Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate N515DRAFT_3233 N515DRAFT_3233 xylose ABC transporter membrane protein
Query= TCDB::O05177 (398 letters) >FitnessBrowser__Dyella79:N515DRAFT_3233 Length = 380 Score = 255 bits (652), Expect = 1e-72 Identities = 139/367 (37%), Positives = 219/367 (59%), Gaps = 8/367 (2%) Query: 29 MLIALVAIMVFFQFYTGGILFRPVNLTNLILQNSFIVIMALGMLLVIVAGHIDLSVGSIV 88 +L+A+ AI VFF TGG N++NL Q + ++A GM+ VI+AG IDLSVGS++ Sbjct: 18 LLLAVAAIWVFFHVATGGDFVTARNVSNLFRQMAITGMLACGMVFVIIAGEIDLSVGSLL 77 Query: 89 AFVGAIAAILTVQWGMNPFLAALICLVIGGIIGAAQGYWIAYHRIPSFIVTLAGMLVFRG 148 +G + A+LTV G + +A + L +G +IG G+W+ R+PSFIV L GML FRG Sbjct: 78 GLLGGVVAVLTVNQGWSTPVAIVAVLGLGVLIGLFNGFWVTRLRVPSFIVGLGGMLAFRG 137 Query: 149 LTLFVLGGKNIGPFPTDFQVISTGFLPDIGGIEGLNTTSMILTVLITVALFYLAWRRRVV 208 + L I P P D + G++ + S +L V I + LA RR Sbjct: 138 VLLGTTHSATIAPVPADLVYLGQGYVSPLW--------STVLGVAIFAVVVALAVLRRRR 189 Query: 209 NVKHGIDVEPFGFFIVQNLLISGAILFLGYQLSTYRGLPNVLIVMLVLIALYSFVTRRTT 268 + I P+ +++ + I A+ L++Y G+P +++++ L+A++S++ +T Sbjct: 190 RAQLQIRQLPWWADLLKVVAIGAALGVFVATLNSYGGIPLPVLILVALLAVFSYLASQTV 249 Query: 269 IGRRVYAMGGNEKATKLSGINTERLSFLTFVNMGVLAGLAGMIIATRLNSATPKAGVGFE 328 +GR +YA+GGN +AT+LSG+N R+ + F MG++ AG++ RL + +P AG E Sbjct: 250 LGRHIYAVGGNLEATRLSGVNVARVKLVVFGIMGLMCAFAGIVNTARLAAGSPSAGTNGE 309 Query: 329 LDVIAACFIGGASASGGVGKITGAVIGAFIMGVMNNGMSIVGLGIDFQQMVKGLVLLAAV 388 LD IAACFIGGAS GG G + GA+IGA +M ++NGMS++ + +Q +VKG +L+ AV Sbjct: 310 LDAIAACFIGGASMRGGAGTVHGALIGALVMASLDNGMSMMDVDTYWQYIVKGAILVLAV 369 Query: 389 FFDVYNK 395 + DV ++ Sbjct: 370 WVDVLSR 376 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: 535 Number of extensions: 32 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: 380 Length adjustment: 30 Effective length of query: 368 Effective length of database: 350 Effective search space: 128800 Effective search space used: 128800 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