Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate WP_012402388.1 BPHY_RS15490 branched-chain amino acid ABC transporter ATP-binding protein/permease
Query= uniprot:G8ALJ0 (294 letters) >NCBI__GCF_000020045.1:WP_012402388.1 Length = 594 Score = 194 bits (494), Expect = 3e-54 Identities = 118/267 (44%), Positives = 160/267 (59%), Gaps = 16/267 (5%) Query: 7 TTTPLLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVG 66 T PLL V+ +FGGLVAVNDVSF G+I +IGPNGAGK+T FN +TG T G Sbjct: 342 TGEPLLVVDKARKQFGGLVAVNDVSFEVKAGQIIGLIGPNGAGKSTTFNLVTGVLQATSG 401 Query: 67 RLTLRHADGKEFLLERMPGYRISQ--KASVARTFQNIRLFGGMSVLENLIVAQHNKLIRA 124 +T R ER+ + K + RTFQ+++L GM+VLEN+ + H + Sbjct: 402 AITFRG--------ERIDALNSREIVKRGIGRTFQHVKLLPGMTVLENVAIGGHLRGRAG 453 Query: 125 SGFSIAGLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMC 184 S+A L G E + A + RV L E EAG+L G QR LEIARA+C Sbjct: 454 VWRSVARLNG-----AEEGRLMAEAARQIRRVGLEEHMYDEAGSLALGKQRILEIARALC 508 Query: 185 TEPVMLCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDY 244 +P +L LDEPAAGL +E +LA LL +R+E + +LL+EHDM VM ++D +VV+++ Sbjct: 509 CDPTLLLLDEPAAGLRYQEKQQLATLLRKLREE-GMSLLLVEHDMDFVMNLTDRLVVMEF 567 Query: 245 GRKISDGDPAFVKNDPAVIRAYLGEEE 271 G +I++G P V+NDPAV+ AYLG E Sbjct: 568 GTRIAEGLPQDVQNDPAVLEAYLGGVE 594 Lambda K H 0.319 0.137 0.397 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: 397 Number of extensions: 21 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: 294 Length of database: 594 Length adjustment: 31 Effective length of query: 263 Effective length of database: 563 Effective search space: 148069 Effective search space used: 148069 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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