Align Glucose/galactose porter (characterized)
to candidate 6936095 Sama_0292 glucose/galactose transporter (RefSeq)
Query= TCDB::P0C105 (412 letters) >FitnessBrowser__SB2B:6936095 Length = 389 Score = 451 bits (1161), Expect = e-131 Identities = 231/385 (60%), Positives = 291/385 (75%), Gaps = 7/385 (1%) Query: 28 LTLLFFMWGFITCLNDILIPHLKNVFQLNYTQSMLIQFCFFGAYFIVSLPAGQLVKRISY 87 +T LFF+WGFIT LNDILIPHLK F+L+YTQ+ML+QFCFFGAYFIVS AG+L+++I Y Sbjct: 1 MTTLFFIWGFITALNDILIPHLKAAFELSYTQAMLVQFCFFGAYFIVSPFAGKLIEKIGY 60 Query: 88 KRGIVVGLIVAAIGCALFIPAASYRVYALFLGALFVLASGVTILQVAANPYVTILGKPET 147 RGIV GL A GC LF PAA VYALFL LFVLASG+TILQV+ANPYV ILG T Sbjct: 61 IRGIVTGLCTMATGCLLFYPAAEVSVYALFLLGLFVLASGITILQVSANPYVAILGAERT 120 Query: 148 AASRLTLTQAFNSLGTTVAPVFGAVLILSAATDATVNAEADAVRFPYLLLALAFTVLAII 207 AASRL+L QA NSLG T+AP+FGA LI AA++A AV+ PYL+LA A + A+ Sbjct: 121 AASRLSLAQAINSLGHTLAPLFGAALIFGAASNA------HAVQLPYLILAGAVLLTAVG 174 Query: 208 FAILKPPDVQEDEPALSDKKEGSAWQYRHLVLGAIGIFVYVGAEVSVGSFLVNFLSDPTV 267 F LK P +Q D + S WQ++HLVLGA+ IF+YVGAEVSVGSFLVN+ S+ + Sbjct: 175 FVFLKLPTLQTDHETQVSHSD-SIWQHKHLVLGALAIFLYVGAEVSVGSFLVNYFSESHI 233 Query: 268 AGLSETDAAHHVAYFWGGAMVGRFIGSAAMRYIDDGKALAFNAFVAIILLFITVATTGHI 327 A LSE +A+ V+Y+WGGAMVGRF+GSA R + LA NA +AI+LL +T+ ++G + Sbjct: 234 AALSEQEASRMVSYYWGGAMVGRFVGSALTRILQPTYVLATNALMAILLLVLTMNSSGAL 293 Query: 328 AMWSVLAIGLFNSIMFPTIFSLALHGLGSHTSQGSGILCLAIVGGAIVPLIQGALADAIG 387 AMWSVLA+G FNSIMFPTIF+LA+ GLG TS+GSG+LC AIVGGAI+PL+QG +AD+ Sbjct: 294 AMWSVLAVGFFNSIMFPTIFTLAIRGLGPLTSRGSGLLCQAIVGGAILPLLQGVVADSSS 353 Query: 388 IHLAFLMPIICYAYIAFYGLIGSKS 412 + +F++P++ Y YI +Y L GSK+ Sbjct: 354 VQFSFVIPMVAYLYIGWYALRGSKA 378 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: 568 Number of extensions: 14 Number of successful extensions: 2 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: 389 Length adjustment: 31 Effective length of query: 381 Effective length of database: 358 Effective search space: 136398 Effective search space used: 136398 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