Align ABC transporter for L-Fucose, permease component 1 (characterized)
to candidate WP_015888140.1 NGR_RS09950 sugar ABC transporter permease
Query= reanno::Smeli:SM_b21104 (298 letters) >NCBI__GCF_000018545.1:WP_015888140.1 Length = 307 Score = 188 bits (478), Expect = 1e-52 Identities = 103/280 (36%), Positives = 161/280 (57%), Gaps = 3/280 (1%) Query: 11 LLLLPAFIVLAVFIVLPLIFSLYSSFTPFRLTKPDSLWVFIGFRNYVNVLTNAEFWVAFG 70 L+L P ++L + P I+ Y++ PD W F+G N+ +L++ +F VA Sbjct: 30 LMLAPTVLILLALTIFPSIYMFYAAVHRIS-PNPDLPWEFVGVGNFARLLSDPQFHVALR 88 Query: 71 RTVLLLTVALNAEMFLGLGLALLVNKATYGQRALRTAMMFPMMFSPVLVGFQFKFLFNDN 130 TV+ VA+ E LGLGLALL+++ L+T +M PMM P+ V +K ++ Sbjct: 89 NTVVFTLVAVALEFLLGLGLALLLDRFIRRLSFLKTVLMIPMMLPPIAVAITWKLIYEPQ 148 Query: 131 IGFVNNALQSLGLTDRAIPWLIDGNLALFSIIVAEVWSSTAVFAILILAGLLAMPKDPVE 190 G +N + LGL +A W D NLA+FSIIVA+VW T +L+LAGL ++P +P E Sbjct: 149 FGVLNEIMFLLGLPVQA--WAGDVNLAMFSIIVADVWQWTPFVFLLMLAGLASLPVEPYE 206 Query: 191 AAHVDGCTPWQTFRYVTWPYLMPFAFIAMTIRSLDVARAYDIVKIMTDGGPAKRTELLWT 250 AA +DG + W+ F +T P+L P IA+ +R +D R +D+V I+T GGPA RT++L Sbjct: 207 AAALDGASSWRQFWDLTLPFLKPVIAIALLLRVMDALRLFDLVFILTGGGPADRTKVLSL 266 Query: 251 LIGRTAYGDARMGMANAMAYVAILLSIFFTVYFFRKLAAA 290 I + AY A G A A++ + ++I + +F +++ A Sbjct: 267 YIYQVAYRFADPGYAAAISLFVLFVTIVLSTWFMKRMRLA 306 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: 248 Number of extensions: 12 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: 307 Length adjustment: 27 Effective length of query: 271 Effective length of database: 280 Effective search space: 75880 Effective search space used: 75880 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 Apr 09 2024. 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