Align Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)
to candidate BWI76_RS26340 BWI76_RS26340 branched-chain amino acid ABC transporter permease
Query= uniprot:G8ALI9 (505 letters) >FitnessBrowser__Koxy:BWI76_RS26340 Length = 426 Score = 369 bits (947), Expect = e-106 Identities = 190/331 (57%), Positives = 250/331 (75%), Gaps = 7/331 (2%) Query: 156 VVVALAFPFTPLADRQLLDIGILLLTYIMLGWGLNIVVGLAGLLDLGYVAFYAVGAYSYA 215 +V+A+A+PF + R +DI L + YI+LG GLN+VVGL+GLL LGY FYA+GAY++A Sbjct: 97 LVIAVAWPF--MVSRGTVDIATLTMIYIILGLGLNVVVGLSGLLVLGYGGFYAIGAYTFA 154 Query: 216 LLAHYFGFSFWVCLPLAGFLAAMSGVLLGFPVLRLRGDYFAIVTLGFGEIIRIILINWYQ 275 LL HY+G FW CLPLAG ++A +G LLGFPVLRLRGDY AIVTLGFGEI+RI+L+N + Sbjct: 155 LLNHYYGLGFWTCLPLAGLVSAAAGFLLGFPVLRLRGDYLAIVTLGFGEIVRILLLNNTE 214 Query: 276 FTGGPNGISGIPRPSFFGIADFTRTPAE-GTAAFHEMFGLEFSPLHRIIFLYYLILVLAL 334 TGGPNGIS IP+P+ FG+ +F+R+ E G F FG+++ P R+IFL YL+ +L + Sbjct: 215 ITGGPNGISQIPKPTLFGL-EFSRSAREGGWDTFSNFFGVKYDPSDRVIFL-YLVALLLV 272 Query: 335 VVNLFTM-RVRKLPLGRAWEALREDDIACASLGINRTNMKLAAFAIAAMFGGFAGSFFAT 393 V++LF + R+ ++PLGRAWEALRED+IAC SLG++ T +KL AF I+A F GFAG+ FA Sbjct: 273 VLSLFVINRLLRMPLGRAWEALREDEIACRSLGLSPTRIKLTAFTISAAFAGFAGTLFAA 332 Query: 394 RQGFISPESFTFIESAIILAIVVLGGMGSQIGVVVAAFLVIGLPEAFRELADYRMLAFGM 453 RQGF+SPESFTF ESA +LAIVVLGGMGSQ V++AA L++ E R+ +Y ML G Sbjct: 333 RQGFVSPESFTFAESAFVLAIVVLGGMGSQFAVILAAVLLVVSRELMRDFNEYSMLMLGA 392 Query: 454 GMVLIMLWRPRGLLAHRDPTI-LLHGRPKGG 483 MVL+M+WRP+GLL P + L +G+ K G Sbjct: 393 LMVLMMIWRPQGLLPMTRPQLKLKNGQAKEG 423 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: 584 Number of extensions: 31 Number of successful extensions: 2 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: 426 Length adjustment: 33 Effective length of query: 472 Effective length of database: 393 Effective search space: 185496 Effective search space used: 185496 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