Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate WP_012330315.1 M446_RS01575 branched-chain amino acid ABC transporter substrate-binding protein
Query= SwissProt::P21175 (373 letters) >NCBI__GCF_000019365.1:WP_012330315.1 Length = 362 Score = 236 bits (602), Expect = 7e-67 Identities = 125/342 (36%), Positives = 192/342 (56%), Gaps = 1/342 (0%) Query: 26 AADTIKIALAGPVTGPVAQYGDMQRAGALMAIEQINKAGGVNGAQLEGVIYDDACDPKQA 85 AA + + +A P TGPVA G+ G A+++ N GG+ G + + DDAC+P QA Sbjct: 17 AAAEVVVGVAVPRTGPVAGIGEQVLQGVQAAVKEANARGGLAGEPIILDVQDDACEPGQA 76 Query: 86 VAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMITPSATAPEITSRGYKLIFRTI 145 V VA + GV VVGHVCSS++ A+D+Y +GV+MI+P++ A +T RG IFR Sbjct: 77 VEVAERFAKAGVGLVVGHVCSSASLAASDVYAAKGVVMISPASNAARLTDRGLPTIFRVS 136 Query: 146 GLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATEVKKTVEDAGIKVAVFEGLNAG 205 G ++ QG ++ +AER++DK IA+L+D +A K + G +F + G Sbjct: 137 GREDDQGRLSATILAERFRDKKIAILYDDTPLSRSLADSTKANLNKIGQNETLFAAIVPG 196 Query: 206 DKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQAGLDARFMGPEGVGNSEITAIAG 265 D ALI +L+ AG++ VY+GG++ EMG L+R A + G ++ G G+ E +AG Sbjct: 197 QTDDAALIKRLQGAGIEVVYYGGHYQEMGKLVRSAAEQGYRPQWFGTSGIATKEFGTLAG 256 Query: 266 DASEGMLATLPRAFEQDPKNKALIDAFKAKNQDPSGIFVLPAYSAVTVIAKGIEKAGEAD 325 AS G+L T + P+ A + A +A DP G FVL Y+A+ + + A ++ Sbjct: 257 PASNGVLMTFNPDLRRKPEAAAAVKALQADGIDPGG-FVLYGYAAMQALVEAGNFARSSN 315 Query: 326 PEKVAEALRANTFETPTGNLGFDEKGDLKNFDFTVYEWHKDA 367 P+ +AE L + F GN+GFD+KGD+ + +Y W A Sbjct: 316 PKTIAETLHSERFNLVLGNVGFDQKGDVTAPGYVLYVWRDGA 357 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: 369 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: 362 Length adjustment: 30 Effective length of query: 343 Effective length of database: 332 Effective search space: 113876 Effective search space used: 113876 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 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