Align Leucine ABC transporter subunit substrate-binding protein LivK (characterized, see rationale)
to candidate WP_018125980.1 B149_RS0114955 branched-chain amino acid ABC transporter substrate-binding protein
Query= uniprot:A0A160A0J6 (375 letters) >NCBI__GCF_000375485.1:WP_018125980.1 Length = 384 Score = 210 bits (535), Expect = 5e-59 Identities = 117/325 (36%), Positives = 187/325 (57%), Gaps = 3/325 (0%) Query: 30 IKIGIAGPKTGPVAQYGDMQFSGSKMAIEQINAKGGVNG-KQLVAVEYDDACDPKQAVAV 88 ++IG P TGP A G+ +G+ AIE + ++GG+ G + D ACDP+QAVA Sbjct: 34 LEIGSISPLTGPYAADGNDIKNGALTAIEVVKSEGGIPGFSDITLSSQDSACDPRQAVAA 93 Query: 89 ANKVVNDGIKFVVGHLCSSSTQPASDIYEDEGVVMITPAATSPDITARGYKMIFRTIGLD 148 ANK++N+ + V+G CSS+T PAS+ +E +VM+TPA+TS +T RG K +FRT G D Sbjct: 94 ANKLINEEVSGVIGAYCSSATIPASETLAEENIVMLTPASTSEKVTERGLKYMFRTCGRD 153 Query: 149 SAQGPAAGNYIADHVKPKIVAVLHDKQQYGEGIASAVKKTLEDKGVKVAVFEGVNAGDKD 208 Q AA +I D +K V ++ DK Y +G+A ++K + G++V + VN GDKD Sbjct: 154 DDQSKAAATFIRDFLKAGNVYIVDDKTTYSQGLADNLEKLCPEYGIEVLAHDHVNQGDKD 213 Query: 209 FSSMIAKLKQANVDFVYYGGYHPELG-LILRQSQEKGLKAKFMGPEGVGNDSISQIAKES 267 FS+++ K+K AN D Y + G L+L Q++ G+ A+ + + V + + +IAK++ Sbjct: 214 FSAVLTKVKAANPDVFYVSLQNSATGALMLTQAKRMGIDAEILAQDAVYHPQLMEIAKDA 273 Query: 268 SEGLLVTLPKSFDQDPANIALADAFKAKKEDPSGPFVFPSYSAVTVIADAIKAAKSEDAG 327 + G+ +T + + + DA+K K DP G + +Y + A+K A S DA Sbjct: 274 ANGVYLTFGYTDKESESYKRFLDAYKPKYGDP-GAYSAYAYDSAMAYLKAVKQAGSADAD 332 Query: 328 KVAEAIHAGTFKTPTGDLSFDKNGD 352 KV +A+ TF+ + + + NGD Sbjct: 333 KVRQALLDMTFEGASKRIDYKSNGD 357 Lambda K H 0.314 0.132 0.372 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: 332 Number of extensions: 17 Number of successful extensions: 4 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: 375 Length of database: 384 Length adjustment: 30 Effective length of query: 345 Effective length of database: 354 Effective search space: 122130 Effective search space used: 122130 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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