Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_050462656.1 AKL27_RS09910 high-affinity branched-chain amino acid ABC transporter permease LivM
Query= uniprot:A0A165KER0 (358 letters) >NCBI__GCF_001189915.1:WP_050462656.1 Length = 408 Score = 261 bits (667), Expect = 2e-74 Identities = 158/357 (44%), Positives = 215/357 (60%), Gaps = 46/357 (12%) Query: 13 VALLVLPLILQSFGNAW-VRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVGAYLF 71 + LL + L+ FG+ V + LAL+YV+L LGLNIVVG+AGLLDLGYV FYAVG Y + Sbjct: 85 MVLLAVALVWPFFGSRGNVDVVTLALIYVVLGLGLNIVVGFAGLLDLGYVGFYAVGGYTY 144 Query: 72 ALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDYLAIV 131 AL+ GL S W +P+AA ++A FG +LG P L+LRGDYLAIV Sbjct: 145 ALLNQYF--------------GL--SFWECLPLAAGMSALFGFLLGFPVLRLRGDYLAIV 188 Query: 132 TLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDI-------- 183 TLGFGEIIR+ LNNL +LT GP G+ I VFG+++ + V G Sbjct: 189 TLGFGEIIRLLLNNL---TSLTGGPDGVSGIPKPTVFGIEMARTASVEGGTTFHDMLGLT 245 Query: 184 ----NSVTLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLL 239 + V Y+L L+LV+ + + RL +GRAW A+R+DEIA +++GIN +KL Sbjct: 246 YQGGHMVIFLYFLGLLLVLFTYFVTSRLIRMPMGRAWEALRDDEIACRSLGINPTKIKLS 305 Query: 240 AFGMGASFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSA 299 AF +GA+F G++G+ F A QG V+PESF+ +ES +I+A+VVLGG+G GVIL A+LL+ Sbjct: 306 AFTLGAAFAGLAGSFFAARQGLVNPESFTFIESALILAIVVLGGMGSQLGVILAAILLTI 365 Query: 300 LPEVLRYVAGPLQAMTDGRLDSAILRQLLIALAMIIIMLLRPRGLWPSPEHGKSLTQ 356 LPEV R A R L+ L M+++M+ RP+GL P+ L Q Sbjct: 366 LPEVAR--------------SFAEYRMLIFGLVMVLMMIWRPQGLLPATRPHVELPQ 408 Lambda K H 0.328 0.144 0.430 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: 374 Number of extensions: 16 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 358 Length of database: 408 Length adjustment: 30 Effective length of query: 328 Effective length of database: 378 Effective search space: 123984 Effective search space used: 123984 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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