Align glucose transporter, periplasmic substrate-binding component (characterized)
to candidate 17627 b3566 D-xylose transporter subunit (NCBI)
Query= reanno::Phaeo:GFF3639 (341 letters) >FitnessBrowser__Keio:17627 Length = 330 Score = 242 bits (618), Expect = 8e-69 Identities = 132/313 (42%), Positives = 192/313 (61%), Gaps = 8/313 (2%) Query: 19 AFAEDVTVGVSWSNFQEERWKTDEAAIKAALEAKGATYVSADAQSSSAKQLSDIESLIAQ 78 A A++V +G++ + + ERW+ D E+ GA A + Q+S IE++I + Sbjct: 21 AHAKEVKIGMAIDDLRLERWQKDRDIFVKKAESLGAKVFVQSANGNEETQMSQIENMINR 80 Query: 79 GVDALIVLAQDAQAIGPAVQAAADEGIPVVAYDRLIEDGRA-FYLTFDNVEVGRMQARAV 137 GVD L+++ + Q + V+ A EGI V+AYDR+I D FY++FDN +VG +QA+A+ Sbjct: 81 GVDVLVIIPYNGQVLSNVVKEAKQEGIKVLAYDRMINDADIDFYISFDNEKVGELQAKAL 140 Query: 138 LEAQPSGNYVMIKGSPTDPNADFLRGGQQEIIQAAIDSGDIKIVGEAYTDGWLPANAQRN 197 ++ P GNY ++ GSP D NA R GQ ++++ +DSG IK+VG+ + DGWLP NA + Sbjct: 141 VDIVPQGNYFLMGGSPVDNNAKLFRAGQMKVLKPYVDSGKIKVVGDQWVDGWLPENALKI 200 Query: 198 MEQILTANDNKVDAVVASNDGTAGGVVAALTAQGMEG-IAVSGQDGDHAALNRVAKGTQT 256 ME LTAN+NK+DAVVASND TAGG + AL+AQG+ G +A+SGQD D A + R+A GTQT Sbjct: 201 MENALTANNNKIDAVVASNDATAGGAIQALSAQGLSGKVAISGQDADLAGIKRIAAGTQT 260 Query: 257 VSVWKDARDLGKAAANIAVEMAEGAVMGDVAGGAAWTSPAG-TELTARFLEPIPVTADNL 315 ++V+K L AA IAVE+ G A T G ++ +R L PI V +N+ Sbjct: 261 MTVYKPITLLANTAAEIAVELGNGQ-----EPKADTTLNNGLKDVPSRLLTPIDVNKNNI 315 Query: 316 SVVVDAGWITKEA 328 V KE+ Sbjct: 316 KDTVIKDGFHKES 328 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: 227 Number of extensions: 10 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: 330 Length adjustment: 28 Effective length of query: 313 Effective length of database: 302 Effective search space: 94526 Effective search space used: 94526 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