Align glucose transporter, ATPase component (characterized)
to candidate GFF2760 HP15_2704 branched-chain amino acid ABC transporter, ATP-binding protein
Query= reanno::Phaeo:GFF3641 (260 letters) >FitnessBrowser__Marino:GFF2760 Length = 252 Score = 123 bits (308), Expect = 4e-33 Identities = 75/230 (32%), Positives = 119/230 (51%), Gaps = 10/230 (4%) Query: 13 TPLVEMKDISISFGGIKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMDAGEI 72 T LVE+K + +FGG+ AV+ VS + G+V ++G NGAGK+TL +++G Y GEI Sbjct: 2 TALVEVKGLDKAFGGVHAVEGVSFSVEAGQVYSVIGPNGAGKTTLFNLITGLYTPTKGEI 61 Query: 73 RVNGDKVEITNPRDARSHNIETIYQTLALADNLDAASNLFLGREL-------VTPFGLVD 125 +NG+ P + + +Q + + N+ A N+ LGR L T F L Sbjct: 62 LLNGESTAKLEPNELAERGMCRTFQQMQICMNMTAIENVMLGRHLQLKSSLFTTLFRLPS 121 Query: 126 DSAMEAECRKIMNRLNPNF---QKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDEPTA 182 EA RK L SA+S G + + IARA+ K++++DEP A Sbjct: 122 LRRNEAAARKRAAELMEYVGCGDYLDAEASAMSYGALKRLEIARALAAEPKVILLDEPAA 181 Query: 183 ALGPHETQMVAELIQQLKAQGIGIFLIDHDVNAVMELCDRASVMKNGQLV 232 L ET + +LI+++ QG + L++HD+ VM + DR V+ G+++ Sbjct: 182 GLNAVETAALEDLIRKIADQGTTVMLVEHDMKLVMGISDRLLVLNYGRVL 231 Lambda K H 0.317 0.135 0.373 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: 138 Number of extensions: 5 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: 260 Length of database: 252 Length adjustment: 24 Effective length of query: 236 Effective length of database: 228 Effective search space: 53808 Effective search space used: 53808 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: 41 (21.7 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