Align Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)
to candidate GFF3114 HP15_3057 leucine/isoleucine/valine transporter permease subunit
Query= uniprot:G8ALI9 (505 letters) >FitnessBrowser__Marino:GFF3114 Length = 423 Score = 396 bits (1018), Expect = e-115 Identities = 203/343 (59%), Positives = 255/343 (74%), Gaps = 5/343 (1%) Query: 128 LSQAERDKRMDHIAAQVQHASRWLGPIAVVVALAFPFTPLADRQLLDIGILLLTYIMLGW 187 L Q+ ++ ++ A+++ W+ VV+AL +PF R +D+ L+L YIML Sbjct: 76 LPQSNKEPMAENRRAKIES---WVLTGIVVLALFWPF--FVSRGAVDLATLVLIYIMLAL 130 Query: 188 GLNIVVGLAGLLDLGYVAFYAVGAYSYALLAHYFGFSFWVCLPLAGFLAAMSGVLLGFPV 247 GLN+VVGLAGLLDLGYVAFYAVGAY++ALL+ Y G SFW+ LP+ LAA+ G++LGFPV Sbjct: 131 GLNVVVGLAGLLDLGYVAFYAVGAYTFALLSQYTGISFWLALPIGALLAALFGLVLGFPV 190 Query: 248 LRLRGDYFAIVTLGFGEIIRIILINWYQFTGGPNGISGIPRPSFFGIADFTRTPAEGTAA 307 LRLRGDY AIVTLGFGEIIRI+L NW TGGPNGI GIP P+ FG+ R EG + Sbjct: 191 LRLRGDYLAIVTLGFGEIIRILLNNWTTLTGGPNGIGGIPDPTLFGMEFGRRVKEEGNTS 250 Query: 308 FHEMFGLEFSPLHRIIFLYYLILVLALVVNLFTMRVRKLPLGRAWEALREDDIACASLGI 367 FHE FG+ +S H++IFLY + LVLA+ L R ++P+GRAWEALRED+IA SLG+ Sbjct: 251 FHETFGIAYSGEHKVIFLYLIALVLAVFTALVIRRFMRMPVGRAWEALREDEIAARSLGL 310 Query: 368 NRTNMKLAAFAIAAMFGGFAGSFFATRQGFISPESFTFIESAIILAIVVLGGMGSQIGVV 427 +RT +KL+AF I A F GFAG+ FA++QGFISPESF F+ESAIILAIVVLGGMGSQIGVV Sbjct: 311 SRTAVKLSAFTIGAFFAGFAGTVFASKQGFISPESFVFLESAIILAIVVLGGMGSQIGVV 370 Query: 428 VAAFLVIGLPEAFRELADYRMLAFGMGMVLIMLWRPRGLLAHR 470 +AA V LPE RE ++YRML FG MVL+M+WRP+GL+ R Sbjct: 371 LAAIAVTILPELAREFSEYRMLIFGAAMVLMMVWRPQGLMPMR 413 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: 579 Number of extensions: 23 Number of successful extensions: 2 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: 505 Length of database: 423 Length adjustment: 33 Effective length of query: 472 Effective length of database: 390 Effective search space: 184080 Effective search space used: 184080 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: 51 (24.3 bits)
This GapMind analysis is from Sep 17 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