Align Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)
to candidate BPHYT_RS31745 BPHYT_RS31745 ABC transporter ATP-binding protein
Query= uniprot:G8ALI9 (505 letters) >FitnessBrowser__BFirm:BPHYT_RS31745 Length = 389 Score = 241 bits (616), Expect = 3e-68 Identities = 148/332 (44%), Positives = 194/332 (58%), Gaps = 52/332 (15%) Query: 171 QLLDIGILLLTYIMLGWGLNIVVGLAGLLDLGYVAFYAVGAYSYALL------AHY---- 220 ++LD +L Y+ML GLNIVVG AGLLDLGY+AFYAVGAY+ ALL AH+ Sbjct: 50 RVLDFAML---YVMLALGLNIVVGFAGLLDLGYIAFYAVGAYTAALLTSPHLAAHFEWIG 106 Query: 221 ------FGFSFWVCLPLAGFLAAMSGVLLGFPVLRLRGDYFAIVTLGFGEIIRIILINW- 273 F +W +P+A LAA++G+ LG P LRLRGDY AIVTLGFGEI+RI + N Sbjct: 107 HMWPSGFHAPYWFVMPVAMVLAAIAGICLGAPTLRLRGDYLAIVTLGFGEIVRIFMNNLD 166 Query: 274 --YQFTGGPNGISGIPRPSFFGIADFTRTPAEGTAAFHEMFGLEFSPLHRIIFLYYLILV 331 T GP GI+G+ + G + H G +F+ +++YY + V Sbjct: 167 RPVNITNGPQGITGVAPVTVAGF---------NLSETHAFLGFQFTT----VYMYYYVFV 213 Query: 332 L-ALVVNLFTMRVRKLPLGRAWEALREDDIACASLGINRTNMKLAAFAIAAMFGGFAGSF 390 L +L+V R++ +GRAW A+RED+IA ++GIN N+KL AFA+ A FGG +G+ Sbjct: 214 LCSLLVVWVCTRLQHSRIGRAWAAIREDEIAAKAMGINTRNVKLLAFAMGASFGGLSGAM 273 Query: 391 FATRQGFISPESFTFIESAIILAIVVLGGMGSQIGVVVAAFLVIGLPEAFR--------- 441 FA QGF+SPESFT ES +LA VVLGGMG GV+ A L+ LPE R Sbjct: 274 FAGFQGFVSPESFTLWESVTVLACVVLGGMGHIPGVIFGAVLLAILPEILRSTMTPLQNA 333 Query: 442 -------ELADYRMLAFGMGMVLIMLWRPRGL 466 + R L +G+ MV+IML RP GL Sbjct: 334 IFGHVIVDTEVIRQLLYGLAMVIIMLRRPEGL 365 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: 536 Number of extensions: 27 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: 505 Length of database: 389 Length adjustment: 32 Effective length of query: 473 Effective length of database: 357 Effective search space: 168861 Effective search space used: 168861 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