Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate WP_011802898.1 PNAP_RS17620 branched-chain amino acid ABC transporter permease
Query= TCDB::Q8DQI0 (292 letters) >NCBI__GCF_000015505.1:WP_011802898.1 Length = 294 Score = 167 bits (424), Expect = 2e-46 Identities = 95/283 (33%), Positives = 167/283 (59%), Gaps = 3/283 (1%) Query: 5 LQQLVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAFIGYFLINSFQMNFFVA 64 L QL+ GL+ G+ YA+L+LG +++G++ ++NFAHG +YM+GAF + +++ F +N++ A Sbjct: 12 LGQLLLGLVNGAFYAMLSLGLAVIFGLLGVVNFAHGALYMLGAFAAWIMLDKFGINYWFA 71 Query: 65 LIVAMLATAILGVVIEFLAYRPLRHSTRIAVLITAIGVSFLLEYGMVYLVGANTRAFP-Q 123 L++A LA GVVIE L + L + L+ G++ ++E L GA+ + +P Sbjct: 72 LVLAPLAVGAFGVVIERLFLKHLYKLDPLYGLLLTFGLALIVEGVFRELYGASGQTYPVP 131 Query: 124 AIQTVRYDLGPISLTNVQLMILGISLILMILLQVIVQKTKMGKAMRAVSVDSDAAQLMGI 183 + +LG + L N + ++ +SL + + I+++T++G +RA + ++ Q GI Sbjct: 132 ELLAGATNLGFMVLPNYRAWVVAVSLAVCLGTWFIIERTRLGAYLRAGTENAALVQTFGI 191 Query: 184 NVNRTISFTFALGSALAGAAGVLIALYYNSLEPLMGVTPGLKSFVAAVLGGIGIIPGAAL 243 NV + T+ G+ALA AGVL A + PLMG + F V+GG+G I G+ + Sbjct: 192 NVPMMVMLTYGAGAALAALAGVLAAPII-QVNPLMGSNLIIVVFAVVVIGGMGSILGSVV 250 Query: 244 GGFVIGLLETFATAFGMSDFRDAIVYGILLLILIVRPAGILGK 286 G +GL+E F + + +V+ +++L+L+VRPAG+ GK Sbjct: 251 TGLALGLVEGMTRVF-YPEASNIVVFVVMVLVLMVRPAGLFGK 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: 252 Number of extensions: 19 Number of successful extensions: 4 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: 294 Length adjustment: 26 Effective length of query: 266 Effective length of database: 268 Effective search space: 71288 Effective search space used: 71288 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 24 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