Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate WP_043748392.1 MNOD_RS09350 branched-chain amino acid ABC transporter substrate-binding protein
Query= SwissProt::P21175 (373 letters) >NCBI__GCF_000022085.1:WP_043748392.1 Length = 367 Score = 237 bits (605), Expect = 3e-67 Identities = 128/353 (36%), Positives = 194/353 (54%), Gaps = 1/353 (0%) Query: 15 MAIAGFASYSMAADTIKIALAGPVTGPVAQYGDMQRAGALMAIEQINKAGGVNGAQLEGV 74 + IAG + A + + +A P +G VA G+ G A++ N GG+ G + Sbjct: 11 LVIAGLFCAAPACAEVVVGVAVPRSGAVAGIGEQVLQGVQAAVKDANGRGGLAGEPIVLD 70 Query: 75 IYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMITPSATAPEIT 134 I DDAC+P QAV VA + V GV+ VVGHVCSS++ A+D+Y GV+MI+P++ A +T Sbjct: 71 IEDDACEPGQAVEVAERFVRTGVRLVVGHVCSSASLAASDVYAANGVVMISPASNAARLT 130 Query: 135 SRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATEVKKTVEDAGI 194 RG IFR G ++ QG ++ +AER++DK IA+L+D +A K + G Sbjct: 131 DRGLSTIFRVSGREDDQGRLSATILAERFRDKKIAILYDDTPLSRSLADSTKANLNKIGQ 190 Query: 195 KVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQAGLDARFMGPEG 254 A+F + G D ALI +L+ +G++ VY+GG++ EMG L+R A + G ++ G G Sbjct: 191 NEALFAAIVPGQTDDAALIKRLQASGIEVVYYGGHYQEMGKLVRTAAEQGYRPQWFGTSG 250 Query: 255 VGNSEITAIAGDASEGMLATLPRAFEQDPKNKALIDAFKAKNQDPSGIFVLPAYSAVTVI 314 + E +AG AS G+L T + P+ A + A +A DP G FVL Y+A+ + Sbjct: 251 IATKEFGTLAGPASNGVLMTFNPDLRRKPEAAAAVKALQADGIDPGG-FVLYGYAAMQAL 309 Query: 315 AKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKNFDFTVYEWHKDA 367 + A DP+ +A L A F GN+GFD+KGD+ + +Y W A Sbjct: 310 VEAGNFAKSTDPKAIAATLHAERFNLVLGNVGFDQKGDVTAPGYVLYVWRDGA 362 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: 368 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 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