Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_045585060.1 AL072_RS29555 high-affinity branched-chain amino acid ABC transporter permease LivM
Query= uniprot:A0A165KER0 (358 letters) >NCBI__GCF_001305595.1:WP_045585060.1 Length = 497 Score = 247 bits (631), Expect = 4e-70 Identities = 149/345 (43%), Positives = 197/345 (57%), Gaps = 45/345 (13%) Query: 12 AVALLVLPLILQSFGNAWVRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVGAYLF 71 AVA+ V+ + + I L L Y++L GLNIVVG AGLLDLGYVAFYAVGAY + Sbjct: 163 AVAIAVVLPMTPLADRMLLDIGILLLTYIMLGWGLNIVVGLAGLLDLGYVAFYAVGAYSY 222 Query: 72 ALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDYLAIV 131 AL+A + S W+ +P+A +LAAF G +LG P L+LRGDY AIV Sbjct: 223 ALLA----------------HYFGLSFWLCLPLAGVLAAFSGVLLGFPVLRLRGDYFAIV 266 Query: 132 TLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRL---------EVFGFD 182 TLGFGEIIRI L N T GP G+ I FG+ R E+FG + Sbjct: 267 TLGFGEIIRIILVNW---YQFTGGPNGISGIPRPSFFGIAEFSRTPADGMAAFHEMFGLE 323 Query: 183 ---INSVTLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLL 239 ++ + YYL L L +V + R++ +GRAW A+RED+IA ++GIN NMKL Sbjct: 324 FSPLHRIVFLYYLILALALVVNVFTLRVRKLPLGRAWEALREDDIACASLGINRTNMKLA 383 Query: 240 AFGMGASFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSA 299 AF + A FGG +G+ F QGF+SPESF+ +ES +I+A+VVLGG+G GV++ +L+ Sbjct: 384 AFAIAAMFGGFAGSFFATRQGFISPESFTFIESAIILAIVVLGGMGSQIGVVVATLLVIG 443 Query: 300 LPEVLRYVAGPLQAMTDGRLDSAILRQLLIALAMIIIMLLRPRGL 344 LPE R +A R L M++IML RPRGL Sbjct: 444 LPEAFRELAD--------------YRMLAFGAGMVVIMLWRPRGL 474 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: 473 Number of extensions: 23 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: 358 Length of database: 497 Length adjustment: 32 Effective length of query: 326 Effective length of database: 465 Effective search space: 151590 Effective search space used: 151590 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 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