Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate H281DRAFT_05513 H281DRAFT_05513 branched-chain amino acid transport system permease protein
Query= uniprot:G8ALJ0 (294 letters) >FitnessBrowser__Burk376:H281DRAFT_05513 Length = 597 Score = 155 bits (391), Expect = 3e-42 Identities = 95/260 (36%), Positives = 149/260 (57%), Gaps = 12/260 (4%) Query: 12 LTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTLR 71 LTVE ++ ++GG++AV+DVSFS G+I +IGPNGAGK+TL N I G Y GR+ L Sbjct: 346 LTVESVSKQYGGVLAVSDVSFSVAAGQIHGLIGPNGAGKSTLVNLIAGNYLCDSGRVRLD 405 Query: 72 HADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIAG 131 AD + K +ARTFQN++L + VLEN+++ + + F+ Sbjct: 406 GADVSNLVTAD------RAKRGLARTFQNLQLVEALPVLENVLLGMSSADGHVANFA-KW 458 Query: 132 LLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVMLC 191 +G REA+++ ++ + L YG ++ +E+ARA+ P ++ Sbjct: 459 WMGRAFDLPERREALEILAFF----GIEHLCQAYPTELSYGHRKLVELARAIAQRPRLML 514 Query: 192 LDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKISDG 251 LDEP AGLN E+ E+A ++ +RD + +LLIEH+M VM++ D + VL+ GR I G Sbjct: 515 LDEPIAGLNGAEAMEVAKVVGRLRDA-GVTILLIEHNMEFVMSLCDSISVLEQGRLIGTG 573 Query: 252 DPAFVKNDPAVIRAYLGEEE 271 P +++D ++RAYLG +E Sbjct: 574 TPEEIRSDERILRAYLGTDE 593 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: 389 Number of extensions: 17 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: 597 Length adjustment: 31 Effective length of query: 263 Effective length of database: 566 Effective search space: 148858 Effective search space used: 148858 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: 50 (23.9 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