Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate WP_029133947.1 A3GO_RS0114160 branched-chain amino acid ABC transporter substrate-binding protein
Query= SwissProt::P21175 (373 letters) >NCBI__GCF_000428045.1:WP_029133947.1 Length = 375 Score = 244 bits (624), Expect = 2e-69 Identities = 134/360 (37%), Positives = 203/360 (56%), Gaps = 9/360 (2%) Query: 5 TQRLSRLFAAMAIAGFASYSMAADTIKIALAGPVTGPVAQYGDMQRAGALMAIEQINKAG 64 T LS MAIA A DTIK+ +AG +G +A YG A + + +N G Sbjct: 13 TVGLSLAIPTMAIA-------ADDTIKLGVAGAHSGDLASYGLPTVNAAKLVVADVNARG 65 Query: 65 GVNGAQLEGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMI 124 G+NG Q+E ++ DD C P+ A A K+V+ GV V+GH+CS +T+ A IY++ GV+++ Sbjct: 66 GINGKQVELLVEDDVCKPEVATNTATKLVSSGVHVVLGHICSGATKAALPIYKNAGVIVM 125 Query: 125 TPSATAPEITSRG-YKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIAT 183 +PSAT PE+T G Y FRTI D+ Q F + K IAV+HDK YG+G+A Sbjct: 126 SPSATNPELTQSGDYPNFFRTIASDDAQAKTQVDFALDNRNLKKIAVIHDKGDYGKGLAE 185 Query: 184 EVKKTVEDAG-IKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQ 242 K+ +E +G +V +FEG+ G D++A++ K+K++G V +GGYHPE ++ Q ++ Sbjct: 186 FAKQFIEKSGNAEVVLFEGVTPGAVDYSAVVQKIKRSGADGVIYGGYHPEASKIVTQMRK 245 Query: 243 AGLDARFMGPEGVGNSEITAIAGDASEGMLATLPRAFEQDPKNKALIDAFKAKNQDPSGI 302 +D F+ +GV + +AG ++EG+ AT + +P A I+A K + G Sbjct: 246 KRIDIDFISGDGVKDDTFIKVAGKSAEGVYATGAKDNSSNPLYTAAIEAHKKTYGEDPGA 305 Query: 303 FVLPAYSAVTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKNFDFTVYE 362 F A++A + +EKAG D + AL+AN T GN+ FDE+GD F VY+ Sbjct: 306 FFDSAHAAAAALLNAVEKAGSTDTAAITNALQANDVATTVGNIHFDERGDAVGVGFAVYQ 365 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: 359 Number of extensions: 19 Number of successful extensions: 3 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: 375 Length adjustment: 30 Effective length of query: 343 Effective length of database: 345 Effective search space: 118335 Effective search space used: 118335 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 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