Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate 5210215 Shew_2658 ABC transporter-related protein (RefSeq)
Query= TCDB::G3LHY8 (358 letters) >FitnessBrowser__PV4:5210215 Length = 227 Score = 113 bits (283), Expect = 4e-30 Identities = 62/179 (34%), Positives = 100/179 (55%), Gaps = 8/179 (4%) Query: 21 DLVLERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHFDGTDVTGMPVQ------KRN 74 DL + +G ++GP+ +GKT+L+ ++ G+D P+ G++ DG D+T + Q + + Sbjct: 27 DLTIAQGEFVAIMGPSGSGKTTLLNMIGGIDSPSSGAVFIDGEDITHLSEQALIAFRRDH 86 Query: 75 VAMVYQQFINYPALTVYNNIASPMRISG-KDAATIDREVRKAAELLKLTPYLDRTPLNLS 133 V ++Q + P LT N+ M++ G +A DR + A++ L D+ P LS Sbjct: 87 VGFIFQDYSLLPVLTALENVEFVMQLQGHSEAECRDRAMALLAQV-GLAAQQDKIPAKLS 145 Query: 134 GGQQQRTALARALVKNASLVLMDEPLANLDYKLREELREELPKIFAQSGAIFVYATTEP 192 GGQQQR A+ARAL V+ DEP ANLD K EL + + + Q G F+++T +P Sbjct: 146 GGQQQRVAVARALAPRPRFVMADEPTANLDAKSTAELLDIMQSLNEQEGTTFIFSTHDP 204 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: 189 Number of extensions: 9 Number of successful extensions: 2 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: 227 Length adjustment: 26 Effective length of query: 332 Effective length of database: 201 Effective search space: 66732 Effective search space used: 66732 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 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