Align High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale)
to candidate WP_012046890.1 BBTA_RS33165 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A159ZYE0 (418 letters) >NCBI__GCF_000015165.1:WP_012046890.1 Length = 338 Score = 146 bits (368), Expect = 1e-39 Identities = 103/345 (29%), Positives = 167/345 (48%), Gaps = 31/345 (8%) Query: 64 ISAMWKSSPGLPVIPAKASNFLTLPTTQRWIVLALIVGALVWPFFGSRGAVDIATLILIY 123 I + +P + +P +A +TL + ++V+ L+ LV P F + T++LIY Sbjct: 4 IEEVGSQAPAVEAVPKRA---MTLSSGTAFVVVLLL---LVVPLFVKNFIIFQMTMLLIY 57 Query: 124 VMLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYALLSHYFGLSFWICLPIAGMMAATFGFL 183 + L LNI+ G +G LG FYAVGAY+ A+L + +++ + LP+AG++ FGFL Sbjct: 58 GLAVLALNILTGGSGQFSLGQSAFYAVGAYTSAILMEQYNINYALTLPVAGVVCFGFGFL 117 Query: 184 LGFPVLRLRGDYLAIVTLGFGEIIRLFLR--NLTDITGGPNGISNIEKPTFFGLTFERKA 241 G P LRL G YLA+ T + L+ TGG G+ + FGL Sbjct: 118 FGQPALRLSGVYLALATFALATAMPQILKLGFFEHWTGGVQGLVVTKPDAPFGL------ 171 Query: 242 AEGLQTFHEYFGLEYNSINKVIFLYLVALLLALAALFVINRLLRMPIGRAWEALREDEIA 301 +++ ++LY L + +A LLR GRA+ A+R++EIA Sbjct: 172 ----------------PMSQDMWLYYFTLAITIAIYIFSVNLLRSRSGRAFMAIRDNEIA 215 Query: 302 CRALGLNPTVIKLSAFTLGAAFAGFAGSFFAARQGLVTPESFTFIESAIILAIVVLGGMG 361 A+G++ K AF + A G AG A V P+S+T + + + +V+GG+G Sbjct: 216 ASAMGIDVATYKTLAFGVSAGITGVAGGLGAIAVQFVAPDSYTIVLAISLFLGMVVGGVG 275 Query: 362 SQLGVILAAIVMILLPEMMREFSE-YRMLMFGALMVLMMIWRPQG 405 G + A +I +P + S+ +FG L+ L++ P G Sbjct: 276 WLPGSFIGAAFIIFVPNIAEGISKGLSGAVFGVLLFLIIFLVPHG 320 Lambda K H 0.331 0.145 0.439 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: 394 Number of extensions: 23 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: 418 Length of database: 338 Length adjustment: 30 Effective length of query: 388 Effective length of database: 308 Effective search space: 119504 Effective search space used: 119504 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 50 (23.9 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