Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate BPHYT_RS26525 BPHYT_RS26525 amino acid ABC transporter substrate-binding protein
Query= SwissProt::P21175 (373 letters) >FitnessBrowser__BFirm:BPHYT_RS26525 Length = 383 Score = 201 bits (512), Expect = 2e-56 Identities = 118/353 (33%), Positives = 193/353 (54%), Gaps = 6/353 (1%) Query: 16 AIAGFASYSMAADT--IKIALAGPVTGPVAQYGDMQRAGALMAIEQIN-KAGGVNGAQLE 72 A+A + +S AAD +KI GP+TGPVA+ G + GA +A+++ N K + G ++ Sbjct: 14 ALATYMPFSWAADPQIVKIGFVGPLTGPVARVGKDLQYGAQLALDEENAKNPMIGGKPVK 73 Query: 73 GV--IYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMITPSATA 130 V + DD DP+ A+ VA K+V+DGV V+GH S + PA+ +Y V MITP +T Sbjct: 74 FVLDVQDDQADPRVAIQVAQKLVDDGVVGVIGHYNSGCSIPASTVYHQANVAMITPGSTN 133 Query: 131 PEITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATEVKKTVE 190 P++T +G+K +FRT+G D + G VAG F+ E+ K K IA++ D+ +G+G+A +K V+ Sbjct: 134 PQLTKQGFKNVFRTMGHDGIGGVVAGHFVVEQMKAKRIAIIDDRTAFGQGLADAFEKGVK 193 Query: 191 DAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQAGLDARFM 250 +A + E N DF A+++ LK V ++FGG + +L++Q + G+ + Sbjct: 194 EANGNIVDREFTNDKAIDFRAILTTLKSKNVDLIFFGGLDEQGAMLVKQMRSLGMSTQLF 253 Query: 251 GPEGVGNSEITAIAGDASEGMLATLP-RAFEQDPKNKALIDAFKAKNQDPSGIFVLPAYS 309 G + ++ IAG A G P A ++ P +A +KA+ ++ +Y Sbjct: 254 GAGALKSNAFLQIAGTAGNGTQDLEPGPALDKLPAAQAFGKRYKARFNQDVELYAPFSYD 313 Query: 310 AVTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKNFDFTVYE 362 A + K I A D K+ ++L T TGN+ FD GDL +T+++ Sbjct: 314 AALAMLKAIHTADSLDRAKIVDSLAKVTVTGVTGNITFDPYGDLIKPPYTLFQ 366 Lambda K H 0.316 0.133 0.377 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: 345 Number of extensions: 10 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 373 Length of database: 383 Length adjustment: 30 Effective length of query: 343 Effective length of database: 353 Effective search space: 121079 Effective search space used: 121079 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 (21.6 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