Align D-lactate transporter, ATP-binding component (characterized)
to candidate Dsui_0627 Dsui_0627 ABC-type branched-chain amino acid transport systems, ATPase component
Query= reanno::Phaeo:GFF1248 (251 letters) >FitnessBrowser__PS:Dsui_0627 Length = 267 Score = 186 bits (473), Expect = 3e-52 Identities = 103/254 (40%), Positives = 154/254 (60%), Gaps = 8/254 (3%) Query: 3 ILEVKNVGKRFGGLQALSDVNLSVRENTVHAIIGPNGAGKSTLLNCLVGKLIPDTGSVMF 62 +LE +V K FGG++AL V+L++RE ++ +IGPNGAGK+T NCL G +P+ G ++F Sbjct: 7 LLEASDVAKHFGGVKALRGVSLTIREGEIYGLIGPNGAGKTTFFNCLTGLYVPNGGRIVF 66 Query: 63 DGKSVLGRAPYEINQMGISRVFQTPEIFGDLSVLENMMIPCFAK-RDGAFEMNAISAVSG 121 G + AP+++ GI+R FQ +F ++ LEN+M+ + R G F AI G Sbjct: 67 AGAELDTSAPHKVAARGIARTFQNIRLFAHMTALENVMVGRHQRTRAGVF--GAIFRTPG 124 Query: 122 QR----DILEKAEHMLEEMNMADKRHMNAASMSRGDKRRLEIGMCLSQEPRLLLLDEPTA 177 R I +AE +L + +AD+ H A +S GD+RRLEI L+ EP+LL LDEP A Sbjct: 125 TRAEEAAIQRRAEELLHYVGIADRAHDLAKHLSYGDQRRLEIARALATEPKLLALDEPAA 184 Query: 178 GMARADTNNTIDLLKQIKSERDITIAIIEHDMHVVFSLADRITVLAQGTPLVEDDPQNIK 237 GM ++T L++ I+ + IT+ +IEHD+ +V L DR+ VL G + ED P ++ Sbjct: 185 GMNASETGELRTLIEGIRKD-GITVLLIEHDVKLVMGLCDRVAVLDYGEKICEDVPAVVQ 243 Query: 238 GNPKVREAYLGESA 251 +P+V AYLG A Sbjct: 244 KDPRVITAYLGAEA 257 Lambda K H 0.318 0.135 0.379 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: 179 Number of extensions: 10 Number of successful extensions: 3 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: 251 Length of database: 267 Length adjustment: 24 Effective length of query: 227 Effective length of database: 243 Effective search space: 55161 Effective search space used: 55161 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