Align L-fucose-proton symporter; 6-deoxy-L-galactose permease; L-fucose permease (characterized)
to candidate Pf6N2E2_1003 Fucose permease
Query= SwissProt::P11551 (438 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1003 Length = 460 Score = 254 bits (648), Expect = 5e-72 Identities = 140/400 (35%), Positives = 223/400 (55%), Gaps = 19/400 (4%) Query: 26 IPFALLCSLFFLWAVANNLNDILLPQFQQAFTLTNFQAGLIQSAFYFGYFIIPIPAGILM 85 + F + SLFF+W +++ L D+L FQ ++ Q+GL+Q+A++ YFII +P G+ M Sbjct: 63 LAFIFVTSLFFMWGLSHGLLDVLNKHFQDTLHISRGQSGLVQTAYFGAYFIIALPVGLFM 122 Query: 86 KKLSYKAGIITGLFLYALGAALFWPAAEIMNYTLFLVGLFIIAAGLGCLETAANPFVTVL 145 ++ YKAGI+ GL L+A+GA LF PA+ + + FLV LF++A GLGCLETAAN + L Sbjct: 123 ERFGYKAGILAGLALFAIGALLFIPASMVGTFMPFLVALFVLACGLGCLETAANLYAAAL 182 Query: 146 GPESSGHFRLNLAQTFNSFGAIIAVVFGQSLILSNVPHQSQDVLDKMSPEQLSAYKHSLV 205 G + RL AQ+FN GA I V G ++ + P + + + L Sbjct: 183 GDPAKSEQRLTFAQSFNGLGAFIGPVIGGAVFFA-------------PPIEFNGNRVDL- 228 Query: 206 LSVQTPYMIIVAIVLLVALLIMLTKFPALQSDNHSDAKQGSFSASLSRLARIRHWRWAVL 265 V Y + IV+L+ + + P ++++ SD SA L + ++ A++ Sbjct: 229 --VSVTYAALAIIVMLMFVAFARIQLPEIRNEKSSDVLLP--SAGEVSLWKKSNFTGALV 284 Query: 266 AQFCYVGAQTACWSYLIRYAVEEIPGMTAGFAANYLTGTMVCFFIGRFTGTWLISRFAPH 325 AQFC VGA ++ I YA++ G++A A+ L+ M+ + +GRF GTW++ Sbjct: 285 AQFCNVGAYVGIGAFFINYAIDHWQGISAQKASYLLSLGMLAYMVGRFAGTWVMRYVPAR 344 Query: 326 KVLAAYALIAMALCLISAFAGGHVGLIALTLCSAFMSIQYPTIFSLGIKNLGQDTKYGSS 385 +L +L++M LC+++ + + A+ FMS+ YPTIF++GI+ LG TK S Sbjct: 345 SLLILNSLVSMVLCIVAIAGFERISIFAVAAIYLFMSVMYPTIFAMGIRGLGTQTKKAGS 404 Query: 386 FIVMTIIGGGIVTPVMGFVSDAAGNIPTAELIPALCFAVI 425 +VMT++GG V +MG ++D G I A +P CFA I Sbjct: 405 CLVMTLVGGAFVPLLMGALADHFG-IAAAFYVPLACFAAI 443 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: 515 Number of extensions: 17 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: 438 Length of database: 460 Length adjustment: 33 Effective length of query: 405 Effective length of database: 427 Effective search space: 172935 Effective search space used: 172935 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: 51 (24.3 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