Align High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized)
to candidate WP_018125396.1 B149_RS0111940 LPS export ABC transporter ATP-binding protein
Query= TCDB::P0A9S7 (255 letters) >NCBI__GCF_000375485.1:WP_018125396.1 Length = 241 Score = 144 bits (362), Expect = 2e-39 Identities = 86/249 (34%), Positives = 140/249 (56%), Gaps = 16/249 (6%) Query: 6 LSVNGLMMRFGGLLAVNNVNLELYPQEIVSLIGPNGAGKTTVFNCLTGFYKPTGGTILLR 65 LS + L R+G V+++ L L +E+V L+GPNGAGKTT F L G KP G + L Sbjct: 5 LSASDLSKRYGRKEVVHSIRLSLGREEVVGLLGPNGAGKTTTFYMLAGIVKPYSGDVYLN 64 Query: 66 DQHLEGLPGQQIARMGVVRTFQHVRLFREMTVIENLLVAQHQQLKTGLFSGLLKTPSFRR 125 +++ LP + AR+GV Q +FR++TV +NL + Q T R Sbjct: 65 GRNITDLPLHERARLGVSYLPQESSIFRKLTVRQNLQIILEQ------------TDMTPR 112 Query: 126 AQSEALDRAATWLERIGLLEHANRQASNLAYGDQRRLEIARCMVTQPEILMLDEPAAGLN 185 Q E RA ++ + + A++ + L+ G++RRLEIAR ++ P+ ++LDEP AG++ Sbjct: 113 QQRE---RADELMDMFSITKLADQASMYLSGGERRRLEIARALIMSPDFILLDEPFAGID 169 Query: 186 PKETKELDELIAELRNHHNTTILLIEHDMKLVMGISDRIYVVNQGTPLANGTPEQIRNNP 245 P ++ E+I+ L++ IL+ +H+++ + I DR Y+V +GT + +GTP I + Sbjct: 170 PIAVIDIQEIISVLKS-MGIGILISDHNVRETLNICDRAYLVYEGTIILDGTPADIVQSS 228 Query: 246 DVIRAYLGE 254 + YLGE Sbjct: 229 RARQIYLGE 237 Lambda K H 0.320 0.137 0.395 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: 160 Number of extensions: 11 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: 255 Length of database: 241 Length adjustment: 24 Effective length of query: 231 Effective length of database: 217 Effective search space: 50127 Effective search space used: 50127 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 46 (22.3 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