Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate 17629 b3568 D-xylose transporter subunit (NCBI)
Query= TCDB::O05177 (398 letters) >FitnessBrowser__Keio:17629 Length = 393 Score = 268 bits (684), Expect = 3e-76 Identities = 154/402 (38%), Positives = 241/402 (59%), Gaps = 15/402 (3%) Query: 1 MSSANTTNEESNVISVGSY--IRS-NIREYGMLIALVAIMVFFQFYTGGILFRPVNLTNL 57 MS +N + + V + G + ++S N++ + M+ A++AIM+FF + T G N++NL Sbjct: 1 MSKSNPSEVKLAVPTSGGFSGLKSLNLQVFVMIAAIIAIMLFFTWTTDGAYLSARNVSNL 60 Query: 58 ILQNSFIVIMALGMLLVIVAGHIDLSVGSIVAFVGAIAAILTVQWGMNPFLAALICLVIG 117 + Q + I+A+GM+ VI++ IDLSVGS++ +G +AAI V G L ++ LV+G Sbjct: 61 LRQTAITGILAVGMVFVIISAEIDLSVGSMMGLLGGVAAICDVWLGWPLPLTIIVTLVLG 120 Query: 118 GIIGAAQGYWIAYHRIPSFIVTLAGMLVFRGLTLFVLGGKNIGPFPTDFQVISTGFLPDI 177 ++GA G+W+AY ++PSFIVTLAGML FRG+ + + G + P I +LP Sbjct: 121 LLLGAWNGWWVAYRKVPSFIVTLAGMLAFRGILIGITNGTTVSPTSAAMSQIGQSYLPA- 179 Query: 178 GGIEGLNTTSMILTVLITVALFYLAWRRRVVNVKHGIDVEPFGFFIVQNLLISGAILFLG 237 +T I+ L +A WR R+ G+ P +V ++ AI+ LG Sbjct: 180 -------STGFIIGALGLMAFVGWQWRGRMRRQALGLQ-SPASTAVVGRQALT-AIIVLG 230 Query: 238 --YQLSTYRGLPNVLIVMLVLIALYSFVTRRTTIGRRVYAMGGNEKATKLSGINTERLSF 295 + L+ YRG+P ++++ +L+ F+ RT GRR+YA+GGN +A +LSGIN ER Sbjct: 231 AIWLLNDYRGVPTPVLLLTLLLLGGMFMATRTAFGRRIYAIGGNLEAARLSGINVERTKL 290 Query: 296 LTFVNMGVLAGLAGMIIATRLNSATPKAGVGFELDVIAACFIGGASASGGVGKITGAVIG 355 F G++ +AG+I+++RL + +P AG ELD IAAC IGG S +GGVG + GAV+G Sbjct: 291 AVFAINGLMVAIAGLILSSRLGAGSPSAGNIAELDAIAACVIGGTSLAGGVGSVAGAVMG 350 Query: 356 AFIMGVMNNGMSIVGLGIDFQQMVKGLVLLAAVFFDVYNKNK 397 AFIM ++NGMS++ + +Q +VKG +LL AV+ D K + Sbjct: 351 AFIMASLDNGMSMMDVPTFWQYIVKGAILLLAVWMDSATKRR 392 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: 569 Number of extensions: 46 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: 398 Length of database: 393 Length adjustment: 31 Effective length of query: 367 Effective length of database: 362 Effective search space: 132854 Effective search space used: 132854 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: 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