Align MFS transporter, FHS family, L-fucose permease (characterized, see rationale)
to candidate 6936095 Sama_0292 glucose/galactose transporter (RefSeq)
Query= uniprot:A0A1I2JXG1 (442 letters) >FitnessBrowser__SB2B:6936095 Length = 389 Score = 375 bits (964), Expect = e-108 Identities = 204/400 (51%), Positives = 267/400 (66%), Gaps = 23/400 (5%) Query: 32 LTSIFFMWGFLTCLNDILIPHLKAVFKLNYAEAMLVQFTFFGAYFLMSLPAGLLVARLGY 91 +T++FF+WGF+T LNDILIPHLKA F+L+Y +AMLVQF FFGAYF++S AG L+ ++GY Sbjct: 1 MTTLFFIWGFITALNDILIPHLKAAFELSYTQAMLVQFCFFGAYFIVSPFAGKLIEKIGY 60 Query: 92 KKGIVAGLAVAGVGAAGFWPAAAMHFYPAFLGALFVLATGITVLQVAANAYVALLGPEKS 151 +GIV GL G F+PAA + Y FL LFVLA+GIT+LQV+AN YVA+LG E++ Sbjct: 61 IRGIVTGLCTMATGCLLFYPAAEVSVYALFLLGLFVLASGITILQVSANPYVAILGAERT 120 Query: 152 ASSRLTLAQALNSLGTFLAPKFGGLLILSAAVLSAEQIAKLSPAEQVAYRVQEAQTVQGP 211 A+SRL+LAQA+NSLG LAP FG LI AA A VQ P Sbjct: 121 AASRLSLAQAINSLGHTLAPLFGAALIFGAA--------------------SNAHAVQLP 160 Query: 212 YLGLAIVLFLLAVFVYLFRLPALTEKTEQASVKQHSLVSPLRHPHVLFGVLAIFFYVGGE 271 YL LA + L AV +LP L +T+ + HS S +H H++ G LAIF YVG E Sbjct: 161 YLILAGAVLLTAVGFVFLKLPTL--QTDHETQVSHS-DSIWQHKHLVLGALAIFLYVGAE 217 Query: 272 VAIGSFLVNYLSMPDIGNMSEQAAANWVAYYWLGAMIGRFIGSALLAKLSPRKLLAIFAA 331 V++GSFLVNY S I +SEQ A+ V+YYW GAM+GRF+GSAL L P +LA A Sbjct: 218 VSVGSFLVNYFSESHIAALSEQEASRMVSYYWGGAMVGRFVGSALTRILQPTYVLATNAL 277 Query: 332 INMALVLTTMMTKGTVAMYSVVSIGLFNSIMFPTIFSLGIERMGPMTGEASSLLIMAIVG 391 + + L++ TM + G +AM+SV+++G FNSIMFPTIF+L I +GP+T S LL AIVG Sbjct: 278 MAILLLVLTMNSSGALAMWSVLAVGFFNSIMFPTIFTLAIRGLGPLTSRGSGLLCQAIVG 337 Query: 392 GAIVPFVQGLFADHIGVQHAFFLPLLCYAYIVFYGLYGSR 431 GAI+P +QG+ AD VQ +F +P++ Y YI +Y L GS+ Sbjct: 338 GAILPLLQGVVADSSSVQFSFVIPMVAYLYIGWYALRGSK 377 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: 478 Number of extensions: 20 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: 442 Length of database: 389 Length adjustment: 31 Effective length of query: 411 Effective length of database: 358 Effective search space: 147138 Effective search space used: 147138 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: 50 (23.9 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