Align ABC transporter for Xylitol, permease component 2 (characterized)
to candidate 3607560 Dshi_0972 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= reanno::Dino:3607127 (272 letters) >FitnessBrowser__Dino:3607560 Length = 276 Score = 185 bits (469), Expect = 1e-51 Identities = 94/251 (37%), Positives = 149/251 (59%), Gaps = 1/251 (0%) Query: 23 FPFYWMVTTSLKTQIVALEAPPVWI-FEPTLSNYREALFEDGVLRTLINSLIIAISTTFL 81 FP W + TS KT+ A+ PPV++ F+ TL NY L + L NS+IIA +T L Sbjct: 26 FPILWTILTSFKTEATAIADPPVFLAFDWTLENYTAVLERSNYAKFLWNSIIIAGGSTIL 85 Query: 82 ALVLGVPAAFALARFEFRGKKDLWFWFITNRMISPIVLALPFFLIARNLGLLDKHITLIL 141 +++ VPAA+++A R KD+ W ++ +M+ + + P +LI LG+LD + L++ Sbjct: 86 GIMIAVPAAWSMAFVPSRRTKDILLWMLSTKMLPAVGVLYPIYLICIELGILDSRVALVV 145 Query: 142 IYLTFNLPIVIWIVTDQFRGIPYDLDEAARLEGASQFTIMRKICLPLAMPGVAVSAIFSF 201 I + NLPI++W++ F+ IP ++ EAAR++GAS + + P+A+PG+A + + +F Sbjct: 146 ILMLMNLPIIVWMLYTYFKEIPGEILEAARMDGASLKEEILYVLTPMAIPGIASTLLLNF 205 Query: 202 IFSWNELMFGLILTRSEAKTAPAMAVSFMEGYNLPYGKIMATSTLIVIPVLIFALIASKQ 261 I +WNE + L LT + A A S+ L + K+ A ST+ + P+LI + KQ Sbjct: 206 ILAWNEAFWTLNLTAANAAPLTAFIASYSSPEGLFFAKLSAASTMAIAPILILGWFSQKQ 265 Query: 262 LVRGLTMGAVK 272 LV GLT GAVK Sbjct: 266 LVSGLTFGAVK 276 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: 238 Number of extensions: 10 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 272 Length of database: 276 Length adjustment: 25 Effective length of query: 247 Effective length of database: 251 Effective search space: 61997 Effective search space used: 61997 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