Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate Dsui_2059 Dsui_2059 ABC-type branched-chain amino acid transport system, permease component
Query= TCDB::Q8DQH9 (318 letters) >FitnessBrowser__PS:Dsui_2059 Length = 287 Score = 167 bits (423), Expect = 3e-46 Identities = 96/280 (34%), Positives = 159/280 (56%), Gaps = 8/280 (2%) Query: 35 YVQILQQIGINIILAVGLNLIVGFSGQFSLGHAGFMAIGAYAAAIIGSKSPTYGAFFGAM 94 Y ++ +G++ +LA+ + L + G SL +A FM +GAY +A++ +F + Sbjct: 11 YSTLVFSVGVHALLALSIWLTLS-CGLLSLANAAFMGVGAYVSALLTLHLEW--SFGSVL 67 Query: 95 LVGALLSGAVALLVGIPTLRLKGDYLAVATLGVSEIIRIFIINGGSLTNGAAGILGIPNF 154 L G + VAL++G P LRL G YLA+ATL E++RI ++N +T G G+ GIP Sbjct: 68 LAGGIAPTLVALIIGAPVLRLSGVYLAMATLAFGEVVRITVLNL-EITGGPEGLNGIPLA 126 Query: 155 TTWQMVYFFVVITTIATLNFLRSPIGRSTLSVREDEIAAESVGVNTTKIKIIAFVFGAIT 214 T + + + RS +GR+ +++EDE+AA +G+N + K++AF GA Sbjct: 127 TEGWHIALILAVAVYGLARLRRSKVGRAFEAIKEDEVAARLMGINVDRYKLLAFSLGAFI 186 Query: 215 ASIAGSLQAGFIGSVVPKDYTFINSINVLIIVVFGGLGSITGAIVSAIVLGILNMLLQDV 274 A +AG+L A F + P++Y F N++++L + V GG S+ G ++ + +L +L LL+ + Sbjct: 187 AGVAGALNAHFTFFISPREYGFENAVDILTMAVLGGTSSLIGPMLGSSILTLLPELLRSL 246 Query: 275 ASVRMIIYALALVLVMIFRPGGLLGTWELSLSR-FFKKSK 313 R ++ LVLV++F P GL WE R FFK+ K Sbjct: 247 QDFRSLVNGAVLVLVVLFLPKGL---WESRRIRAFFKRLK 283 Lambda K H 0.327 0.143 0.403 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: 196 Number of extensions: 8 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: 318 Length of database: 287 Length adjustment: 27 Effective length of query: 291 Effective length of database: 260 Effective search space: 75660 Effective search space used: 75660 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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