Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate SM_b20630 SM_b20630 sugar uptake ABC transporter ATP-binding protein
Query= reanno::Dino:3607124 (338 letters) >FitnessBrowser__Smeli:SM_b20630 Length = 361 Score = 336 bits (861), Expect = 6e-97 Identities = 179/351 (50%), Positives = 231/351 (65%), Gaps = 16/351 (4%) Query: 4 IKIDKINKFYGTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRIEIG 63 + + I K YG + + I+L IE+G+FVVFVGPSGCGKSTLLR +AGLE VS G I I Sbjct: 10 VVLSDIRKSYGGLEVIHGIDLTIEEGDFVVFVGPSGCGKSTLLRMIAGLEEVSEGEIAIK 69 Query: 64 GRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAARVLQL 123 GRDVT ++P++R +AMVFQSYALYPHM+V EN+ FG+K+ +P R+A+ + +L++ Sbjct: 70 GRDVTDLDPSERGIAMVFQSYALYPHMSVSENLGFGLKMARTDPAEIARRVAQVSAILKI 129 Query: 124 EDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGLHKQL 183 + LDR+PGQLSGGQRQRVAIGRAIV+ P VFLFDEPLSNLDA+LRV MR+E+ LH++L Sbjct: 130 DHLLDRRPGQLSGGQRQRVAIGRAIVRKPDVFLFDEPLSNLDAELRVSMRIEIARLHREL 189 Query: 184 GATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPAMNVFS 243 G TM+YVTHDQ EAMT+AD+IVVL GRIEQ GSP D+Y P + FVA FIGSP MN Sbjct: 190 GNTMVYVTHDQTEAMTLADQIVVLRDGRIEQAGSPRDVYEDPANMFVAGFIGSPRMNFLD 249 Query: 244 SD------VGLQDISLDAS----------AAFVGCRPEHIEIVPDGDGHIAATVHVKERL 287 ++ + + + +L+A+ +G RPEHI + G IAA V E L Sbjct: 250 AEWQGDGTIRVGETTLEAAIDGGSLKHGERLLLGIRPEHIAVAEPGPERIAAQVEFSEYL 309 Query: 288 GGESLLYLGLKGGGQIVARVGGDDETKVGAAVSLRFSRHRLHQFDEAGRAI 338 GG LY L+ G +V + G +S R F E GR + Sbjct: 310 GGTRYLYCQLEDGQSLVVEQREGPNWQAGEKLSFAVPDDRRRFFAEDGRRL 360 Lambda K H 0.320 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: 386 Number of extensions: 19 Number of successful extensions: 2 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: 338 Length of database: 361 Length adjustment: 29 Effective length of query: 309 Effective length of database: 332 Effective search space: 102588 Effective search space used: 102588 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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