Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate WP_085771912.1 B1812_RS12645 LPS export ABC transporter ATP-binding protein
Query= uniprot:G8ALJ0 (294 letters) >NCBI__GCF_002117405.1:WP_085771912.1 Length = 288 Score = 116 bits (290), Expect = 7e-31 Identities = 82/264 (31%), Positives = 132/264 (50%), Gaps = 33/264 (12%) Query: 11 LLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTL 70 +L + +L + V DVS GE ++GPNGAGKTT+F ITG P GR+TL Sbjct: 51 VLAIHNLAKSYKTRRVVEDVSLHVRRGEAVGLLGPNGAGKTTVFYMITGLVKPDSGRITL 110 Query: 71 RHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLI----VAQHNKLIRASG 126 DG + + +P YR + + Q + +F G++V EN++ + + +K RA Sbjct: 111 ---DGYD--VTPLPMYR-RARLGIGYLPQEMSVFRGLTVEENILAVLEIVEPDKKKRAE- 163 Query: 127 FSIAGLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTE 186 + GL L+ RL A + G +RR EIARA+ Sbjct: 164 -QLDGL--------------------LEEFRLAHLRKTPAIAVSGGERRRCEIARAIAGR 202 Query: 187 PVMLCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGR 246 P + LDEP AG++P G + DL+ +++ + IGVL+ +H + + ++D ++ G Sbjct: 203 PSFMLLDEPFAGIDPIAIGGIQDLVRHLK-QRGIGVLITDHSVRETLGLTDRAYIIYNGH 261 Query: 247 KISDGDPAFVKNDPAVIRAYLGEE 270 +++G PA + +P V R YLGE+ Sbjct: 262 VLTEGAPAEIVANPDVRRIYLGED 285 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: 203 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: 288 Length adjustment: 26 Effective length of query: 268 Effective length of database: 262 Effective search space: 70216 Effective search space used: 70216 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 Apr 09 2024. 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