Align MFS transporter, FHS family, L-fucose permease (characterized, see rationale)
to candidate CCNA_01159 CCNA_01159 transporter, major facilitator superfamily
Query= uniprot:A0A1I2JXG1 (442 letters) >FitnessBrowser__Caulo:CCNA_01159 Length = 451 Score = 235 bits (600), Expect = 2e-66 Identities = 152/431 (35%), Positives = 221/431 (51%), Gaps = 37/431 (8%) Query: 27 MAMGVLTSIFFMWGFLTCLNDILIPHLKAVFKLNYAEAMLVQFTFFGAYFLMSLPAGLLV 86 +A+ +T +FF+W +T L D L+ +K VF L EA L F FF AY +MSLP+ + Sbjct: 18 LAIVYVTCLFFIWALVTNLLDPLLKTMKTVFTLTPVEASLTGFAFFIAYGIMSLPSAAFL 77 Query: 87 ARLGYKKGIVAGLAVAGVGAAGFWPAAAMHFYPAFLGALFVLATGITVLQVAANAYVALL 146 ++LGY + ++ GL G AA +H + FL LFV A+G+T+LQVAAN +A + Sbjct: 78 SKLGYARSVMVGLGGIVAGCFIAIAAAKLHTFGVFLVGLFVTASGVTLLQVAANPLIASM 137 Query: 147 GPEKSASSRLTLAQALNSLGTFLAPKFGGLLILSAAVLSAEQIAKLSPAEQVAYRVQEAQ 206 G + +S RL L+QA NSLG FG +L + + + + EQ V Sbjct: 138 GKPEESSFRLNLSQAFNSLGAACGLWFGANFLLKGEIFEKDAVITDAMREQALGFVSNVY 197 Query: 207 TVQGPYLGLAIVLFLLAVFVYLFRLPALTEKTEQASVKQHSLVSP---LRHPHVLFGVLA 263 +GL + LF+L +F+ + +K +A+ K LV+P L G + Sbjct: 198 LA----IGLGLALFILLIFM-------VRQKITEAAPKTGQLVNPFTALTSKWANLGAIG 246 Query: 264 IFFYVGGEVAIGSFLVNYLSMPDIGNMSEQAAANWVAYYWLGAMIGRFIGSALLAKLSPR 323 IF YVG EVAI L+ +L I ++S + A +Y + AMIGRF GSALL + Sbjct: 247 IFLYVGAEVAISLHLLLFLEQSHILDISAEQAGKLTTFYMVFAMIGRFAGSALLKTIKDY 306 Query: 324 KLLAIFAAINMALVLTTMMTK----------------------GTVAMYSVVSIGLFNSI 361 +LAI A +AL L ++TK G + ++ + IGLFNSI Sbjct: 307 VMLAIVAVGAIALCLVVILTKDMTPSAHAGTVNLLLASAPVTTGLIPAFAALLIGLFNSI 366 Query: 362 MFPTIFSLGIERMGPMTGEASSLLIMAIVGGAIVPFVQGLFADHIG-VQHAFFLPLLCYA 420 MFPTIF+L ++R T S LL MAIVGGA +P + G + F PLLCY Sbjct: 367 MFPTIFTLTLQRSSAPTSATSGLLCMAIVGGAFLPLAFAKIEEMTGSMAMGFAAPLLCYV 426 Query: 421 YIVFYGLYGSR 431 Y++++ L + Sbjct: 427 YVLWFALVAKK 437 Lambda K H 0.327 0.140 0.414 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: 469 Number of extensions: 19 Number of successful extensions: 4 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: 442 Length of database: 451 Length adjustment: 33 Effective length of query: 409 Effective length of database: 418 Effective search space: 170962 Effective search space used: 170962 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 (21.7 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