Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate GFF2365 PS417_12060 sugar ABC transporter permease
Query= TCDB::O05177 (398 letters) >FitnessBrowser__WCS417:GFF2365 Length = 325 Score = 162 bits (411), Expect = 1e-44 Identities = 120/378 (31%), Positives = 185/378 (48%), Gaps = 71/378 (18%) Query: 20 IRSNIREYGMLIALVAIMVFFQFYTGGILFRPVNLTNLILQNSFIVIMALGMLLVIVAGH 79 +R ++ +G+ + + + V F + N +++ Q S I+A+GM VI+ Sbjct: 18 LRLSLDRFGLPLVFILLCVVMAF-SSEYFMTWRNWMDILRQTSINGILAVGMTYVILTKG 76 Query: 80 IDLSVGSIVAFVGAIAAILTVQWGMNPFLAALICLVIGGIIGAAQGYWIAYHRIPSFIVT 139 IDLSVGSI+AF G +A++ A QGY + Sbjct: 77 IDLSVGSILAFAGLCSAMV-----------------------ATQGYGL-------LAAV 106 Query: 140 LAGMLVFRGLTLFVLGGKNIGPFPTDFQVISTGFLPDIGGIEGLNTTSMILTVLITVALF 199 AGM F G L V+ G F V + P + + G+ + + +T ++ Sbjct: 107 SAGM--FAGAMLGVVNG---------FMVANLSIPPFVATL-GMLSIARGMTFILN---- 150 Query: 200 YLAWRRRVVNVKHGIDVEPFGFFIVQNLLISGAILFLGYQLSTYRGLPNVLIVMLVLIAL 259 D P + A L LG G+P +I+ V+ + Sbjct: 151 ---------------DGSPITD-------LPDAYLALGIGKIGPIGVP--IIIFAVVALI 186 Query: 260 YSFVTRRTTIGRRVYAMGGNEKATKLSGINTERLSFLTFVNMGVLAGLAGMIIATRLNSA 319 + V R TT GR VYA+GGNEK+ + SGI ++ F +V G+LAGLAG++++ R SA Sbjct: 187 FWMVLRYTTYGRYVYAVGGNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVVLSARTTSA 246 Query: 320 TPKAGVGFELDVIAACFIGGASASGGVGKITGAVIGAFIMGVMNNGMSIVGLGIDFQQMV 379 P+AGV +ELD IAA IGG S SGG G I G + GA ++GV+NNG++++G+ +QQ+ Sbjct: 247 LPQAGVSYELDAIAAVVIGGTSLSGGTGSIVGTLFGALLIGVINNGLNLLGVSSYYQQVA 306 Query: 380 KGLVLLAAVFFDVYNKNK 397 KGL+++ AV DV+ K K Sbjct: 307 KGLIIVFAVLIDVWRKKK 324 Lambda K H 0.329 0.145 0.422 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: 462 Number of extensions: 31 Number of successful extensions: 3 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: 398 Length of database: 325 Length adjustment: 29 Effective length of query: 369 Effective length of database: 296 Effective search space: 109224 Effective search space used: 109224 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 (21.8 bits) S2: 49 (23.5 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