Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate WP_052473043.1 SUTH_RS01380 branched-chain amino acid ABC transporter substrate-binding protein
Query= SwissProt::P21175 (373 letters) >NCBI__GCF_000828635.1:WP_052473043.1 Length = 460 Score = 205 bits (522), Expect = 2e-57 Identities = 121/335 (36%), Positives = 185/335 (55%), Gaps = 4/335 (1%) Query: 30 IKIALAGPVTGPVAQYGDMQRAGALMAIEQINKAG---GVNGAQLEGVIYDDACDPKQAV 86 +KI P+TG +A G GA +AI++ N AG G + E + DD DPK Sbjct: 41 VKIGSVAPLTGGIAHLGKDNENGARLAIDEANAAGVSLGGKKVKFELMSEDDQSDPKVGN 100 Query: 87 AVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMITPSATAPEITSRGYKLIFRTIG 146 VA K+V+ V VVGH+ S +T PA+ IY + MI+ SAT P +T +G+K +FR +G Sbjct: 101 TVAQKLVDAKVAGVVGHLNSGTTIPASAIYNTANLPMISGSATNPALTEQGFKGVFRVVG 160 Query: 147 LDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATEVKKTVEDAGIKVAVFEGLNAGD 206 D+ QGP ++A + K KT+AV+ D YGEG+A EV+KT + AGIKV E Sbjct: 161 RDDQQGPAIANYLASQNKPKTVAVIDDATAYGEGLANEVEKTFKAAGIKVLPREKGTDKT 220 Query: 207 KDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQAGLDARFMGPEGVGNSEITAIAGD 266 D+ A+++K+K V++GG G LL+QA++ + A F +G ++ +AG Sbjct: 221 VDWKAVLTKVKGKKPDAVFYGGMDATGGPLLKQARELKMTAVFAFGDGACTDKMAELAGP 280 Query: 267 ASEGMLATLPRAFEQDPKNKALIDAFKAKNQDPSGIFVLPAYSAVTVIAKGIEKAGEADP 326 A+EG+L + K +DA+KAK + ++ Y A ++ ++KA DP Sbjct: 281 AAEGLLCS-QAGIPVQAAGKKFLDAYKAKFKVEPILYSPFTYDAANLLIAAMKKADSPDP 339 Query: 327 EKVAEALRANTFETPTGNLGFDEKGDLKNFDFTVY 361 K AL A+ + +GN+ FDEKGD K+ + T++ Sbjct: 340 AKYLPALAASDYTGASGNIQFDEKGDRKDAEMTIF 374 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: 485 Number of extensions: 29 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: 460 Length adjustment: 31 Effective length of query: 342 Effective length of database: 429 Effective search space: 146718 Effective search space used: 146718 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 Apr 09 2024. 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