Align Glucose/galactose transporter (characterized, see rationale)
to candidate N515DRAFT_1222 N515DRAFT_1222 MFS transporter, FHS family, L-fucose permease
Query= uniprot:A0KXM0 (423 letters) >FitnessBrowser__Dyella79:N515DRAFT_1222 Length = 422 Score = 242 bits (618), Expect = 1e-68 Identities = 146/415 (35%), Positives = 215/415 (51%), Gaps = 15/415 (3%) Query: 12 SSVSEAGNGNYRFALVSLTSLFFMWGFITCLNDILIPHLKAVFSLNYTQAMLIQFCFFGA 71 SS AG AL+ SLFF+WG LND+LIP K F LN QA L+Q F+ Sbjct: 4 SSSRAAGRSPLPLALI--VSLFFLWGVANNLNDVLIPQFKKAFVLNDFQAGLVQSAFYLG 61 Query: 72 YFLVSIPAGQLVKRLGYQKGIVTGLVIASIGCGLFYPAASFATYGLFLGALFVLASGITI 131 YFLV++PAG ++R GY+ +V GL + +G LF+PAA TYG FL ALFV+ASG+ Sbjct: 62 YFLVAMPAGIYMRRFGYKSAVVFGLALYGLGALLFWPAAQQGTYGFFLFALFVIASGLAF 121 Query: 132 LQVAANPYVNALGSSETASSRLNLTQAFNALGTTVAPFFGSILILSVAASVSSELAQANA 191 L+ +ANP+V LG E+A+ RLNL QAFN LG+ G I S +LA +A Sbjct: 122 LETSANPFVTLLGPRESAARRLNLAQAFNPLGSITGILIGQHFIFSGVEHTPEQLAALSA 181 Query: 192 ---------EAEVVKLPYLLLAAALAVLAIIFAKLDLPVIREHSQAAAEEVQTHLGKTSA 242 E V+LPYL + + ++ P + + A + H Sbjct: 182 AERAAFVAHETAAVQLPYLAIGLVVLAWGLLILLTRFPAVHAVEEGAVP--RDHGALARL 239 Query: 243 LQSMHLVLGAVGIFVYVGAEVSIGSFLVNFLGEAHIVGMPEEQAAHYIAYYWGGAMVGRF 302 L + F YVGA+V + S+L+ ++ +A + G P + AA+Y+ M GRF Sbjct: 240 LGDRRFLATLAAQFFYVGAQVGVWSYLIRYV-QATMPGTPAKLAANYMLVSLACFMAGRF 298 Query: 303 IGSAVMQKIPAGTVLAFNAFMAALLVLVAMTTSGSVAMWAILGVGLFNSIMFPTIFSLAL 362 GSA+M+ + +LA A + L + A+ G A++ F S+M+PTIF+L + Sbjct: 299 AGSALMRYVAPRRLLALFAAVNVALTVFAVAVPGVAGACALVACSFFMSVMYPTIFALGV 358 Query: 363 RDLGPHTSQ-GSGILCLAIVGGAIVPLLQGVLADNLGIQLAFILPVVCYGFILFY 416 G + GS +L + I+GGA++ G ++D GI A ++P + IL + Sbjct: 359 EGRGDDERKLGSALLVMTIIGGAVLTAAMGAVSDAAGISRAMLVPAASFVVILLF 413 Lambda K H 0.326 0.138 0.402 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: 486 Number of extensions: 25 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: 423 Length of database: 422 Length adjustment: 32 Effective length of query: 391 Effective length of database: 390 Effective search space: 152490 Effective search space used: 152490 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