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_010629602.1 BZY95_RS02765 branched-chain amino acid ABC transporter permease
Query= TCDB::Q8DQI0 (292 letters) >NCBI__GCF_002151265.1:WP_010629602.1 Length = 295 Score = 160 bits (404), Expect = 4e-44 Identities = 91/286 (31%), Positives = 164/286 (57%), Gaps = 5/286 (1%) Query: 3 LMLQQLVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAFIGYFLINSFQMNFF 62 + + QL+ GLI G+ YALL+LG +++G++K++NFAHG +YM+GAF + +N++ Sbjct: 11 VFMGQLLLGLINGAFYALLSLGLAVIFGLLKIVNFAHGAMYMLGAFATLLGMRYLGINYW 70 Query: 63 VALIVAMLATAILGVVIEFLAYRPLRHSTRIAVLITAIGVSFLLEYGMVYLVGANTRAF- 121 AL++A L +LG++IE + R + H + L+ G++ + E +V G + + Sbjct: 71 AALLLAPLFVGLLGMLIERVLLRRIGHLDHLYGLLLTFGLALIFEGTLVNFFGVSGARYP 130 Query: 122 -PQAIQTVRYDLGPISLTNVQLMILGISLILMILLQVIVQKTKMGKAMRAVSVDSDAAQL 180 P+A+Q Y G + L + +L +L++ I+++T++G +RA + + Q Sbjct: 131 TPEALQG-GYQTGFMFLPKYRAWVLLAALVVCFATWYIIERTRLGAYLRAGTENPALMQA 189 Query: 181 MGINVNRTISFTFALGSALAGAAGVLIALYYNSLEPLMGVTPGLKSFVAAVLGGIGIIPG 240 G+NV ++ T+ G ALA AGVL A Y + P MG + F V+GG+G I G Sbjct: 190 FGVNVPLLVTLTYGFGVALAAFAGVLAAPLY-PVSPTMGSNLLIVVFAVVVIGGMGSILG 248 Query: 241 AALGGFVIGLLETFATAFGMSDFRDAIVYGILLLILIVRPAGILGK 286 A + G +GL+E + + + +++ +++L+L++RPAG+ GK Sbjct: 249 AIVTGLAMGLIEGLTKVY-YPEAANTVIFLVMILVLLLRPAGLFGK 293 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: 263 Number of extensions: 17 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: 295 Length adjustment: 26 Effective length of query: 266 Effective length of database: 269 Effective search space: 71554 Effective search space used: 71554 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