAKRTE 246 EAA +DG TPW+ FRY+T P Y + F+ M I ++ R + +V +MT+GGP + Sbjct: 204 EAARMDGATPWERFRYITLPMMRYNLAIGFLLMLIYNI---RNFSMVWVMTEGGPGVSSS 260 Query: 247 LLWTLIGRTAYGDARMGMANAMAYVAILLSIFFTVYFFR 285 L +I RTA+ D +G+A+A++ + ++ + F+ Y+ + Sbjct: 261 TLPVMIYRTAFVDFNVGLASALSVLLFVVLLVFSYYYIK 299 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: 286 Number of extensions: 11 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: 308 Length adjustment: 27 Effective length of query: 271 Effective length of database: 281 Effective search space: 76151 Effective search space used: 76151 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