Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate SMc01949 SMc01949 high-affinity branched-chain amino acid ABC transporter ATP-binding protein
Query= uniprot:G8ALJ0 (294 letters) >FitnessBrowser__Smeli:SMc01949 Length = 295 Score = 374 bits (961), Expect = e-108 Identities = 183/271 (67%), Positives = 221/271 (81%) Query: 3 TQSMTTTPLLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYT 62 T +MT P+L VE L+MRFGGL+A+ND SF A GEITA+IGPNGAGKTT+FNCITGFY Sbjct: 5 TDTMTKDPILKVERLSMRFGGLMAINDFSFEAERGEITALIGPNGAGKTTVFNCITGFYK 64 Query: 63 PTVGRLTLRHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLI 122 PT+G +T+R G EFLLER+P + I++KA VARTFQNIR+F G++VLENL+VAQHNKL+ Sbjct: 65 PTMGMITMRQKSGAEFLLERLPDFEITKKAKVARTFQNIRMFSGLTVLENLLVAQHNKLM 124 Query: 123 RASGFSIAGLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARA 182 RASG++I GL G P+Y RE+++LA++WL++ L E AD AG+LPYGAQRRLEIARA Sbjct: 125 RASGYTILGLFGFPAYREASRESIELARHWLEKASLTERADDPAGDLPYGAQRRLEIARA 184 Query: 183 MCTEPVMLCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVL 242 MCT P +LCLDEPAAGLNPRES L LL IR + +LLIEHDMSVVM ISDHVVVL Sbjct: 185 MCTGPELLCLDEPAAGLNPRESLALNALLQEIRRDTGTSILLIEHDMSVVMEISDHVVVL 244 Query: 243 DYGRKISDGDPAFVKNDPAVIRAYLGEEEDE 273 +YG+KISDG+P FVKNDP VI AYLG E++E Sbjct: 245 EYGQKISDGNPDFVKNDPRVIAAYLGVEDEE 275 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: 279 Number of extensions: 2 Number of successful extensions: 1 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: 295 Length adjustment: 26 Effective length of query: 268 Effective length of database: 269 Effective search space: 72092 Effective search space used: 72092 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