Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate WP_014449569.1 LFE_RS07230 ABC transporter ATP-binding protein
Query= TCDB::G3LHY8 (358 letters) >NCBI__GCF_000284315.1:WP_014449569.1 Length = 231 Score = 90.9 bits (224), Expect = 3e-23 Identities = 58/176 (32%), Positives = 88/176 (50%), Gaps = 10/176 (5%) Query: 24 LERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHFDGTDVTGMP------VQKRNVAM 77 L G L G + AGK++L+ L+ +DRPT G + DV+ + + R++ Sbjct: 33 LPAGVFVALTGASGAGKSTLLHLVGTIDRPTMGRVIHGDRDVSELSEYDLASFRNRHIGF 92 Query: 78 VYQQFINYPALTVYNNIASPMRISGK----DAATIDREVRKAAELLKLTPYLDRTPLNLS 133 V+Q P T N+ P I+GK + I+ R+ + + L+ L P LS Sbjct: 93 VFQFHHLLPEFTALENVLMPSWIAGKSLMEEVGVIENRARELLDRVGLSGRLSHKPSELS 152 Query: 134 GGQQQRTALARALVKNASLVLMDEPLANLDYKLREELREELPKIFAQSGAIFVYAT 189 GG+QQR A+ARALV N S++L DEP NLD E+ + L + + G + AT Sbjct: 153 GGEQQRVAIARALVMNPSILLADEPTGNLDTHTSFEVFDLLRTVNHEQGITLIMAT 208 Lambda K H 0.319 0.136 0.392 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: 215 Number of extensions: 15 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: 358 Length of database: 231 Length adjustment: 26 Effective length of query: 332 Effective length of database: 205 Effective search space: 68060 Effective search space used: 68060 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 (21.7 bits) S2: 47 (22.7 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