Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate WP_092348696.1 BLU87_RS11835 branched-chain amino acid ABC transporter substrate-binding protein
Query= SwissProt::P21175 (373 letters) >NCBI__GCF_900107645.1:WP_092348696.1 Length = 371 Score = 249 bits (637), Expect = 7e-71 Identities = 138/363 (38%), Positives = 204/363 (56%), Gaps = 5/363 (1%) Query: 1 MKKGTQRLSRLFAAMAIAGFASYSMAADTIKIALAGPVTGPVAQYGDMQRAGALMAIEQI 60 MKK T +S L A+++ + AADTIK+ +AGP +G +A YG A + ++Q+ Sbjct: 1 MKKITVLISTLTLALSMI---TVGFAADTIKLGVAGPHSGDLAPYGIPAMKAAQLVVKQV 57 Query: 61 NKAGGVNGAQLEGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEG 120 N GG+ G Q+E +I DD C P+ A A K+V DG V+GH+CS +T+ A IY+D Sbjct: 58 NANGGILGKQVELLIQDDQCKPEIATNTATKLVTDGADVVLGHICSGATKAALGIYKDAK 117 Query: 121 VLMITPSATAPEITSRG-YKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGE 179 + +++PSAT P +T G Y FRTI D+MQ +A F K +AV+HDK YG+ Sbjct: 118 IPVMSPSATNPPLTQSGDYPNFFRTIASDDMQAKLAVDFAINTLGVKKVAVIHDKGDYGK 177 Query: 180 GIATEVKKTVEDAG-IKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLR 238 G A K+ ++++G ++V +FEG+ G D+++++ K+++ + + FGGYHPE L+ Sbjct: 178 GFADFAKQYLDESGKVEVVLFEGITPGAMDYSSIVQKVRRNKAEALIFGGYHPEASKLVS 237 Query: 239 QAKQAGLDARFMGPEGVGNSEITAIAGDASEGMLATLPRAFEQDPKNKALIDAFKAKNQD 298 Q + L F+ +GV + +AGDA+ G T PR + N A F+A+ Sbjct: 238 QMSRKRLKTVFISDDGVKDDSFLKVAGDAANGAYMTGPRDLSKIALNAAATAEFQAEYGA 297 Query: 299 PSGIFVLPAYSAVTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKNFDF 358 G F YSA + IEKAG D E V ALR ETP G + FD KGD + F Sbjct: 298 EPGAFFQEGYSAALALLNAIEKAGSTDYEAVTNALRTEYVETPVGKIKFDSKGDAEGVGF 357 Query: 359 TVY 361 +VY Sbjct: 358 SVY 360 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: 367 Number of extensions: 16 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: 373 Length of database: 371 Length adjustment: 30 Effective length of query: 343 Effective length of database: 341 Effective search space: 116963 Effective search space used: 116963 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: 49 (23.5 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