Align Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)
to candidate WP_041938756.1 FRAAL_RS03130 branched-chain amino acid ABC transporter permease
Query= uniprot:G8ALI9 (505 letters) >NCBI__GCF_000058485.1:WP_041938756.1 Length = 515 Score = 213 bits (543), Expect = 1e-59 Identities = 135/359 (37%), Positives = 198/359 (55%), Gaps = 36/359 (10%) Query: 151 LGPIAVVVALAFPF---TPLADRQLLDIGILLLTYIMLGWGLNIVVGLAGLLDLGYVAFY 207 L + + VA+ P T + DIGI Y +L GLN+VVG AGLLDLGY+AF+ Sbjct: 178 LNLVLLAVAILAPLVVSTAAQQSMVNDIGI----YALLALGLNVVVGYAGLLDLGYIAFF 233 Query: 208 AVGAYSYALLAHY--------FGFSFWVCLPLAGFLAAMSGVLLGFPVLRLRGDYFAIVT 259 A+GAY+ A F + + P+A LAA++GV+LG P LRLRGDY AIVT Sbjct: 234 AIGAYATAYFTSQTAMPWHAPFVLNPFFVFPIALVLAALAGVILGAPTLRLRGDYLAIVT 293 Query: 260 LGFGEIIRIILINWYQFTGGPNGISGIPRPSFFGIADFTRTPAEGTAAFHEMFGLEFSPL 319 LGFGEII ++ N T G G G+P S ++ G+++ Sbjct: 294 LGFGEIIHLVANNADGITNGARGAFGVPHLSI------------------DLLGIDYKWG 335 Query: 320 HRIIFLYYLILVLALVVNLFTMRVRKLPLGRAWEALREDDIACASLGINRTNMKLAAFAI 379 + YYL+L + + V + R+ + +GR+W A+RED+IA + G+ MKL AFAI Sbjct: 336 IDPLPYYYLLLAIVIGVMIAFGRLERSRIGRSWAAIREDEIAAEATGVATLRMKLLAFAI 395 Query: 380 AAMFGGFAGSFFATRQGFISPESFTFIESAIILAIVVLGGMGSQIGVVVAAFLVIGLPEA 439 A GFAG FA++Q F +P+SF+ S ++A+V+ GGMGS++GVVV A ++ GL Sbjct: 396 GASVSGFAGVLFASKQ-FFNPQSFSLQASFFVVAVVIFGGMGSRLGVVVGAVVLQGLAFY 454 Query: 440 FRELAD--YRMLAFGMGMVLIMLWRPRGLLAHRDPTILLHGRPKGGAGGPAAGSAAAGG 496 R+ R + FG +V++M++RP+GL+ R + +G + G+A GG Sbjct: 455 LRDKVQPADRYIYFGAVIVIMMIFRPQGLVPSRRRRREIELAEEGIGAADSLGAAPTGG 513 Lambda K H 0.329 0.144 0.438 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: 706 Number of extensions: 46 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: 505 Length of database: 515 Length adjustment: 34 Effective length of query: 471 Effective length of database: 481 Effective search space: 226551 Effective search space used: 226551 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 (21.8 bits) S2: 52 (24.6 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