Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate HSERO_RS00895 HSERO_RS00895 ABC transporter
Query= uniprot:G8ALJ0 (294 letters) >FitnessBrowser__HerbieS:HSERO_RS00895 Length = 255 Score = 198 bits (503), Expect = 1e-55 Identities = 119/259 (45%), Positives = 164/259 (63%), Gaps = 12/259 (4%) Query: 11 LLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTL 70 LL + ++ RFGGL A+N V + G+I +IGPNGAGKTT FN ITG Y P G L Sbjct: 5 LLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFEL 64 Query: 71 RHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIA 130 DGK + + ++ KA +ARTFQNIRLFG M+VLEN++V H + + ++ Sbjct: 65 ---DGKPY--SPSAPHEVA-KAGIARTFQNIRLFGEMTVLENVMVGCHVRTRQ----NVF 114 Query: 131 GLLGLPSYTRTEREAV-DLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVM 189 G + R E A+ + ++ LD V + +FA A +L YG QRRLEIARA+ T+P + Sbjct: 115 GAVFRHKAAREEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQL 174 Query: 190 LCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKIS 249 L LDEPAAG+N E L +LL I+ E K +LLIEHD+ ++M + + + VLDYG+ I+ Sbjct: 175 LALDEPAAGMNATEKLGLRELLVKIQAEGKT-ILLIEHDVKLMMGLCNRITVLDYGKPIA 233 Query: 250 DGDPAFVKNDPAVIRAYLG 268 +G PA V+ +PAVI AYLG Sbjct: 234 EGVPADVQKNPAVIEAYLG 252 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: 201 Number of extensions: 9 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: 255 Length adjustment: 25 Effective length of query: 269 Effective length of database: 230 Effective search space: 61870 Effective search space used: 61870 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