Align ABC transporter for Xylitol, permease component 2 (characterized)
to candidate GFF2207 HP15_2161 sugar ABC transporter, permease protein
Query= reanno::Dino:3607127 (272 letters) >FitnessBrowser__Marino:GFF2207 Length = 269 Score = 166 bits (419), Expect = 6e-46 Identities = 88/271 (32%), Positives = 140/271 (51%), Gaps = 3/271 (1%) Query: 1 MTSTRSLFSQIALLVLIITVCVFPFYWMVTTSLKTQIVALEAPPVWIFEPTLSNYREALF 60 M TRS I L +L++ P YW++ S KT L +W TL NY Sbjct: 2 MRQTRSKNVGITLFILLLLT---PIYWLLNMSFKTNQEILGGLTLWPQNFTLDNYAVIFT 58 Query: 61 EDGVLRTLINSLIIAISTTFLALVLGVPAAFALARFEFRGKKDLWFWFITNRMISPIVLA 120 + INS+I + L++ +PAA+A +R++F G K L+FW ++NRM P V Sbjct: 59 DPSWYNGYINSMIYVSINVVITLLVALPAAYAFSRYKFLGDKHLFFWLLSNRMAPPAVFL 118 Query: 121 LPFFLIARNLGLLDKHITLILIYLTFNLPIVIWIVTDQFRGIPYDLDEAARLEGASQFTI 180 LPFF + ++GL D HI + L + FN+P+ +WI+ G+P + DE A ++G S Sbjct: 119 LPFFQLYSSIGLFDTHIAVALAHCLFNVPLAVWILEGFMSGVPREYDEMAYIDGYSFPKF 178 Query: 181 MRKICLPLAMPGVAVSAIFSFIFSWNELMFGLILTRSEAKTAPAMAVSFMEGYNLPYGKI 240 K+ LP+ G+ V+A F+F+FSW EL+ LT +A+ A+ + + +G + Sbjct: 179 FVKVFLPMIRSGIGVTAFFAFMFSWVELLLARTLTSVDAQPIGAIMTRTIGASGIDWGVL 238 Query: 241 MATSTLIVIPVLIFALIASKQLVRGLTMGAV 271 A +L +IP L+ + +G +G V Sbjct: 239 AAAGSLTIIPGLLVIWFVRNHVAKGFALGRV 269 Lambda K H 0.331 0.143 0.431 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: 249 Number of extensions: 12 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: 272 Length of database: 269 Length adjustment: 25 Effective length of query: 247 Effective length of database: 244 Effective search space: 60268 Effective search space used: 60268 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 47 (22.7 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