Align Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)
to candidate H281DRAFT_04061 H281DRAFT_04061 amino acid/amide ABC transporter membrane protein 2, HAAT family
Query= uniprot:G8ALI9 (505 letters) >FitnessBrowser__Burk376:H281DRAFT_04061 Length = 389 Score = 240 bits (612), Expect = 7e-68 Identities = 151/331 (45%), Positives = 194/331 (58%), Gaps = 50/331 (15%) Query: 171 QLLDIGILLLTYIMLGWGLNIVVGLAGLLDLGYVAFYAVGAYSYALL------------A 218 ++LD +L Y+ML GLN+VVG AGLLDLGY+AFYAVGAY+ ALL A Sbjct: 50 RVLDFAML---YVMLALGLNVVVGFAGLLDLGYIAFYAVGAYTAALLSSPHLTSQFEWIA 106 Query: 219 HY----FGFSFWVCLPLAGFLAAMSGVLLGFPVLRLRGDYFAIVTLGFGEIIRIILINW- 273 H F + +P A +AA GV+LG P LRLRGDY AIVTLGFGEI+RI L N Sbjct: 107 HLAPNGLHVPFLIIVPCAMAVAAFFGVILGAPTLRLRGDYLAIVTLGFGEIVRIFLNNLD 166 Query: 274 --YQFTGGPNGISGIPRPSFFGIADFTRTPAEGTAAFHEMFGLEFSPLHRIIFLYYLILV 331 T GP GI+GI + DF+ A H +FG +F ++ YYL ++ Sbjct: 167 RPVNITNGPKGITGIDSVH---LGDFS------LAQTHSLFGFQFPSVYSY---YYLFVL 214 Query: 332 LALVVNLFTMRVRKLPLGRAWEALREDDIACASLGINRTNMKLAAFAIAAMFGGFAGSFF 391 AL+V R++ +GRAW A+RED+IA ++GIN N+KL AFA+ A FGG +G+ F Sbjct: 215 AALLVIWVCTRLQHSRIGRAWAAIREDEIAAKAMGINTRNVKLLAFAMGASFGGLSGAMF 274 Query: 392 ATRQGFISPESFTFIESAIILAIVVLGGMGSQIGVVVAAFLVIGLPEAFR---------- 441 QGF+SPESFT ES ++LA VVLGGMG GV++ A L+ LPE R Sbjct: 275 GAFQGFVSPESFTLPESIVVLACVVLGGMGHIPGVILGAVLLAVLPEFLRSTMGPLQHML 334 Query: 442 ---ELAD---YRMLAFGMGMVLIMLWRPRGL 466 E+ D R L + + MVLIML+R GL Sbjct: 335 FGHEIVDTEVIRQLVYALAMVLIMLYRSEGL 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: 520 Number of extensions: 30 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