Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate BWI76_RS26350 BWI76_RS26350 branched chain amino acid ABC transporter substrate-binding protein
Query= SwissProt::P21175 (373 letters) >FitnessBrowser__Koxy:BWI76_RS26350 Length = 369 Score = 415 bits (1067), Expect = e-121 Identities = 195/365 (53%), Positives = 272/365 (74%), Gaps = 4/365 (1%) Query: 13 AAMAIAGFASYSMA----ADTIKIALAGPVTGPVAQYGDMQRAGALMAIEQINKAGGVNG 68 A IAG + +M+ A IK+A+ G ++GPVAQ+GDM+ GA AI+ IN GG+ G Sbjct: 5 AKTVIAGLVALAMSQAAFAKDIKVAVVGAMSGPVAQWGDMEFNGARQAIKDINAQGGIKG 64 Query: 69 AQLEGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMITPSA 128 +L V YDDACDPKQAVAVANK+VNDG+++V+GH+CSSSTQPA+DIYEDEG+LMI+P A Sbjct: 65 DKLVAVEYDDACDPKQAVAVANKIVNDGIQYVIGHLCSSSTQPASDIYEDEGILMISPGA 124 Query: 129 TAPEITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATEVKKT 188 T PE+T RGY+ I RT GLD+ QGP A K+I E K + IA++HDKQQYGEG+A V+++ Sbjct: 125 TNPELTQRGYQYIMRTAGLDSSQGPTAAKYIMETVKPQRIAIIHDKQQYGEGLARSVQES 184 Query: 189 VEDAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQAGLDAR 248 ++ G + F+G+ AG+KDF+AL+++LKK + FVY+GGY+PEMG +LRQA+ GL Sbjct: 185 LKKGGANIVFFDGITAGEKDFSALLARLKKENIDFVYYGGYYPEMGQMLRQARSVGLKTV 244 Query: 249 FMGPEGVGNSEITAIAGDASEGMLATLPRAFEQDPKNKALIDAFKAKNQDPSGIFVLPAY 308 FMGPEGVGN+ ++ IAGDA+EGML T+P+ ++QDP N A++DA KA+ +DPSG +V Y Sbjct: 245 FMGPEGVGNASLSNIAGDAAEGMLVTMPKRYDQDPANSAIVDALKAEKKDPSGPYVWITY 304 Query: 309 SAVTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKNFDFTVYEWHKDAT 368 +AV +A+ +++A +P + + L+A+ +T G L +DEKGDLK F+F V++WH D + Sbjct: 305 AAVQSLAQAMDRAASQEPLDLIKDLKAHGAKTVIGPLNWDEKGDLKGFEFGVFQWHADGS 364 Query: 369 RTEVK 373 T K Sbjct: 365 STLAK 369 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: 464 Number of extensions: 25 Number of successful extensions: 1 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: 369 Length adjustment: 30 Effective length of query: 343 Effective length of database: 339 Effective search space: 116277 Effective search space used: 116277 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 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