Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate BPHYT_RS15595 BPHYT_RS15595 ABC transporter
Query= uniprot:G8ALJ0 (294 letters) >FitnessBrowser__BFirm:BPHYT_RS15595 Length = 257 Score = 215 bits (548), Expect = 7e-61 Identities = 122/257 (47%), Positives = 167/257 (64%), Gaps = 10/257 (3%) Query: 12 LTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTLR 71 L+V+ + RFGGL A+++V +G+I +IGPNGAGKTT FN ITG YTP G L Sbjct: 7 LSVKGVNKRFGGLQALSEVGLEIKSGQIYGLIGPNGAGKTTFFNVITGLYTPDSGEFKL- 65 Query: 72 HADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIAG 131 DG+ + + Y+++ KA +ARTFQNIRLFGGM+ LEN++V +H +R I Sbjct: 66 --DGENYTPTAV--YQVA-KAGIARTFQNIRLFGGMTALENVMVGRH---VRTKHGLIGA 117 Query: 132 LLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVMLC 191 + P+ + ERE + A L+ V + ++AD+ + NL YG QRRLEIARA+ T+P +L Sbjct: 118 VFQTPAERKEEREIKERAIELLEYVGIAQYADYTSRNLSYGHQRRLEIARALATDPKLLA 177 Query: 192 LDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKISDG 251 LDEPAAG+N E EL LL IR + K +LLIEHD+ +VM + + + VLDYG+ I+ G Sbjct: 178 LDEPAAGMNATEKVELTKLLDKIRADGKT-ILLIEHDVKLVMGLCNQMTVLDYGKVIAQG 236 Query: 252 DPAFVKNDPAVIRAYLG 268 P V+ DP VI AYLG Sbjct: 237 LPQDVQKDPKVIEAYLG 253 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: 12 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: 257 Length adjustment: 25 Effective length of query: 269 Effective length of database: 232 Effective search space: 62408 Effective search space used: 62408 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: 47 (22.7 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