Align leucine-specific-binding protein LivK (characterized)
to candidate H281DRAFT_06096 H281DRAFT_06096 amino acid/amide ABC transporter substrate-binding protein, HAAT family
Query= CharProtDB::CH_107418 (369 letters) >FitnessBrowser__Burk376:H281DRAFT_06096 Length = 383 Score = 187 bits (474), Expect = 5e-52 Identities = 113/338 (33%), Positives = 179/338 (52%), Gaps = 6/338 (1%) Query: 26 IKVAVVGAMSGPIAQWG-DMEFNGARQAIKDINAKG---GIKGDKLVGVEYDDACDPKQA 81 +K+ VG ++GP+A+ G D+++ GA+ AI + NA+ G K K V DD DP+ A Sbjct: 30 VKIGFVGPLTGPVARVGKDLQY-GAQLAIDEENARHPTVGGKPVKFVLDVQDDQADPRVA 88 Query: 82 VAVANKIVNDGIKYVIGHLCSSSTQPASDIYEDEGILMISPGATNPELTQRGYQHIMRTA 141 + VA K+V+DG+ VIGH S + PAS +Y + MI+PG+TNP+LT++GY+++ RT Sbjct: 89 IQVAQKLVDDGVVGVIGHYNSGCSIPASTVYHQANVAMITPGSTNPQLTKQGYKNVFRTM 148 Query: 142 GLDSSQGPTAAKYILETVKPQRIAIIHDKQQYGEGLARSVQDGLKAANANVVFFDGITAG 201 G D G A +++E +K +RI II D+ +G+GLA + + G K AN N+V + Sbjct: 149 GHDGIGGVVAGHFVVEQMKAKRIGIIDDRTAFGQGLADAFEKGAKEANGNIVVREFTNDK 208 Query: 202 EKDFSALIARLKKENIDFVYYGGYYPEMGQMLRQARSVGLKTQFMGPEGVGNASLSNIAG 261 DF A++ LK N+D +++GG + +++Q RS+G+ Q G + + + IAG Sbjct: 209 AVDFRAILTTLKSRNVDLIFFGGLDEQGAMLIKQMRSLGMNAQLFGAGALKSNAFLQIAG 268 Query: 262 DAAEGMLVTMP-KRYDQDPANQGIVDALKADKKDPSGPYVWITYAAVQSLATALERTGSD 320 A +G P D+ PA KA Y Y A ++ A+ S Sbjct: 269 TAGDGTQDLEPGPALDKQPAALEFGKRYKARFNQDVELYAPFAYDAALAMLKAIHTANSL 328 Query: 321 EPLALVKDLKANGANTVIGPLNWDEKGDLKGFDFGVFQ 358 + +V L V G + +D GDL + +FQ Sbjct: 329 DRSKIVDSLSKVNVTGVTGQIAFDPYGDLIKPPYTLFQ 366 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: 392 Number of extensions: 9 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: 383 Length adjustment: 30 Effective length of query: 339 Effective length of database: 353 Effective search space: 119667 Effective search space used: 119667 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 17 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