Align small component of D-alanine uptake system, with Psest_0347 (actP-like) (characterized)
to candidate Echvi_1266 Echvi_1266 putative solute:sodium symporter small subunit
Query= reanno::psRCH2:GFF345 (87 letters) >FitnessBrowser__Cola:Echvi_1266 Length = 85 Score = 89.7 bits (221), Expect = 6e-24 Identities = 41/84 (48%), Positives = 57/84 (67%) Query: 4 NDKENAAAYWKANVRLITWSLVVWALVSYGFGILLRPLVAGIPVGGTDLGFWFAQQGSII 63 + +E AYW+ NV+++ L VW VS+G GILL ++ + +GG LGFWFAQQG+I Sbjct: 2 SQQEKMKAYWRRNVKILLSLLAVWFTVSFGCGILLVDVLNKVQIGGFKLGFWFAQQGAIY 61 Query: 64 TFIAIIFHYAWRLNKLDKEFGVEE 87 F+ +IF Y + LNKLD+EF V E Sbjct: 62 VFVILIFVYVFLLNKLDREFDVHE 85 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: 47 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: 85 Length adjustment: 9 Effective length of query: 78 Effective length of database: 76 Effective search space: 5928 Effective search space used: 5928 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