Align small component of D-alanine uptake system, with Psest_0347 (actP-like) (characterized)
to candidate WP_010629690.1 BZY95_RS03240 DUF4212 domain-containing protein
Query= reanno::psRCH2:GFF345 (87 letters) >NCBI__GCF_002151265.1:WP_010629690.1 Length = 86 Score = 135 bits (339), Expect = 1e-37 Identities = 62/87 (71%), Positives = 75/87 (86%), Gaps = 1/87 (1%) Query: 1 MADNDKENAAAYWKANVRLITWSLVVWALVSYGFGILLRPLVAGIPVGGTDLGFWFAQQG 60 MAD DK NAA YWKANVRLIT ++VWA VSYG +L RPL++GIP+GGTDLGFWFAQQG Sbjct: 1 MAD-DKINAAEYWKANVRLITGCMIVWAFVSYGCAMLFRPLLSGIPIGGTDLGFWFAQQG 59 Query: 61 SIITFIAIIFHYAWRLNKLDKEFGVEE 87 SI+TFI +IF YAW++NKLD++FG+ E Sbjct: 60 SILTFIGLIFFYAWKMNKLDQKFGLGE 86 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: 74 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: 86 Length adjustment: 9 Effective length of query: 78 Effective length of database: 77 Effective search space: 6006 Effective search space used: 6006 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 24 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