Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate 1937025 b3460 leucine/isoleucine/valine transporter subunit (NCBI)
Query= SwissProt::P21175 (373 letters) >FitnessBrowser__Keio:1937025 Length = 367 Score = 418 bits (1074), Expect = e-121 Identities = 198/363 (54%), Positives = 272/363 (74%), Gaps = 3/363 (0%) Query: 11 LFAAMAIAGFASYSMAADTIKIALAGPVTGPVAQYGDMQRAGALMAIEQINKAGGVNGAQ 70 L A F++ ++A D IK+A+ G ++GPVAQYGD + GA A+ IN GG+ G + Sbjct: 8 LLAGCIALAFSNMALAED-IKVAVVGAMSGPVAQYGDQEFTGAEQAVADINAKGGIKGNK 66 Query: 71 LEGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMITPSATA 130 L+ V YDDACDPKQAVAVANKVVNDG+K+V+GH+CSSSTQPA+DIYEDEG+LMITP+ATA Sbjct: 67 LQIVKYDDACDPKQAVAVANKVVNDGIKYVIGHLCSSSTQPASDIYEDEGILMITPAATA 126 Query: 131 PEITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATEVKKTVE 190 PE+T+RGY+LI RT GLD+ QGP A K+I E+ K + IA++HDKQQYGEG+A V+ ++ Sbjct: 127 PELTARGYQLILRTTGLDSDQGPTAAKYILEKVKPQRIAIVHDKQQYGEGLARAVQDGLK 186 Query: 191 DAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQAGLDARFM 250 V F+G+ AG+KDF+ L+++LKK + FVY+GGYHPEMG +LRQA+ AGL +FM Sbjct: 187 KGNANVVFFDGITAGEKDFSTLVARLKKENIDFVYYGGYHPEMGQILRQARAAGLKTQFM 246 Query: 251 GPEGVGNSEITAIAGDASEGMLATLPRAFEQDPKNKALIDAFKAKNQDPSGIFVLPAYSA 310 GPEGV N ++ IAG+++EG+L T P+ ++Q P NK ++DA KAK QDPSG FV Y+A Sbjct: 247 GPEGVANVSLSNIAGESAEGLLVTKPKNYDQVPANKPIVDAIKAKKQDPSGAFVWTTYAA 306 Query: 311 VTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKNFDFTVYEWHKDATRT 370 + + G+ ++ DP ++A+ L+AN+ +T G L +DEKGDLK F+F V++WH + T T Sbjct: 307 LQSLQAGLNQSD--DPAEIAKYLKANSVDTVMGPLTWDEKGDLKGFEFGVFDWHANGTAT 364 Query: 371 EVK 373 + K Sbjct: 365 DAK 367 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: 466 Number of extensions: 19 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: 367 Length adjustment: 30 Effective length of query: 343 Effective length of database: 337 Effective search space: 115591 Effective search space used: 115591 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