Align ABC transporter substrate-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate WP_092344940.1 BLU87_RS03940 branched-chain amino acid ABC transporter substrate-binding protein
Query= TCDB::Q8DQI1 (386 letters) >NCBI__GCF_900107645.1:WP_092344940.1 Length = 387 Score = 187 bits (475), Expect = 4e-52 Identities = 114/364 (31%), Positives = 192/364 (52%), Gaps = 18/364 (4%) Query: 28 AVNTAGNSVEEKTIKIGFNFEESGSLAAYGTAEQKGAQLAVDEINAAGGID--GKQ--IE 83 AV A ++ +TIKIGFN +G + G + A++ + ++N AGG+D GK+ +E Sbjct: 14 AVMLAVPAMATQTIKIGFNIPMTGDIPEVGEGSKNAAEMYLADVNGAGGLDVGGKKYMLE 73 Query: 84 VVDKDNKSETAEAASVTTNLVTQSKVSAVVGPATSGATAAAVANATKAGVPLISPSATQD 143 + DN+S+ A + L+ Q +V A++GP +S A + VP+ISP +T Sbjct: 74 FIYMDNESKADSAVNAALKLIEQEEVVAIIGPNSSKQAVPGGGTANENRVPMISPWSTNP 133 Query: 144 GLTKGQDYLFIGTFQDSFQGKIISNYVSEKLNAKKVVLYTDNASDYAKGIAKSFRESYK- 202 T + ++F F D FQG +++++ ++K AK + D A+DY+ G+A+ F+ +++ Sbjct: 134 NTTLDRPWVFRAAFLDPFQGPVVADFAAKKFGAKTAAVLFDVANDYSVGLAEVFKSAWEA 193 Query: 203 ---GEIVADETFVAGDTDFQAALTKMKGKDFDAIVVPGYYNEAGKIVNQARGMGIDKPIV 259 G +VA E+ D DF A LT + D I VP YN+ I+ QAR +G P + Sbjct: 194 KGLGPVVAYESNGTKDQDFSAQLTTIIKAKPDFIFVPENYNQVALIIPQARDLGYKGPFM 253 Query: 260 GGDGFNGEEFVQQATAEKASNIYFISGFSTTVEVSAKAKAFLDAYRAKYNEEPSTFAALA 319 G D + + V + E+ + YF + ++ A K F+D Y KY EP+ +AAL Sbjct: 254 GSDAWGTPDLV-KLCGEQCNGQYFSTHYAAAGAKGA-TKVFIDRYMEKYGAEPADYAALT 311 Query: 320 YDSVHLVANAAKGA--------KNSGEIKNNLAKTKDFEGVTGQTSFDADHNTVKTAYMM 371 +DS+ L+ K A K I++ LA K F+GVTG + F+ + +K A ++ Sbjct: 312 WDSIGLMVEGIKNAGVVDSNPRKMRKAIRDGLAAIKSFDGVTGSSKFNEQGDPIKCAVVV 371 Query: 372 TMNN 375 +++ Sbjct: 372 KISD 375 Lambda K H 0.310 0.126 0.337 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: 339 Number of extensions: 20 Number of successful extensions: 5 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: 386 Length of database: 387 Length adjustment: 30 Effective length of query: 356 Effective length of database: 357 Effective search space: 127092 Effective search space used: 127092 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 (21.8 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