Align glucose transporter, periplasmic substrate-binding component (characterized)
to candidate BPHYT_RS32820 BPHYT_RS32820 xylose ABC transporter substrate-binding protein
Query= reanno::Phaeo:GFF3639 (341 letters) >FitnessBrowser__BFirm:BPHYT_RS32820 Length = 342 Score = 230 bits (587), Expect = 3e-65 Identities = 131/325 (40%), Positives = 196/325 (60%), Gaps = 6/325 (1%) Query: 7 VSALAFAATASMAFAEDVTVGVSWSNFQEERWKTDEAAIKAALEAKGATYVSADAQSSSA 66 +++L+ A + A + +G + + ERW D AA E GA A +S A Sbjct: 19 LASLSLVAPLAHASKDHPEIGFCIDDLRVERWSRDRDYFVAAAEKLGAKVSVQSADASEA 78 Query: 67 KQLSDIESLIAQGVDALIVLAQDAQAIGPAVQAAADEGIPVVAYDRLIEDGRA-FYLTFD 125 +Q+S IE+LI++GVD ++++ +++ +G V A GI VV+YDRLI D Y++FD Sbjct: 79 RQISQIENLISRGVDVIVIVPFNSKTLGNVVAEAKKAGIKVVSYDRLILDADVDAYISFD 138 Query: 126 NVEVGRMQARAVLEAQPSGNYVMIKGSPTDPNADFLRGGQQEIIQAAIDSGDIKIVGEAY 185 N +VG +QA+ V AQP GNY ++ G+PTD NA LR GQ +I++ AID GDIK+VG+ + Sbjct: 139 NEKVGELQAQGVYNAQPKGNYFLLGGAPTDNNAKMLREGQLKILKPAIDKGDIKVVGQQW 198 Query: 186 TDGWLPANAQRNMEQILTANDNKVDAVVASNDGTAGGVVAALTAQGMEG-IAVSGQDGDH 244 W + A R +E LTAN+NK+DA+VASNDGTAGG + AL AQ M G + VSGQD D Sbjct: 199 VPEWSASTALRIVEDALTANNNKIDAIVASNDGTAGGAIQALAAQHMAGKVPVSGQDADL 258 Query: 245 AALNRVAKGTQTVSVWKDARDLGKAAANIAVEMAEGAVMGDVAGGAAWTSPAGTELTARF 304 AA+ RV GTQT++V+K + + AA ++V +A+ G+ + ++ Sbjct: 259 AAVKRVIAGTQTMTVYKPLKLIAGEAAKLSVALAK----GEKPAFNSQYDNGKKKVDTVL 314 Query: 305 LEPIPVTADNLSVVVDAGWITKEAL 329 L+P +T N+ VVV G+ ++ L Sbjct: 315 LQPTLLTKSNVDVVVKDGFYSQAQL 339 Lambda K H 0.313 0.128 0.362 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: 226 Number of extensions: 8 Number of successful extensions: 3 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: 341 Length of database: 342 Length adjustment: 29 Effective length of query: 312 Effective length of database: 313 Effective search space: 97656 Effective search space used: 97656 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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