Align L-fucose-proton symporter; 6-deoxy-L-galactose permease; L-fucose permease (characterized)
to candidate CA265_RS15045 CA265_RS15045 MFS transporter
Query= SwissProt::P11551 (438 letters) >FitnessBrowser__Pedo557:CA265_RS15045 Length = 535 Score = 105 bits (261), Expect = 5e-27 Identities = 69/230 (30%), Positives = 104/230 (45%), Gaps = 22/230 (9%) Query: 21 SRSYIIPFALLCSLFFLWAVANNLNDILLPQFQQAFTLTNFQAGLIQSAFYFGYFIIPIP 80 +++Y + ++FF W N I +P + F LT F++ LI FY GYFI + Sbjct: 6 TKNYGTALYTIITVFFFWGFVAASNGIFIPFCKTHFKLTQFESQLIDFTFYGGYFIGSLI 65 Query: 81 AGI--------LMKKLSYKAGIITGLFLYALGAALFWPAAEIMNYTLFLVGLFIIAAGLG 132 ++ K+ YK GII GL + A GA L PA ++ L F+IA G Sbjct: 66 LYFASQASKVDILNKIGYKKGIIAGLIISAGGALLMIPAVHSGSFLFILFAFFVIALGFS 125 Query: 133 CLETAANPFVTVLGPESSGHFRLNLAQTFNSFGAIIAVVFGQSLILSNVPHQSQDVLDKM 192 +TAANPFV LG SG RLNLA N+FG ++ V ++ V++ Sbjct: 126 LQQTAANPFVVALGEPESGAHRLNLAGGINNFGGLMGPVIVSVVLFGTANDAVAKVVE-- 183 Query: 193 SPEQLSAYKHSLVLSVQTPYMIIVAIVLLVALLIMLTKFPALQSDNHSDA 242 + S+ Y I+ + L VA+ ++K P + S +A Sbjct: 184 ------------ISSINNLYYILAGLFLGVAIFFGVSKLPDVTSTEKIEA 221 Score = 80.1 bits (196), Expect = 2e-19 Identities = 43/111 (38%), Positives = 62/111 (55%), Gaps = 1/111 (0%) Query: 319 ISRFAPHKVLAAYALIAMALCLISAFAGGHVGLIALTLCSAFMSIQYPTIFSLGIKNLGQ 378 I + P K LA + + +I GHV + A SI +P+IFSL I LG+ Sbjct: 403 IGQEKPAKTLAIFGTLGAIAMIIGLLTTGHVAIFAFVSGGLCCSIMWPSIFSLAITGLGK 462 Query: 379 DTKYGSSFIVMTIIGGGIVTPVMGFVSDAAGNIPTAELIPALCFAVIFIFA 429 T GSSF++M I+GG I+ P+ G ++D+AG I + +IP L FA + FA Sbjct: 463 YTSQGSSFLIMMILGGSIIPPIQGELADSAG-IHNSYIIPVLGFAYLIFFA 512 Lambda K H 0.329 0.140 0.425 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: 575 Number of extensions: 28 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 438 Length of database: 535 Length adjustment: 34 Effective length of query: 404 Effective length of database: 501 Effective search space: 202404 Effective search space used: 202404 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 52 (24.6 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