Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate WP_109940760.1 DLD82_RS08835 ATP-binding cassette domain-containing protein
Query= reanno::Dino:3607124 (338 letters) >NCBI__GCF_003173335.1:WP_109940760.1 Length = 348 Score = 212 bits (540), Expect = 1e-59 Identities = 105/262 (40%), Positives = 165/262 (62%), Gaps = 10/262 (3%) Query: 19 LFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRIEIGGRDVTTVEPADRDLA 78 L ++ LDI GE++V +GP+G GK+ LL T+AG SG+I + GRD+T + P DR++ Sbjct: 16 LRNVTLDITPGEYLVIIGPTGAGKTILLETIAGFYPPDSGKIIMDGRDITNIPPKDRNIC 75 Query: 79 MVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAARVLQLEDYLDRKPGQLSGGQ 138 MV+Q Y L+PH+TV EN+ FG+K +P+ +++ E AR+L ++ L RKP LSGG+ Sbjct: 76 MVYQDYMLFPHLTVEENIGFGLKTRKKDPEYIRKKTVEMARLLSIDHLLHRKPETLSGGE 135 Query: 139 RQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGLHKQLGATMIYVTHDQVEAM 198 +QR AI R++V P++ L DEPLS LD + R ++R EL +H T++++TH+ E Sbjct: 136 QQRAAIARSLVMEPNLLLLDEPLSALDGQTRDKLRTELRRIHDITNVTVVHITHNFEEVF 195 Query: 199 TMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPAMNVFSSDVGLQD----ISLD 254 ++AD++ ++N+G I Q+G+P +++ KP S F+A F G N+F QD I +D Sbjct: 196 SLADRVAIMNKGEIVQIGNPDEVFRKPESEFIASFTGME--NIFKGSCSHQDGISAIKID 253 Query: 255 A----SAAFVGCRPEHIEIVPD 272 SA +G R + I P+ Sbjct: 254 GHIVYSATCLGEREVYATIRPE 275 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: 292 Number of extensions: 11 Number of successful extensions: 1 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: 348 Length adjustment: 29 Effective length of query: 309 Effective length of database: 319 Effective search space: 98571 Effective search space used: 98571 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 24 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