Align ABC transporter for L-Fucose, permease component 1 (characterized)
to candidate BPHYT_RS35665 BPHYT_RS35665 ABC transporter permease
Query= reanno::Smeli:SM_b21104 (298 letters) >FitnessBrowser__BFirm:BPHYT_RS35665 Length = 296 Score = 141 bits (356), Expect = 2e-38 Identities = 84/282 (29%), Positives = 148/282 (52%), Gaps = 2/282 (0%) Query: 4 SKLSAPTLLLLPAFIVLAVFIVLPLIFSLYSSFTPFRLTKPDSLWVFIGFRNYVNVLTNA 63 S+L AP LL+ P+ +VLA+FI+ IF++ + +++ ++ F G +N+ + ++ Sbjct: 7 SRLQAPWLLIAPS-LVLALFIISYPIFNIVWQ-SLHEVSRFGAIRDFTGLQNFYTIFSDP 64 Query: 64 EFWVAFGRTVLLLTVALNAEMFLGLGLALLVNKATYGQRALRTAMMFPMMFSPVLVGFQF 123 F A RT++ + + + + +AL++N+ YG+ RT +M P S + + Sbjct: 65 AFLAAARRTLVWTICVVGGTVLISVPVALVLNQDFYGRGVARTIVMLPWSVSLTMTAVVW 124 Query: 124 KFLFNDNIGFVNNALQSLGLTDRAIPWLIDGNLALFSIIVAEVWSSTAVFAILILAGLLA 183 ++ FND+ G VN LQ LGL I WL LA I + S ++L GL + Sbjct: 125 RWAFNDDYGMVNVTLQRLGLISGPIHWLATPELAFPVEIAVGILVSVPFTVTILLGGLSS 184 Query: 184 MPKDPVEAAHVDGCTPWQTFRYVTWPYLMPFAFIAMTIRSLDVARAYDIVKIMTDGGPAK 243 +P D EAA +DG + WQ FR +T P L PF + + + + V ++ I+ +MT GGP Sbjct: 185 VPGDIYEAARMDGASAWQQFRKLTMPLLRPFINMTILLNVIYVFNSFPIIWVMTQGGPDN 244 Query: 244 RTELLWTLIGRTAYGDARMGMANAMAYVAILLSIFFTVYFFR 285 T +L T + + R G A A++ + +++ F++ + R Sbjct: 245 STHILVTYLYELGFRLGRPGEAAAVSLIMLVMLFIFSIAYLR 286 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: 284 Number of extensions: 14 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: 296 Length adjustment: 26 Effective length of query: 272 Effective length of database: 270 Effective search space: 73440 Effective search space used: 73440 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