Align Monosaccharide-transporting ATPase, component of Xylose transporter, XylFGH (XylF (R), 359 aas; XylG (C), 525 aas; XylH (M), 389 aas (characterized)
to candidate 3608606 Dshi_1999 inner-membrane translocator (RefSeq)
Query= TCDB::A6LW12 (389 letters) >FitnessBrowser__Dino:3608606 Length = 435 Score = 231 bits (588), Expect = 4e-65 Identities = 133/399 (33%), Positives = 218/399 (54%), Gaps = 38/399 (9%) Query: 23 SKMAAILIATAAIWVLFTFLTDGNFLTTRNLSNLFRQMSITGVLAIGMVFVIILGEIDLS 82 +++ ++ A + ++F LTDG FLT RN+ NL Q ++A GMVF+I+ IDL+ Sbjct: 27 TRLLGMIGAFVLVCLVFNLLTDGRFLTARNIFNLSIQTVSVAIMATGMVFIIVTRHIDLA 86 Query: 83 AGSTLGLLGGIAA---------ILNVWFGFSAIPTV--VITLILGVIMGAWNGYWIAFRN 131 G+ L A + + G AIP + ++ L+ G ++GA+ GY + + Sbjct: 87 VGALLATCSAAMAMTQTAILPQVFGLELGHPAIPWIAMLVGLVTGTVIGAFQGYLVGYLM 146 Query: 132 VPSFIVTLASMLVFRGVLIGITGGNTVAPLTADFKAIG--QAYLPTVVGYILVVLAIVGS 189 +P+FIVTL +LV+R V +T G T+ PL F +G L + +I+ ++A+V + Sbjct: 147 IPAFIVTLGGLLVWRNVAWYMTNGQTIGPLDPTFMTLGGINGTLGATLSWIVGLVAVVAA 206 Query: 190 AYLILGNRKNKIKYNIEVRPMALDVLTIVGIGVISLVLVLILNDYQ-------------- 235 + + RKNKI ++ V+P+ ++ + + V L V ILN Y+ Sbjct: 207 CWALWSGRKNKIAHDAPVKPVWAELTVMGVVSVAILGFVAILNSYEVPTARLRRLFEARG 266 Query: 236 -----------GFPIPVFIMLLLALILAFVGTKTIFGRRIYGIGGNRDAARLSGINVKKH 284 G P V +++ +A+ + + KT FGR I+ GGN DAA LSGIN + Sbjct: 267 EVMPEGYTEVYGIPYSVLLLIAVAVAMTVIAKKTRFGRYIFATGGNPDAAELSGINTRML 326 Query: 285 IIVIYSVLGLLCAVAGILLTSRLNAGSVSAGQNAEMDAIASCVIGGASLAGGSGTVAGAL 344 + +++++G LCA++ I+ ++RL S G E+ IA+ VIGG +LAGG GT+ GA+ Sbjct: 327 TVKVFALMGALCAISAIVASARLTNHSNDIGTLDELRVIAAAVIGGTALAGGIGTIYGAI 386 Query: 345 VGALVMASIDNGMSMMNTPTFWQYIVKGLILLIAVWMDI 383 +GAL+M S+ +GM+M+ Q IV G +L+ AV +DI Sbjct: 387 LGALIMQSLQSGMAMVGVDAPLQNIVVGTVLVAAVLIDI 425 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: 422 Number of extensions: 25 Number of successful extensions: 4 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: 435 Length adjustment: 31 Effective length of query: 358 Effective length of database: 404 Effective search space: 144632 Effective search space used: 144632 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