Align ABC transporter for L-Fucose, permease component 1 (characterized)
to candidate SM_b20659 SM_b20659 sugar uptake ABC transporter permease
Query= reanno::Smeli:SM_b21104 (298 letters) >FitnessBrowser__Smeli:SM_b20659 Length = 310 Score = 146 bits (369), Expect = 5e-40 Identities = 92/287 (32%), Positives = 141/287 (49%), Gaps = 3/287 (1%) Query: 11 LLLLPAFIVLAVFIVLPLIFSLYSSFTPFRLTKPDSLWVFIGFRNYVNVLTNAEFWVAFG 70 L +LPA + L F+ PL ++ FT R+ + VFIG NY + ++ FW++ Sbjct: 26 LFMLPAAVFLICFLTYPLGLGVWLGFTDTRIGRDG---VFIGIENYEFLARDSVFWLSVY 82 Query: 71 RTVLLLTVALNAEMFLGLGLALLVNKATYGQRALRTAMMFPMMFSPVLVGFQFKFLFNDN 130 T+L VA + LGL LALL+N+ + R ++ P + VL F ++++ Sbjct: 83 NTLLYTFVASILKFVLGLWLALLLNENLPFKSFFRAIVLLPWVVPTVLSALAFWWIYDSQ 142 Query: 131 IGFVNNALQSLGLTDRAIPWLIDGNLALFSIIVAEVWSSTAVFAILILAGLLAMPKDPVE 190 ++ +L LG+ D I +L D N A S+I A VW AI +LAGL +P E Sbjct: 143 FSIISWSLMQLGIIDGPINFLGDPNNARASVIAANVWRGIPFVAISLLAGLQTIPASLQE 202 Query: 191 AAHVDGCTPWQTFRYVTWPYLMPFAFIAMTIRSLDVARAYDIVKIMTDGGPAKRTELLWT 250 AA +DG T WQ FRYVT P L P + MT L + ++ ++T GGP T L+ T Sbjct: 203 AASLDGATSWQRFRYVTLPMLTPIIAVVMTFSVLFTFTDFQLIYVLTKGGPVNATHLMAT 262 Query: 251 LIGRTAYGDARMGMANAMAYVAILLSIFFTVYFFRKLAAARQQIGAE 297 L + ++G A+A I + ++ F L + Q G + Sbjct: 263 LSFQRGIPGGQLGEGAAIAVAMIPFLLAAIMFSFFGLQRRKWQQGGQ 309 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: 307 Number of extensions: 16 Number of successful extensions: 1 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: 310 Length adjustment: 27 Effective length of query: 271 Effective length of database: 283 Effective search space: 76693 Effective search space used: 76693 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