Align Monosaccharide-transporting ATPase, component of Xylose transporter, XylFGH (XylF (R), 359 aas; XylG (C), 525 aas; XylH (M), 389 aas (characterized)
to candidate 16645 b2546 predicted sugar transporter subunit: membrane component of ABC superfamily (NCBI)
Query= TCDB::A6LW12 (389 letters) >FitnessBrowser__Keio:16645 Length = 332 Score = 150 bits (379), Expect = 5e-41 Identities = 110/367 (29%), Positives = 182/367 (49%), Gaps = 68/367 (18%) Query: 28 ILIATAAIWVLFTFLTDGNFLTTRNLSNLFRQMSITGVLAIGMVFVIILGEIDLSAGSTL 87 +L+ A ++++F+ G F++ N N+ R + G+ A M +II GEID+S G + Sbjct: 29 LLVVIAILYLVFSLNAPG-FISLNNQMNVLRDAATIGIAAWAMTLIIISGEIDVSVGPMV 87 Query: 88 GLLGGIAAILNVWFGFSAIPTVVITLILGVIMGAWNGYWIAFRNVPSFIVTLASMLVFRG 147 + A L + +P V L++ +++GA G TLA +L RG Sbjct: 88 AFVSVCLAFLLQF----EVPLAVACLLV-LLLGALMG-------------TLAGVL--RG 127 Query: 148 VLIGITGGNTVAPLTADFKAIGQAYLPTVVGYILVVLAIVGSAYLILGNRKNKIKYNIEV 207 V +P+ V + + A+ G + I N Sbjct: 128 VF----------------------NVPSFVATLGLWSALRGMGLFMTNALPVPIDEN--- 162 Query: 208 RPMALDVLTIVGIGVISLVLVLILNDYQGFPIPVFIMLLLALILAFVGTKTIFGRRIYGI 267 +VL +G + G P+ IM++L + F+ KT FGR ++ + Sbjct: 163 -----EVLDWLG------------GQFLGVPVSALIMIVLFALFVFISRKTAFGRSVFAV 205 Query: 268 GGNRDAARLSGINVKKHIIVIYSVLGLLCAVAGILLTSRLNAGSVSAGQNAEMDAIASCV 327 GGN AA+L GINV++ I+I+++ GLL AV GILL +RL +G+ A E D IA+ V Sbjct: 206 GGNATAAQLCGINVRRVRILIFTLSGLLAAVTGILLAARLGSGNAGAANGLEFDVIAAVV 265 Query: 328 IGGASLAGGSGTVAGALVGALVMASIDNGMSMMNTPTFWQYIVKGLILLIAVWMDI---- 383 +GG +L+GG G++ G L+G LV+ I NG+ ++ +F+Q +V+G+I+++AV +I Sbjct: 266 VGGTALSGGRGSLFGTLLGVLVITLIGNGLVLLGINSFFQQVVRGVIIVVAVLANILLTQ 325 Query: 384 -SSKNKK 389 SSK K+ Sbjct: 326 RSSKAKR 332 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: 336 Number of extensions: 23 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: 389 Length of database: 332 Length adjustment: 29 Effective length of query: 360 Effective length of database: 303 Effective search space: 109080 Effective search space used: 109080 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: 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