Align Monosaccharide-transporting ATPase; EC 3.6.3.17 (characterized, see rationale)
to candidate N515DRAFT_3233 N515DRAFT_3233 xylose ABC transporter membrane protein
Query= uniprot:B2SYR4 (338 letters) >FitnessBrowser__Dyella79:N515DRAFT_3233 Length = 380 Score = 159 bits (403), Expect = 8e-44 Identities = 114/379 (30%), Positives = 187/379 (49%), Gaps = 77/379 (20%) Query: 31 QQITEYSLIVIFVVMFATMSL----TVDHFFSIENMLGLALSISQIGMVSCTMMFCLASR 86 Q Y ++ + + + A T F + N+ L ++ GM++C M+F + + Sbjct: 8 QLFARYKILALLLAVAAIWVFFHVATGGDFVTARNVSNLFRQMAITGMLACGMVFVIIAG 67 Query: 87 DFDLSVGSTVAF-AGVLCAMVLNATGNTFIAIVAA------------------------V 121 + DLSVGS + GV+ + +N +T +AIVA V Sbjct: 68 EIDLSVGSLLGLLGGVVAVLTVNQGWSTPVAIVAVLGLGVLIGLFNGFWVTRLRVPSFIV 127 Query: 122 AAGGVIGF-------VNGAVIA-------YL---------------RINALITTLATMEI 152 GG++ F + A IA YL I A++ LA + Sbjct: 128 GLGGMLAFRGVLLGTTHSATIAPVPADLVYLGQGYVSPLWSTVLGVAIFAVVVALAVLRR 187 Query: 153 VR-------------GLGFIVSHGQAVGVSSDTFIALGGLSFFGVSLPIWVTLLCFIVFG 199 R L +V+ G A+GV T + GG + LP+ + + VF Sbjct: 188 RRRAQLQIRQLPWWADLLKVVAIGAALGVFVATLNSYGG-----IPLPVLILVALLAVFS 242 Query: 200 VMLNQTVYGRNTLAIGGNPEASRLAGINVERTRVYIFLIQGAVTALAGVILASRITSGQP 259 + +QTV GR+ A+GGN EA+RL+G+NV R ++ +F I G + A AG++ +R+ +G P Sbjct: 243 YLASQTVLGRHIYAVGGNLEATRLSGVNVARVKLVVFGIMGLMCAFAGIVNTARLAAGSP 302 Query: 260 NAAQGFELNVISACVLGGVSLLGGRATISGVVIGVLIMGTVENVMNLMNIDAFYQYLVRG 319 +A EL+ I+AC +GG S+ GG T+ G +IG L+M +++N M++M++D ++QY+V+G Sbjct: 303 SAGTNGELDAIAACFIGGASMRGGAGTVHGALIGALVMASLDNGMSMMDVDTYWQYIVKG 362 Query: 320 AILLAAVLLDQLKNRGSRD 338 AIL+ AV +D L +R RD Sbjct: 363 AILVLAVWVDVL-SRPQRD 380 Lambda K H 0.326 0.139 0.396 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: 364 Number of extensions: 28 Number of successful extensions: 5 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: 338 Length of database: 380 Length adjustment: 29 Effective length of query: 309 Effective length of database: 351 Effective search space: 108459 Effective search space used: 108459 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: 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