Align Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)
to candidate 209488 DVU0549 high-affinity branched-chain amino acid ABC transporter, permease protein
Query= uniprot:G8ALI9 (505 letters) >MicrobesOnline__882:209488 Length = 407 Score = 313 bits (802), Expect = 7e-90 Identities = 173/351 (49%), Positives = 226/351 (64%), Gaps = 22/351 (6%) Query: 140 IAAQVQHASRWLGPIAVVVALAFPFTP-LADRQLLDIGILLLTYIMLGWGLNIVVGLAGL 198 + A+V+ +R P + V + F P L +I I L Y+MLG GLNIVVGL+G Sbjct: 78 LMARVRSDARLRTPALLAVLVVFAVLPMLVSTYQTNIMISALLYVMLGLGLNIVVGLSGQ 137 Query: 199 LDLGYVAFYAVGAYSYALLAHYFGFSFWVCLPLAGFLAAMSGVLLGFPVLRLRGDYFAIV 258 L LGYVAFYAVGAY+YALL FG FW LP+ G LAA+ G+LLGFPVLRL+GDY AIV Sbjct: 138 LVLGYVAFYAVGAYAYALLNADFGLGFWTVLPIGGALAAVFGILLGFPVLRLKGDYLAIV 197 Query: 259 TLGFGEIIRIILINWYQFTGGPNGISGIPRPSFFGIADFTRTPAEGTAAFHEMFGLEFSP 318 TLGFGEI+R++L NW T GP+GIS I RP +FG+E S Sbjct: 198 TLGFGEIVRLVLENWGSVTRGPSGISKIARPG--------------------LFGMELSV 237 Query: 319 LHRIIFLYYLILVLALVVNLFTMRVRKLPLGRAWEALREDDIACASLGINRTNMKLAAFA 378 ++YYLIL + R++ +GRAW+ALRED+IAC ++GI+ T KL AFA Sbjct: 238 SEATTYIYYLILAAVIFTIFAVGRLKDSRIGRAWQALREDEIACEAMGIDLTTTKLTAFA 297 Query: 379 IAAMFGGFAGSFFATRQGFISPESFTFIESAIILAIVVLGGMGSQIGVVVAAFLVIGLPE 438 + A + GFAG FA + FI+P SFTF+ESA+ILA+VVLGGMGS +GVV+ A ++I LPE Sbjct: 298 LGACWAGFAGVIFAAKTTFINPASFTFLESAMILAMVVLGGMGSTLGVVLGALVLILLPE 357 Query: 439 AFRELADYRMLAFGMGMVLIMLWRPRGLLAHRDPTILLHGRPKGGAGGPAA 489 R ++YRML FG MVL+M++RP+GL++ R ++ P+ G G A Sbjct: 358 YLRAFSEYRMLIFGAAMVLMMVFRPQGLVSCRSREYDVND-PEAGKSGEKA 407 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: 558 Number of extensions: 29 Number of successful extensions: 3 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: 407 Length adjustment: 33 Effective length of query: 472 Effective length of database: 374 Effective search space: 176528 Effective search space used: 176528 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