Align Inositol transport system sugar-binding protein (characterized)
to candidate BWI76_RS00285 BWI76_RS00285 D-ribose ABC transporter substrate-binding protein
Query= reanno::WCS417:GFF2331 (309 letters) >FitnessBrowser__Koxy:BWI76_RS00285 Length = 296 Score = 141 bits (356), Expect = 2e-38 Identities = 89/293 (30%), Positives = 157/293 (53%), Gaps = 10/293 (3%) Query: 8 TALALSMLLASGVASAADLKIGVSMSAFDDTFLTYLREDMDKQAKSYPKGDGVQLQFEDA 67 +A+ALS +++ A A D I + +S ++ F L+E K+A G L D+ Sbjct: 11 SAVALSATVSAN-AMAKDT-IALVISTLNNPFFVSLKEGAQKEADKL----GYNLVVLDS 64 Query: 68 RADVVKQLSQVENFISQKVDAIIVNPVDTASTANIIKAATAAKIPLVFVNRRPDSQTLAP 127 + + K+L+ V++ + +++NP D+ + N +K A AKIP++ ++R+ + Sbjct: 65 QNNPAKELANVQDLTVRGTKLLLINPTDSDAVGNAVKLANQAKIPVITLDRQASKGDV-- 122 Query: 128 GVAAVTSDDVEAGKLQMQYIAEKLGGKGNIVILLGDLANNSTTNRTKGVKEVLTKYPGIK 187 V+ + SD+V GK+ YIA+K+G I+ L G ++ R +G ++ + + Sbjct: 123 -VSHIASDNVLGGKMAGDYIAKKVGENAKIIELQGIAGTSAARERGEGFQQAVAAHK-FN 180 Query: 188 IEQEQTGIWLRDRGMTLVNDWLTQGRDFQAVLSNNDEMAIGAAMALKSAGKKGVLIAGVD 247 + Q + R +G+ ++ + LT D QAV + NDEMA+GA AL++AGK V++ G D Sbjct: 181 VLASQPADFDRTKGLNVMQNLLTAHPDVQAVFAQNDEMALGALRALQTAGKSDVMVVGFD 240 Query: 248 GTPDGLNAITKGDMTVSAFQDAKGQADKSVETARKMAKNEPIEQNVVIPFQLI 300 GTPDG A+ G + + Q + K VETA K+ K E +E + + +L+ Sbjct: 241 GTPDGEKAVNSGKLAATIAQLPEQIGVKGVETADKVLKGEKVETSYPLELKLV 293 Lambda K H 0.314 0.131 0.357 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: 238 Number of extensions: 15 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: 309 Length of database: 296 Length adjustment: 27 Effective length of query: 282 Effective length of database: 269 Effective search space: 75858 Effective search space used: 75858 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 48 (23.1 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