Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate BWI76_RS26365 BWI76_RS26365 branched chain amino acid ABC transporter substrate-binding protein
Query= SwissProt::P21175 (373 letters) >FitnessBrowser__Koxy:BWI76_RS26365 Length = 372 Score = 412 bits (1060), Expect = e-120 Identities = 198/360 (55%), Positives = 266/360 (73%), Gaps = 2/360 (0%) Query: 14 AMAIAGFASYSMAADTIKIALAGPVTGPVAQYGDMQRAGALMAIEQINKAGGVNGAQLEG 73 A IA S + A+ IK+A+ G ++GPVAQYGD + GA AI IN GG+ G +L+ Sbjct: 15 AGCIALIMSGTAMAEDIKVAVVGAMSGPVAQYGDQEFTGAEQAIADINAKGGIKGNKLQM 74 Query: 74 VIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMITPSATAPEI 133 V YDDACDPKQAVAVANKV+NDG+K+V+GH+CSSSTQPA+DIYEDEGVLMITP+ATAPE+ Sbjct: 75 VKYDDACDPKQAVAVANKVINDGIKYVIGHLCSSSTQPASDIYEDEGVLMITPAATAPEL 134 Query: 134 TSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATEVKKTVEDAG 193 T+RGY LI RT GLD+ QGP A K+I E+ K + IA++HDKQQYGEG+A V+ ++ G Sbjct: 135 TARGYHLILRTTGLDSDQGPTAAKYILEKVKPQRIAIVHDKQQYGEGLARAVQDNLKKGG 194 Query: 194 IKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQAGLDARFMGPE 253 V F+G+ AG+KDF+ L+++LKK + FVY+GGYHPEMG +LRQ++ AGL +FMGPE Sbjct: 195 ANVVFFDGITAGEKDFSTLVARLKKENIDFVYYGGYHPEMGQILRQSRAAGLKTQFMGPE 254 Query: 254 GVGNSEITAIAGDASEGMLATLPRAFEQDPKNKALIDAFKAKNQDPSGIFVLPAYSAVTV 313 GV N ++ IAG ++EGML T P+ ++Q P NK ++DA KAK QDPSG FV Y+A+ Sbjct: 255 GVANVSLSNIAGASAEGMLVTKPKNYDQVPANKPIVDAIKAKKQDPSGAFVWTTYAALQS 314 Query: 314 IAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKNFDFTVYEWHKDATRTEVK 373 + G+ ++ DP ++A+ L+ T +T G L ++EKGDLK F+F V+ WH + T T+ K Sbjct: 315 LQAGLNQS--EDPAEIAKYLKGATVDTVMGPLTWNEKGDLKGFEFGVFTWHANGTATDAK 372 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: 458 Number of extensions: 20 Number of successful extensions: 2 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: 372 Length adjustment: 30 Effective length of query: 343 Effective length of database: 342 Effective search space: 117306 Effective search space used: 117306 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