Align leucine-specific-binding protein LivK (characterized)
to candidate WP_012405805.1 BPHY_RS32955 branched-chain amino acid ABC transporter substrate-binding protein
Query= CharProtDB::CH_107418 (369 letters) >NCBI__GCF_000020045.1:WP_012405805.1 Length = 382 Score = 182 bits (462), Expect = 1e-50 Identities = 110/339 (32%), Positives = 183/339 (53%), Gaps = 6/339 (1%) Query: 16 AISHTAMADDIKVAVVGAMSGPIAQWG-DMEFNGARQAIKDINAKGGI---KGDKLVGVE 71 + + A + +K+ VG ++GP+A+ G D+++ GA+ A+ + NAK K K V Sbjct: 20 SFAFAADPETVKIGFVGPLTGPVARVGKDLQY-GAQLALDEENAKQPTIAGKPVKFVLDV 78 Query: 72 YDDACDPKQAVAVANKIVNDGIKYVIGHLCSSSTQPASDIYEDEGILMISPGATNPELTQ 131 DD DP+ A+ VA K+V+DG+ VIGH S + PAS +Y + + MI+PG+TNP+LT+ Sbjct: 79 QDDQADPRVAIQVAQKLVDDGVVGVIGHYNSGCSIPASAVYHNANVAMITPGSTNPQLTK 138 Query: 132 RGYQHIMRTAGLDSSQGPTAAKYILETVKPQRIAIIHDKQQYGEGLARSVQDGLKAANAN 191 +G++++ RT G D G A +++E +K +RI II D+ +G+GLA + + G+K AN N Sbjct: 139 QGFKNVFRTMGHDGIGGVVAGHFVVEQMKAKRIGIIDDRTAFGQGLADAFEKGVKEANGN 198 Query: 192 VVFFDGITAGEKDFSALIARLKKENIDFVYYGGYYPEMGQMLRQARSVGLKTQFMGPEGV 251 +V + DF A++ LK +N+D +++GG + +++Q RS+G++ Q G + Sbjct: 199 IVSREFTNDKAVDFRAILTSLKSKNVDVIFFGGLDEQGAMLVKQMRSLGMQAQLFGAGAL 258 Query: 252 GNASLSNIAGDAAEGMLVTMP-KRYDQDPANQGIVDALKADKKDPSGPYVWITYAAVQSL 310 + + IAG + E P D+ PA Q KA Y Y A ++ Sbjct: 259 KSNAFLQIAGASGERTQDLEPGPALDKLPAAQDFGKRYKARFNQDVELYAPFAYDAALAM 318 Query: 311 ATALERTGSDEPLALVKDLKANGANTVIGPLNWDEKGDL 349 A+ S + +V+ L V G + +D GDL Sbjct: 319 IKAIHDANSLDRQKIVESLAKVSLTGVTGKITFDPYGDL 357 Lambda K H 0.315 0.133 0.386 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: 381 Number of extensions: 13 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: 369 Length of database: 382 Length adjustment: 30 Effective length of query: 339 Effective length of database: 352 Effective search space: 119328 Effective search space used: 119328 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.5 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