Align Glucose/galactose porter (characterized)
to candidate 7025147 Shewana3_2310 glucose/galactose transporter (RefSeq)
Query= TCDB::P0C105 (412 letters) >FitnessBrowser__ANA3:7025147 Length = 423 Score = 550 bits (1416), Expect = e-161 Identities = 281/424 (66%), Positives = 335/424 (79%), Gaps = 15/424 (3%) Query: 1 MATSIPTNNPLHTETSSQK---NYGFALTSLTLLFFMWGFITCLNDILIPHLKNVFQLNY 57 MA+SI T++ HT + S+ NY FAL SLT LFFMWGFITCLNDILIPHLK VF LNY Sbjct: 1 MASSINTSS--HTSSVSEAGNGNYRFALVSLTSLFFMWGFITCLNDILIPHLKAVFSLNY 58 Query: 58 TQSMLIQFCFFGAYFIVSLPAGQLVKRISYKRGIVVGLIVAAIGCALFIPAASYRVYALF 117 TQ+MLIQFCFFGAYF+VS+PAGQLVKR+ Y++GIV GL++A+IGC LF PAAS+ Y LF Sbjct: 59 TQAMLIQFCFFGAYFLVSIPAGQLVKRLGYQKGIVTGLVIASIGCGLFYPAASFATYGLF 118 Query: 118 LGALFVLASGVTILQVAANPYVTILGKPETAASRLTLTQAFNSLGTTVAPVFGAVLILSA 177 LGALFVLASG+TILQVAANPYV LG ETA+SRL LTQAFN+LGTTVAP FG++LILS Sbjct: 119 LGALFVLASGITILQVAANPYVNALGSSETASSRLNLTQAFNALGTTVAPFFGSILILSV 178 Query: 178 ATD-----ATVNAEADAVRFPYLLLALAFTVLAIIFAILKPPDVQEDEPALSDKKEG--- 229 A A NAEA+ V+ PYLLLA A VLAIIFA L P ++E A +++ + Sbjct: 179 AASVSSELAQANAEAEVVKLPYLLLAAALAVLAIIFAKLDLPVIREHSQAAAEEVQTHLG 238 Query: 230 --SAWQYRHLVLGAIGIFVYVGAEVSVGSFLVNFLSDPTVAGLSETDAAHHVAYFWGGAM 287 SA Q HLVLGA+GIFVYVGAEVS+GSFLVNFL + + G+ E AAH++AY+WGGAM Sbjct: 239 KTSALQSMHLVLGAVGIFVYVGAEVSIGSFLVNFLGEAHIVGMPEEQAAHYIAYYWGGAM 298 Query: 288 VGRFIGSAAMRYIDDGKALAFNAFVAIILLFITVATTGHIAMWSVLAIGLFNSIMFPTIF 347 VGRFIGSA M+ I G LAFNAF+A +L+ + + T+G +AMW++L +GLFNSIMFPTIF Sbjct: 299 VGRFIGSAVMQKIPAGTVLAFNAFMAALLVLVAMTTSGSVAMWAILGVGLFNSIMFPTIF 358 Query: 348 SLALHGLGSHTSQGSGILCLAIVGGAIVPLIQGALADAIGIHLAFLMPIICYAYIAFYGL 407 SLAL LG HTSQGSGILCLAIVGGAIVPL+QG LAD +GI LAF++P++CY +I FYG Sbjct: 359 SLALRDLGPHTSQGSGILCLAIVGGAIVPLLQGVLADNLGIQLAFILPVVCYGFILFYGA 418 Query: 408 IGSK 411 GSK Sbjct: 419 KGSK 422 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: 698 Number of extensions: 30 Number of successful extensions: 3 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: 423 Length adjustment: 32 Effective length of query: 380 Effective length of database: 391 Effective search space: 148580 Effective search space used: 148580 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