Align small component of D-alanine uptake system, with Psest_0347 (actP-like) (characterized)
to candidate 201984 SO2858 conserved hypothetical protein (NCBI ptt file)
Query= reanno::psRCH2:GFF345 (87 letters) >FitnessBrowser__MR1:201984 Length = 88 Score = 87.0 bits (214), Expect = 4e-23 Identities = 42/87 (48%), Positives = 57/87 (65%) Query: 1 MADNDKENAAAYWKANVRLITWSLVVWALVSYGFGILLRPLVAGIPVGGTDLGFWFAQQG 60 MA + + A YW N+RL+ L +WA VS+G GILL ++ I G LGFWFAQQG Sbjct: 1 MAFENNDKAKGYWNENLRLVLSLLAIWAAVSFGCGILLVDVLNEIHFMGFKLGFWFAQQG 60 Query: 61 SIITFIAIIFHYAWRLNKLDKEFGVEE 87 S+ F+A+IF YA + N LDK++ V+E Sbjct: 61 SMYVFVALIFVYAAKANALDKKYNVQE 87 Lambda K H 0.326 0.142 0.469 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: 52 Number of extensions: 1 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: 87 Length of database: 88 Length adjustment: 9 Effective length of query: 78 Effective length of database: 79 Effective search space: 6162 Effective search space used: 6162 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: 38 (20.7 bits) S2: 38 (19.2 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