Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate CA265_RS04345 CA265_RS04345 lipoprotein-releasing system ATP-binding protein LolD
Query= TCDB::G3LHY8 (358 letters) >FitnessBrowser__Pedo557:CA265_RS04345 Length = 216 Score = 86.3 bits (212), Expect = 7e-22 Identities = 50/169 (29%), Positives = 84/169 (49%), Gaps = 6/169 (3%) Query: 1 MLELRNAAKMVGADYHIYPTDLVLERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHF 60 ML+ K G + + +++G + ++GP+ AGK++L+ ++ LD+P GS+ Sbjct: 1 MLKATGIRKSYGNLQILKGVNFEVQKGEIVSIIGPSGAGKSTLLHILGTLDKPDDGSVQL 60 Query: 61 DGTDVTGM------PVQKRNVAMVYQQFINYPALTVYNNIASPMRISGKDAATIDREVRK 114 GT + + + +N+ V+Q P + NI P I+ + + + Sbjct: 61 KGTVINKLNGDLLSTFRNQNIGFVFQFHHLLPEFSAIENICIPAFIAKTNKKQAETRAFE 120 Query: 115 AAELLKLTPYLDRTPLNLSGGQQQRTALARALVKNASLVLMDEPLANLD 163 +L L P LSGG+QQR A+ARAL+ N S++L DEP NLD Sbjct: 121 LLDLFGLKDRAQHKPNQLSGGEQQRVAIARALINNPSIILADEPSGNLD 169 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: 160 Number of extensions: 12 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: 216 Length adjustment: 25 Effective length of query: 333 Effective length of database: 191 Effective search space: 63603 Effective search space used: 63603 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