Align ABC transporter for L-Fucose, permease component 1 (characterized)
to candidate SM_b21220 SM_b21220 sugar ABC transporter permease
Query= reanno::Smeli:SM_b21104 (298 letters) >FitnessBrowser__Smeli:SM_b21220 Length = 293 Score = 159 bits (401), Expect = 9e-44 Identities = 96/283 (33%), Positives = 153/283 (54%), Gaps = 5/283 (1%) Query: 11 LLLLPAFIVLAVFIVLPLIFSLYSSFTPFRLTKPDSLWVFIGFRNYVNVLTNAEFWVAFG 70 LL+LP +V+ I PL+ ++ SFT +L + F+G NY+ +L + F A Sbjct: 12 LLMLPLLVVMTAVIGWPLVDTVRLSFTDAKLVGTEG--GFVGTANYIKMLGGSNFQRALV 69 Query: 71 RTVLLLTVALNAEMFLGLGLALLVNKATYGQRALRTAMMFPMMFSPVLVGFQFKFLFNDN 130 T +++ AEM LG+ ALL+N+ G+ ALR M+ P V+ ++ ++N Sbjct: 70 TTTWFAVISVAAEMVLGVLAALLLNQQFRGRTALRALMILPWALPTVVNATLWRLIYNPE 129 Query: 131 IGFVNNALQSLGLTDRAIPWLIDGNLALFSIIVAEVWSSTAVFAILILAGLLAMPKDPVE 190 G +N AL LGL D WL + AL ++IVA+ W + + A++ LA L A+P+D Sbjct: 130 YGALNAALTQLGLLDSYRSWLGEPGTALAALIVADCWKNFPLVALIALAALQAVPRDITA 189 Query: 191 AAHVDGCTPWQTFRYVTWPYLMPFAFIAMTIRSLDVARAYDIVKIMTDGGPAKRTELLWT 250 A+ VDG P+ FR+V PYL +A+ +R+++ + +DI+ +MT GGPA T L Sbjct: 190 ASLVDGAGPFNRFRFVIMPYLAGPLLVALVLRTIEAFKVFDIIWVMTRGGPANSTRTLSI 249 Query: 251 LIGRTAYGDARMGMANAMA-YVAILLSIFFTVY--FFRKLAAA 290 L+ + A+ R G ++A V +L++I Y RK A A Sbjct: 250 LVYQEAFSFQRAGSGASLALIVTLLVTILAAAYAALLRKAAGA 292 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: 246 Number of extensions: 10 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: 298 Length of database: 293 Length adjustment: 26 Effective length of query: 272 Effective length of database: 267 Effective search space: 72624 Effective search space used: 72624 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