Align Monosaccharide-transporting ATPase, component of Xylose transporter, XylFGH (XylF (R), 359 aas; XylG (C), 525 aas; XylH (M), 389 aas (characterized)
to candidate N515DRAFT_3233 N515DRAFT_3233 xylose ABC transporter membrane protein
Query= TCDB::A6LW12 (389 letters) >FitnessBrowser__Dyella79:N515DRAFT_3233 Length = 380 Score = 376 bits (966), Expect = e-109 Identities = 190/366 (51%), Positives = 257/366 (70%) Query: 24 KMAAILIATAAIWVLFTFLTDGNFLTTRNLSNLFRQMSITGVLAIGMVFVIILGEIDLSA 83 K+ A+L+A AAIWV F T G+F+T RN+SNLFRQM+ITG+LA GMVFVII GEIDLS Sbjct: 14 KILALLLAVAAIWVFFHVATGGDFVTARNVSNLFRQMAITGMLACGMVFVIIAGEIDLSV 73 Query: 84 GSTLGLLGGIAAILNVWFGFSAIPTVVITLILGVIMGAWNGYWIAFRNVPSFIVTLASML 143 GS LGLLGG+ A+L V G+S +V L LGV++G +NG+W+ VPSFIV L ML Sbjct: 74 GSLLGLLGGVVAVLTVNQGWSTPVAIVAVLGLGVLIGLFNGFWVTRLRVPSFIVGLGGML 133 Query: 144 VFRGVLIGITGGNTVAPLTADFKAIGQAYLPTVVGYILVVLAIVGSAYLILGNRKNKIKY 203 FRGVL+G T T+AP+ AD +GQ Y+ + +L V L + R+ + + Sbjct: 134 AFRGVLLGTTHSATIAPVPADLVYLGQGYVSPLWSTVLGVAIFAVVVALAVLRRRRRAQL 193 Query: 204 NIEVRPMALDVLTIVGIGVISLVLVLILNDYQGFPIPVFIMLLLALILAFVGTKTIFGRR 263 I P D+L +V IG V V LN Y G P+PV I++ L + +++ ++T+ GR Sbjct: 194 QIRQLPWWADLLKVVAIGAALGVFVATLNSYGGIPLPVLILVALLAVFSYLASQTVLGRH 253 Query: 264 IYGIGGNRDAARLSGINVKKHIIVIYSVLGLLCAVAGILLTSRLNAGSVSAGQNAEMDAI 323 IY +GGN +A RLSG+NV + +V++ ++GL+CA AGI+ T+RL AGS SAG N E+DAI Sbjct: 254 IYAVGGNLEATRLSGVNVARVKLVVFGIMGLMCAFAGIVNTARLAAGSPSAGTNGELDAI 313 Query: 324 ASCVIGGASLAGGSGTVAGALVGALVMASIDNGMSMMNTPTFWQYIVKGLILLIAVWMDI 383 A+C IGGAS+ GG+GTV GAL+GALVMAS+DNGMSMM+ T+WQYIVKG IL++AVW+D+ Sbjct: 314 AACFIGGASMRGGAGTVHGALIGALVMASLDNGMSMMDVDTYWQYIVKGAILVLAVWVDV 373 Query: 384 SSKNKK 389 S+ ++ Sbjct: 374 LSRPQR 379 Lambda K H 0.326 0.142 0.410 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: 448 Number of extensions: 16 Number of successful extensions: 1 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: 389 Length of database: 380 Length adjustment: 30 Effective length of query: 359 Effective length of database: 350 Effective search space: 125650 Effective search space used: 125650 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 (21.6 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