Align Inositol transport system ATP-binding protein (characterized)
to candidate Dsui_0627 Dsui_0627 ABC-type branched-chain amino acid transport systems, ATPase component
Query= reanno::Phaeo:GFF717 (261 letters) >FitnessBrowser__PS:Dsui_0627 Length = 267 Score = 120 bits (300), Expect = 4e-32 Identities = 76/235 (32%), Positives = 119/235 (50%), Gaps = 9/235 (3%) Query: 1 MSMSQPLIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPT 60 MS L+ + KHFG V AL GVS+ + GE + L+G NGAGK+TF ++G++ P Sbjct: 1 MSERPILLEASDVAKHFGGVKALRGVSLTIREGEIYGLIGPNGAGKTTFFNCLTGLYVPN 60 Query: 61 KGDILFEGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIG------ 114 G I+F G L + P A GIA Q++ + M+ N +G + G Sbjct: 61 GGRIVFAGAELDTSAPHKVAARGIARTFQNIRLFAHMTALENVMVGRHQRTRAGVFGAIF 120 Query: 115 --PLKLFDHDYANRITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLIL 172 P + R E + +GI R D A LS G+++ + IARA+ K+L L Sbjct: 121 RTPGTRAEEAAIQRRAEELLHYVGIADRAHDLA-KHLSYGDQRRLEIARALATEPKLLAL 179 Query: 173 DEPTSALGVRQTANVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTL 227 DEP + + +T + I+ +RK G+ V+ I H+V+ + + DR VL+ G+ + Sbjct: 180 DEPAAGMNASETGELRTLIEGIRKDGITVLLIEHDVKLVMGLCDRVAVLDYGEKI 234 Lambda K H 0.321 0.137 0.395 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: 169 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: 261 Length of database: 267 Length adjustment: 25 Effective length of query: 236 Effective length of database: 242 Effective search space: 57112 Effective search space used: 57112 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 (21.9 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