Align Glucose/galactose porter (characterized)
to candidate Echvi_3909 Echvi_3909 Fucose permease
Query= TCDB::P0C105 (412 letters) >FitnessBrowser__Cola:Echvi_3909 Length = 469 Score = 405 bits (1041), Expect = e-117 Identities = 227/455 (49%), Positives = 292/455 (64%), Gaps = 62/455 (13%) Query: 12 HTETSSQKNYGFALTSLTLLFFMWGFITCLNDILIPHLKNVFQLNYTQSMLIQFCFFGAY 71 + E S + Y L +T+LFFMWGFITC+NDILIPHL+ VF L Q+MLIQ FFGAY Sbjct: 14 NVEFDSGQQYLGPLFLVTMLFFMWGFITCMNDILIPHLQQVFTLQNWQAMLIQTAFFGAY 73 Query: 72 FIVSL-------PAGQLVKRISYKRGIVVGLIVAAIGCALFIPAASYRVYALFLGALFVL 124 F +SL G + RI YK GI++GL+++A+GC F PAAS + FL ALFVL Sbjct: 74 FFISLGYYLISITKGDPIGRIGYKNGIILGLVISAVGCLFFYPAASLVSFGFFLFALFVL 133 Query: 125 ASGVTILQVAANPYVTILGKPETAASRLTLTQAFNSLGTTVAPVFGAVLILSAATDATVN 184 ASG+TILQ+AANPYVTILGKP A+SRL +TQAFNSLGTT+AP+ G LI A D V+ Sbjct: 134 ASGITILQIAANPYVTILGKPSGASSRLNMTQAFNSLGTTIAPLIGGYLIFGAIGD--VD 191 Query: 185 AEADAVRFPYLLLALAFTVLAIIFAILKPPDVQEDEPALSDKKEGSAWQYRHLVLGAIGI 244 AD+V+ PY+ LAL ++A+IF + K P++ +SD A ++RHL+LG I Sbjct: 192 ISADSVKMPYVALALTLLLIALIFKLFKLPEIGSQGVIISD---SGALKHRHLMLGIGAI 248 Query: 245 FVYVGAEVSVGSFLVNFLSDPTVAGLSETDAAHHVAYFWGGAMVGRFIGSAAMR------ 298 F YVG EV+VGS L+NF P +AGL E +A+H++A FWGGAMVGRF G+ A+ Sbjct: 249 FAYVGGEVTVGSNLINFARLPEIAGLDEAEASHYLALFWGGAMVGRFFGAVALADFKHNL 308 Query: 299 ------------------YIDDGK----ALAF---NAFVAII------------------ 315 Y+ G+ ALAF N V II Sbjct: 309 NRFLIIGAITAISYVTIYYVYGGEMALYALAFIGLNIVVIIIGQFIPNRTLWLFGITGIG 368 Query: 316 LLFITVATTGHIAMWSVLAIGLFNSIMFPTIFSLALHGLGSHTSQGSGILCLAIVGGAIV 375 LL I + T+G +A+WS++A+GLFNSIMFPTIFSLA+ GLG +T+Q S +L +AIVGGAIV Sbjct: 369 LLVIGLLTSGQLALWSIVALGLFNSIMFPTIFSLAIKGLGKYTAQASSLLVMAIVGGAIV 428 Query: 376 PLIQGALADAIG-IHLAFLMPIICYAYIAFYGLIG 409 PL+QG LAD G + L+FL+P+ CY YI FYG+ G Sbjct: 429 PLLQGLLADISGSVQLSFLVPLACYLYIVFYGMKG 463 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: 718 Number of extensions: 39 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 412 Length of database: 469 Length adjustment: 32 Effective length of query: 380 Effective length of database: 437 Effective search space: 166060 Effective search space used: 166060 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