Align Glucose/galactose porter (characterized)
to candidate Pf6N2E2_1003 Fucose permease
Query= TCDB::P0C105 (412 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1003 Length = 460 Score = 269 bits (687), Expect = 1e-76 Identities = 151/399 (37%), Positives = 227/399 (56%), Gaps = 8/399 (2%) Query: 12 HTETSSQKNYGFALTSLTLLFFMWGFITCLNDILIPHLKNVFQLNYTQSMLIQFCFFGAY 71 H + SS + A +T LFFMWG L D+L H ++ ++ QS L+Q +FGAY Sbjct: 55 HEKLSSTR---LAFIFVTSLFFMWGLSHGLLDVLNKHFQDTLHISRGQSGLVQTAYFGAY 111 Query: 72 FIVSLPAGQLVKRISYKRGIVVGLIVAAIGCALFIPAASYRVYALFLGALFVLASGVTIL 131 FI++LP G ++R YK GI+ GL + AIG LFIPA+ + FL ALFVLA G+ L Sbjct: 112 FIIALPVGLFMERFGYKAGILAGLALFAIGALLFIPASMVGTFMPFLVALFVLACGLGCL 171 Query: 132 QVAANPYVTILGKPETAASRLTLTQAFNSLGTTVAPVFGAVLILSAATDATVNAEADAVR 191 + AAN Y LG P + RLT Q+FN LG + PV G + + + N D V Sbjct: 172 ETAANLYAAALGDPAKSEQRLTFAQSFNGLGAFIGPVIGGAVFFAPPIEFNGN-RVDLVS 230 Query: 192 FPYLLLALAFTVLAIIFAILKPPDVQEDEPA---LSDKKEGSAWQYRHLVLGAIGIFVYV 248 Y LA+ ++ + FA ++ P+++ ++ + L E S W+ + + F V Sbjct: 231 VTYAALAIIVMLMFVAFARIQLPEIRNEKSSDVLLPSAGEVSLWKKSNFTGALVAQFCNV 290 Query: 249 GAEVSVGSFLVNFLSDPTVAGLSETDAAHHVAYFWGGAMVGRFIGSAAMRYIDDGKALAF 308 GA V +G+F +N+ D G+S A++ ++ MVGRF G+ MRY+ L Sbjct: 291 GAYVGIGAFFINYAIDHW-QGISAQKASYLLSLGMLAYMVGRFAGTWVMRYVPARSLLIL 349 Query: 309 NAFVAIILLFITVATTGHIAMWSVLAIGLFNSIMFPTIFSLALHGLGSHTSQGSGILCLA 368 N+ V+++L + +A I++++V AI LF S+M+PTIF++ + GLG+ T + L + Sbjct: 350 NSLVSMVLCIVAIAGFERISIFAVAAIYLFMSVMYPTIFAMGIRGLGTQTKKAGSCLVMT 409 Query: 369 IVGGAIVPLIQGALADAIGIHLAFLMPIICYAYIAFYGL 407 +VGGA VPL+ GALAD GI AF +P+ C+A IA+YGL Sbjct: 410 LVGGAFVPLLMGALADHFGIAAAFYVPLACFAAIAWYGL 448 Lambda K H 0.328 0.141 0.420 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: 554 Number of extensions: 30 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: 412 Length of database: 460 Length adjustment: 32 Effective length of query: 380 Effective length of database: 428 Effective search space: 162640 Effective search space used: 162640 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