Align required for pyruvate transport, with AZOBR_RS02940 (characterized)
to candidate Dsui_0289 Dsui_0289 putative membrane protein
Query= reanno::azobra:AZOBR_RS02935 (100 letters) >FitnessBrowser__PS:Dsui_0289 Length = 105 Score = 99.8 bits (247), Expect = 8e-27 Identities = 49/98 (50%), Positives = 66/98 (67%), Gaps = 1/98 (1%) Query: 2 KENAQRILANPKFQELVQKRSAFAWTLSIAMLVIYFGFILLVAFGKGFLGTPIG-SGVTT 60 +E +RI ANPKF EL KR+ F WTL++ ML+ Y+G+I ++AF K L + SGV T Sbjct: 4 QELTKRIRANPKFHELKSKRNVFGWTLTVIMLLAYYGYIAIIAFDKALLAQKLSESGVMT 63 Query: 61 WGIPVGLFTIISAFILTGIYVHRANGEFDELNRQIMEE 98 GIPVG+ I+ +TG+YV RAN EFD L QI++E Sbjct: 64 VGIPVGVGLILFTVAITGLYVRRANSEFDALTEQIVQE 101 Lambda K H 0.326 0.142 0.424 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: 49 Number of extensions: 3 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: 100 Length of database: 105 Length adjustment: 11 Effective length of query: 89 Effective length of database: 94 Effective search space: 8366 Effective search space used: 8366 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 40 (20.0 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