Align Glucose/galactose porter (characterized)
to candidate 5209419 Shew_1890 glucose/galactose transporter (RefSeq)
Query= TCDB::P0C105 (412 letters) >FitnessBrowser__PV4:5209419 Length = 421 Score = 525 bits (1353), Expect = e-154 Identities = 265/404 (65%), Positives = 319/404 (78%), Gaps = 10/404 (2%) Query: 18 QKNYGFALTSLTLLFFMWGFITCLNDILIPHLKNVFQLNYTQSMLIQFCFFGAYFIVSLP 77 Q+NY FAL SLT LFFMWGFITCLNDILIPHLK F LNY ++MLIQFCFFGAYF+VS+P Sbjct: 17 QENYRFALVSLTSLFFMWGFITCLNDILIPHLKAAFSLNYAEAMLIQFCFFGAYFLVSMP 76 Query: 78 AGQLVKRISYKRGIVVGLIVAAIGCALFIPAASYRVYALFLGALFVLASGVTILQVAANP 137 AG+LVK + Y++GIV GL++AA+GCALF PAA+ Y LFLGALFVLASG+TILQVAANP Sbjct: 77 AGKLVKALGYQKGIVTGLLIAALGCALFYPAAALATYGLFLGALFVLASGITILQVAANP 136 Query: 138 YVTILGKPETAASRLTLTQAFNSLGTTVAPVFGAVLILSAATDAT-----VNAEADAVRF 192 YV LG ETA+SRL LTQAFN+LGTTVAP FGAVLILS A +A+ AEA+ V+ Sbjct: 137 YVNALGSVETASSRLNLTQAFNALGTTVAPYFGAVLILSVAVEASETLTQAQAEAEVVKL 196 Query: 193 PYLLLALAFTVLAIIFAILKPPDVQE-----DEPALSDKKEGSAWQYRHLVLGAIGIFVY 247 PYL+LA A VLA++FA L P ++E ++ + + SA Q HLVLGA+GIFVY Sbjct: 197 PYLILATALGVLALVFAKLDLPQIKEHCQSGEQGEVVHNGKTSALQSLHLVLGAVGIFVY 256 Query: 248 VGAEVSVGSFLVNFLSDPTVAGLSETDAAHHVAYFWGGAMVGRFIGSAAMRYIDDGKALA 307 VGAEVS+GSFLVNFL+ +AGLSE AA ++ Y+WGGAMVGRFIGSA M+ + G L Sbjct: 257 VGAEVSIGSFLVNFLAQDDIAGLSEASAASYITYYWGGAMVGRFIGSAVMQKVPAGTVLG 316 Query: 308 FNAFVAIILLFITVATTGHIAMWSVLAIGLFNSIMFPTIFSLALHGLGSHTSQGSGILCL 367 FNA +A +L+ + + +TG +AMW++LA+GLFNSIMFPTIFSLAL LG HTSQGSG+LCL Sbjct: 317 FNALMAALLVALAMTSTGTVAMWAILAVGLFNSIMFPTIFSLALRDLGPHTSQGSGVLCL 376 Query: 368 AIVGGAIVPLIQGALADAIGIHLAFLMPIICYAYIAFYGLIGSK 411 AIVGGAI+PL+QG LAD IGI AF +PIICY +I FYG+ GSK Sbjct: 377 AIVGGAILPLLQGVLADNIGIQHAFFLPIICYLFIMFYGVKGSK 420 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: 675 Number of extensions: 25 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: 421 Length adjustment: 31 Effective length of query: 381 Effective length of database: 390 Effective search space: 148590 Effective search space used: 148590 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