Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate RR42_RS01630 RR42_RS01630 branched-chain amino acid ABC transporter ATP-binding protein
Query= uniprot:G8ALJ0 (294 letters) >FitnessBrowser__Cup4G11:RR42_RS01630 Length = 307 Score = 190 bits (482), Expect = 4e-53 Identities = 108/258 (41%), Positives = 153/258 (59%), Gaps = 9/258 (3%) Query: 11 LLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTL 70 +L ++++++ FGG+ A+ D+SF EI AIIGPNGAGK+++ N I G Y P GR+ Sbjct: 56 ILDLQNISLAFGGVKALTDISFDVREHEIRAIIGPNGAGKSSMLNVINGVYHPQQGRIVF 115 Query: 71 RHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIA 130 R G+E R + + +ARTFQNI LF GM+VL+N++ ++ + SG +A Sbjct: 116 R---GEE---RRKMHPTAAARQGIARTFQNIALFKGMTVLDNIMTGRNTRF--RSGL-LA 166 Query: 131 GLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVML 190 L E + + +D + + G LPYG Q+R+E+ARA+ EP ML Sbjct: 167 NALWWGPARNEEMQHRRKVEEVIDFLEIQAIRKTPVGRLPYGLQKRVELARALAAEPSML 226 Query: 191 CLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKISD 250 LDEP AG+N E ++ + + + ++LIEHDM VVM ISD VVVLDYG+KI D Sbjct: 227 LLDEPMAGMNVEEKQDMCRFILDVNHQFGTTIVLIEHDMGVVMDISDRVVVLDYGKKIGD 286 Query: 251 GDPAFVKNDPAVIRAYLG 268 G P VK +P VIRAYLG Sbjct: 287 GTPEAVKANPDVIRAYLG 304 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: 221 Number of extensions: 9 Number of successful extensions: 3 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: 307 Length adjustment: 27 Effective length of query: 267 Effective length of database: 280 Effective search space: 74760 Effective search space used: 74760 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: 48 (23.1 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