Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate BPHYT_RS04435 BPHYT_RS04435 ABC transporter
Query= uniprot:G8ALJ0 (294 letters) >FitnessBrowser__BFirm:BPHYT_RS04435 Length = 646 Score = 194 bits (493), Expect = 4e-54 Identities = 117/269 (43%), Positives = 162/269 (60%), Gaps = 14/269 (5%) Query: 8 TTPLLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGR 67 T +L + + M+F GL A+NDV + G I +IGPNG+GK+T+ N +TG Y PT G Sbjct: 388 TEDILQLRGILMQFSGLKALNDVDLTVQRGTIHGLIGPNGSGKSTMMNVLTGIYVPTAGT 447 Query: 68 LTLRHADGKEFLLERMPGYRISQKA--SVARTFQNIRLFGGMSVLENLIVAQHNKLIRAS 125 L R A + G +Q A +ARTFQN++LFG M+ LEN++V H+ + Sbjct: 448 LEYRGAS--------LAGKTSAQIALSGIARTFQNVQLFGEMTALENVLVGLHHTF--NA 497 Query: 126 GFSIAGLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCT 185 + GL+ Y R ER A + A L V L A EA NLPYG QR LEIARA+ Sbjct: 498 NLADVGLMS-SRYRREERAARERAFGMLRFVGLDNVAAEEARNLPYGKQRLLEIARALAL 556 Query: 186 EPVMLCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYG 245 +P +L LDEPAAGL + EL ++ +RD H I V+LIEH M VVM++ D V VLD+G Sbjct: 557 DPQLLLLDEPAAGLTAPDIKELVAIIRKVRD-HGITVVLIEHHMDVVMSVCDRVSVLDFG 615 Query: 246 RKISDGDPAFVKNDPAVIRAYLGEEEDEE 274 +KI++G PA ++++ VI AYLG + ++ Sbjct: 616 QKIAEGKPADIQSNEKVIEAYLGGQPADQ 644 Lambda K H 0.319 0.137 0.397 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: 409 Number of extensions: 25 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: 294 Length of database: 646 Length adjustment: 32 Effective length of query: 262 Effective length of database: 614 Effective search space: 160868 Effective search space used: 160868 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (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