Align Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)
to candidate WP_068173840.1 HTA01S_RS16515 ABC transporter ATP-binding protein
Query= uniprot:G8ALI9 (505 letters) >NCBI__GCF_001592305.1:WP_068173840.1 Length = 361 Score = 233 bits (593), Expect = 1e-65 Identities = 137/329 (41%), Positives = 190/329 (57%), Gaps = 48/329 (14%) Query: 171 QLLDIGILLLTYIMLGWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLA------------ 218 ++LDI +L Y++L GLNIVVG AGLLDLGY+AF+AVGAY +ALL Sbjct: 36 RILDIALL---YVLLALGLNIVVGYAGLLDLGYIAFFAVGAYVFALLGSPHLIDTFPAIK 92 Query: 219 ----HYFGFSFWVCLPLAGFLAAMSGVLLGFPVLRLRGDYFAIVTLGFGEIIRIILINW- 273 S W+ + +A +A + G++LG P L+LRGDY AI+TLGFGEIIRI L+N Sbjct: 93 AMFPEGLHISIWIVMIIAAVIAGVVGMILGAPTLKLRGDYLAIITLGFGEIIRIFLLNMD 152 Query: 274 --YQFTGGPNGISGIPRPSFFGIADFTRTPAEGTAAFHEMFGLEFSPLHRIIFLYYLILV 331 T GP GIS I S FG+ D + G +F + YYL L Sbjct: 153 RPVNITNGPKGISQIDTISVFGL-DLGQRLTIGDYSFQP-----------VTLYYYLFLF 200 Query: 332 LALVVNLFTMRVRKLPLGRAWEALREDDIACASLGINRTNMKLAAFAIAAMFGGFAGSFF 391 + + + R++ +GRAW A+RED+IA ++G+N N+KL AF + A FGG +G F Sbjct: 201 FVVGAVILSYRLQDSRIGRAWMAIREDEIAAKAMGLNTRNLKLLAFGMGATFGGVSGVLF 260 Query: 392 ATRQGFISPESFTFIESAIILAIVVLGGMGSQIGVVVAAFLVIGLPEAFRELAD------ 445 A+ Q F+SPESF+ +ES +++A+VVLGG+G GV++ A L+ GLPE R +A Sbjct: 261 ASFQRFVSPESFSLMESVMVVAMVVLGGIGHIPGVILGALLLAGLPELLRHVAHPLTAMT 320 Query: 446 --------YRMLAFGMGMVLIMLWRPRGL 466 R L + MV++ML RP+GL Sbjct: 321 DGRLAPEILRQLLIALAMVVVMLIRPKGL 349 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: 515 Number of extensions: 28 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: 361 Length adjustment: 32 Effective length of query: 473 Effective length of database: 329 Effective search space: 155617 Effective search space used: 155617 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 24 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