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_093393374.1 BM091_RS03050 branched-chain amino acid ABC transporter permease
Query= TCDB::Q8DQI0 (292 letters) >NCBI__GCF_900114975.1:WP_093393374.1 Length = 301 Score = 266 bits (679), Expect = 6e-76 Identities = 131/301 (43%), Positives = 204/301 (67%), Gaps = 9/301 (2%) Query: 1 MNLMLQQLVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAFIGYFLINSFQM- 59 M LQQ +NGL +G +YAL+ALGYTMVYG++KLINFAHGD++ +GA++G L+ S + Sbjct: 1 MEEFLQQFINGLCVGGIYALIALGYTMVYGVLKLINFAHGDLFTIGAYLGLTLLISLGLA 60 Query: 60 -------NFFVALIVAMLATAILGVVIEFLAYRPLRHSTRIAVLITAIGVSFLLEYGMVY 112 F+ ++ M A+LGV++E +AYRPLRHS R++ +++A+G S + ++ Sbjct: 61 DHIGPVAGIFLLSLMVMGLVAVLGVILERVAYRPLRHSPRLSAVVSALGASIFFQNAVML 120 Query: 113 LVGANTRAFPQ-AIQTVRYDLGPISLTNVQLMILGISLILMILLQVIVQKTKMGKAMRAV 171 + GA + +PQ + + ++ + + +++++L S+I+M+ L + +QKT +G A+RA Sbjct: 121 IYGARFQVYPQDLLPKIALNIFGLYIPLIRILVLAASVIMMLALYLFIQKTTIGTAIRAA 180 Query: 172 SVDSDAAQLMGINVNRTISFTFALGSALAGAAGVLIALYYNSLEPLMGVTPGLKSFVAAV 231 ++D AAQLMGINVN I+ F +G AL G AGV++ L Y ++ MG GLK+F AA+ Sbjct: 181 AIDQKAAQLMGINVNAVITLVFIIGPALGGFAGVMVGLLYGQIKFTMGWIYGLKAFTAAI 240 Query: 232 LGGIGIIPGAALGGFVIGLLETFATAFGMSDFRDAIVYGILLLILIVRPAGILGKNVKEK 291 LGGIG IPGA LGG ++G++E A+ ++DAI + +L++ILIVRP G+LG+ V EK Sbjct: 241 LGGIGNIPGAMLGGLILGVIEALGAAYLSIAWKDAIAFLVLIVILIVRPTGLLGERVAEK 300 Query: 292 V 292 V Sbjct: 301 V 301 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: 274 Number of extensions: 15 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: 301 Length adjustment: 26 Effective length of query: 266 Effective length of database: 275 Effective search space: 73150 Effective search space used: 73150 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