Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate GFF3115 HP15_3058 leucine/isoleucine/valine transporter ATP-binding subunit
Query= uniprot:G8ALJ0 (294 letters) >FitnessBrowser__Marino:GFF3115 Length = 251 Score = 262 bits (670), Expect = 5e-75 Identities = 137/259 (52%), Positives = 190/259 (73%), Gaps = 9/259 (3%) Query: 11 LLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTL 70 +L V++L+MRFGGL+AV++VS EI +IIGPNGAGKTT+FNC++GFY PT G++ Sbjct: 1 MLEVQNLSMRFGGLLAVDEVSLDVQEHEIVSIIGPNGAGKTTVFNCMSGFYKPTGGKILF 60 Query: 71 RHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIA 130 +GKE ++ P Y+IS+ V RTFQ++RLF M+V+ENL+VAQH L + I+ Sbjct: 61 ---EGKE--VQGKPDYKISRLGMV-RTFQHVRLFSQMTVVENLLVAQHRHL---NTNLIS 111 Query: 131 GLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVML 190 GL+ PSY + E++++D A YWLDRV LL+ A+ EAGNL YG QRRLEIAR M TEP +L Sbjct: 112 GLIQTPSYRKKEQKSLDRAAYWLDRVGLLDMANREAGNLAYGQQRRLEIARCMVTEPKLL 171 Query: 191 CLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKISD 250 LDEPAAGLNP E+ EL L+ +++++ + V+LIEHDMS+VM ISD + V++ GR ++ Sbjct: 172 MLDEPAAGLNPAETKELNQLIISLKEDYNVSVVLIEHDMSLVMDISDRINVINQGRPLAS 231 Query: 251 GDPAFVKNDPAVIRAYLGE 269 G P ++ + VI+AYLGE Sbjct: 232 GTPEEIRQNDDVIKAYLGE 250 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: 211 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: 251 Length adjustment: 25 Effective length of query: 269 Effective length of database: 226 Effective search space: 60794 Effective search space used: 60794 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