Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate Dsui_3464 Dsui_3464 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component
Query= reanno::Dino:3607124 (338 letters) >FitnessBrowser__PS:Dsui_3464 Length = 263 Score = 157 bits (397), Expect = 3e-43 Identities = 89/211 (42%), Positives = 127/211 (60%), Gaps = 7/211 (3%) Query: 1 MAGIKIDKINKFY----GTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVS 56 M+ I I + K + G AL DINL ++ GEFV +GPSGCGKSTLL +AG + S Sbjct: 1 MSDILIKDVQKVFKTPGGDVTALKDINLTVKQGEFVCLLGPSGCGKSTLLNAVAGFQPPS 60 Query: 57 SGRIEIGGRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAE 116 +G I I G+ + T P D MVFQ YAL+P MTV +N+ FG+++ E + + Sbjct: 61 AGEIVIEGKKILTPGP---DRGMVFQEYALFPWMTVAQNIAFGLQIQKKEKAEIDLTVNQ 117 Query: 117 AARVLQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVEL 176 +L L+D+ DR P LSGG RQRVAI R + + + L DEP LDA R ++ EL Sbjct: 118 LLDLLHLKDFRDRFPKDLSGGMRQRVAIARVLALDSPIMLMDEPFGALDALTRRNLQDEL 177 Query: 177 EGLHKQLGATMIYVTHDQVEAMTMADKIVVL 207 + ++L T+++VTH E++ +AD+IVV+ Sbjct: 178 LRIWEKLNKTILFVTHSIEESIYLADRIVVM 208 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: 221 Number of extensions: 7 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: 263 Length adjustment: 26 Effective length of query: 312 Effective length of database: 237 Effective search space: 73944 Effective search space used: 73944 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: 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