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_027721621.1 H589_RS0108435 branched-chain amino acid ABC transporter substrate-binding protein
Query= TCDB::Q8DQI1 (386 letters) >NCBI__GCF_000425265.1:WP_027721621.1 Length = 393 Score = 191 bits (484), Expect = 4e-53 Identities = 122/373 (32%), Positives = 191/373 (51%), Gaps = 20/373 (5%) Query: 32 AGNSVEEKTIKIGFNFEESGSLAAYGTAEQKGAQLAVDEINAAGGID--GKQI--EVVDK 87 AG S EE+ IKIGFN +G + G A + A++ + +INA GG++ GK+I + + Sbjct: 23 AGCSKEEEKIKIGFNIPLTGDIPKVGEASKNAAEMLLADINAQGGLEVGGKKIPLQFFYE 82 Query: 88 DNKSETAEAASVTTNLVTQSKVSAVVGPATSGATAAAVANATKAGVPLISPSATQDGLTK 147 DN+S+ A +V L+ Q+ V A++GP +S A P++SP +T TK Sbjct: 83 DNESKAESAVNVALKLIEQNGVVAIIGPNSSKQAVPAGGTCNDNRTPMVSPWSTNPDTTK 142 Query: 148 GQDYLFIGTFQDSFQGKIISNYVSEKLNAKKVVLYTDNASDYAKGIAKSFRESYK----G 203 + ++F F D FQG + N+ +++ A K + D ++DY+KG+A+ F++ ++ G Sbjct: 143 NRPWVFRAAFLDPFQGPVAVNFATKQFKATKAAVLFDVSNDYSKGLAEIFKDVFEKKNGG 202 Query: 204 E-IVADETFVAGDTDFQAALTKMKGKDFDAIVVPGYYNEAGKIVNQARGMGIDKPIVGGD 262 E +VA E+ D DF A LTK+ D I VP YN+ IV QAR +G P +G D Sbjct: 203 ESVVAFESHGTKDQDFSAQLTKIINSKPDFIFVPDNYNQVALIVKQARDLGWTGPFMGSD 262 Query: 263 GFNGEEFVQQATAEKASNIYFISGFSTTVEVSAKAKAFLDAYRAKYNEEPSTFAALAYDS 322 + E ++ + F S K F+D Y AKY E P AAL +D+ Sbjct: 263 AWGSAELMKLCGDDCKGQ--FFSTHYAAAGAKGATKEFIDRYEAKYGETPDDVAALTWDA 320 Query: 323 VHLVANAAKGAKNSG--------EIKNNLAKTKDFEGVTGQTSFDADHNTVKTAYMMTM- 373 LV A + A + I++ L+ K+F G+TG FD+ + +K A ++ + Sbjct: 321 ARLVLQAIQDAGSYNPNVKDERKAIRDALSSIKEFAGITGSMKFDSQGDPIKCAVVVRID 380 Query: 374 NNGKVEAAEVVKP 386 +NG AE V P Sbjct: 381 DNGNFVFAESVCP 393 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: 316 Number of extensions: 15 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: 393 Length adjustment: 30 Effective length of query: 356 Effective length of database: 363 Effective search space: 129228 Effective search space used: 129228 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