Align small component of L-lactate and L-malate uptake system (characterized)
to candidate WP_009154192.1 SACMADRAFT_RS12545 DUF4212 domain-containing protein
Query= reanno::PV4:5209924 (88 letters) >NCBI__GCF_000244955.1:WP_009154192.1 Length = 103 Score = 90.9 bits (224), Expect = 3e-24 Identities = 41/76 (53%), Positives = 53/76 (69%) Query: 12 YWRENLRLVLGLLAIWAAVSFGCGILLVDVLNEIHFMGFKLGFWFAQQGAMYVFVALIFV 71 YWR NLRL L LL+IW V FG GIL V+ LN++ F G+ LGFW AQQG++Y F+ LI + Sbjct: 20 YWRRNLRLKLILLSIWFVVPFGGGILFVEQLNQVSFGGYPLGFWIAQQGSIYTFLVLILI 79 Query: 72 YVAKANALDKKYNVHE 87 Y + + LD K+ V E Sbjct: 80 YAVRMDRLDDKFGVSE 95 Lambda K H 0.329 0.143 0.455 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: 51 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: 88 Length of database: 103 Length adjustment: 10 Effective length of query: 78 Effective length of database: 93 Effective search space: 7254 Effective search space used: 7254 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: 39 (21.3 bits) S2: 39 (19.6 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