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_2060 Dsui_2060 branched-chain amino acid ABC-type transport system, permease component
Query= TCDB::Q8DQI0 (292 letters) >FitnessBrowser__PS:Dsui_2060 Length = 293 Score = 205 bits (521), Expect = 1e-57 Identities = 103/292 (35%), Positives = 180/292 (61%), Gaps = 3/292 (1%) Query: 3 LMLQQLVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAFIGYFLINSFQMNFF 62 ++ QQL+N L LGSVYAL ALG+T+V+G++ +IN +HG ++M+G++ +++ + Sbjct: 1 MLEQQLLNALTLGSVYALFALGFTLVFGVLAVINLSHGAVFMVGSYAALAMVSHLNAPLW 60 Query: 63 VALIVAMLATAILGVVIEFLAYRPLR--HSTRIAVLITAIGVSFLLEYGMVYLVGANTRA 120 VA++ AM+ + +G++++ L +PLR ++ + +I IGV +L L GA Sbjct: 61 VAMLGAMVVSGTIGLLVDVLVLKPLRARNAPHLIPMIATIGVGIMLTSAAQGLFGAEVLR 120 Query: 121 FPQAIQTV-RYDLGPISLTNVQLMILGISLILMILLQVIVQKTKMGKAMRAVSVDSDAAQ 179 FP+ + + +G + + +++ I+ I+ +LM +L I+++T++G+A+RA++ AA Sbjct: 121 FPEDVMPAGEFMVGDVHVRALEIAIVAIAFLLMAVLFTILKRTQLGRALRAIAESPKAAY 180 Query: 180 LMGINVNRTISFTFALGSALAGAAGVLIALYYNSLEPLMGVTPGLKSFVAAVLGGIGIIP 239 L+GINV T + +AL G AGVLI L +N++ P MG K +LGG+G I Sbjct: 181 LLGINVEGLFHITSFVAAALGGIAGVLIGLNFNAITPFMGQPMLHKGIAVIILGGMGDIR 240 Query: 240 GAALGGFVIGLLETFATAFGMSDFRDAIVYGILLLILIVRPAGILGKNVKEK 291 GA +GG +G E + A+ S DA+ +G+L LIL+VRP+G+ G+ ++ K Sbjct: 241 GALIGGLFLGFAEVISKAYLSSQMGDAVAFGLLFLILLVRPSGLFGRKLERK 292 Lambda K H 0.330 0.146 0.407 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: 218 Number of extensions: 16 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: 292 Length of database: 293 Length adjustment: 26 Effective length of query: 266 Effective length of database: 267 Effective search space: 71022 Effective search space used: 71022 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 (21.8 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