Align small component of L-lactate and L-malate uptake system (characterized)
to candidate WP_052668290.1 NITAL_RS21000 DUF4212 domain-containing protein
Query= reanno::PV4:5209924 (88 letters) >NCBI__GCF_000969705.1:WP_052668290.1 Length = 93 Score = 82.4 bits (202), Expect = 1e-21 Identities = 39/79 (49%), Positives = 53/79 (67%), Gaps = 1/79 (1%) Query: 10 EGYWRENLRLVLGLLAIWAAVSFGCGILLVDVLNEI-HFMGFKLGFWFAQQGAMYVFVAL 68 + YWR N+RL+ LLA+W AVSFG GIL V LN++ +GFWFAQQG++ FV L Sbjct: 7 KAYWRRNVRLIGALLAVWFAVSFGAGILFVQPLNDLGTIFNVPIGFWFAQQGSIITFVVL 66 Query: 69 IFVYVAKANALDKKYNVHE 87 I +YV + + LD ++ V E Sbjct: 67 IGIYVLRMDRLDDEFGVAE 85 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: 50 Number of extensions: 2 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: 88 Length of database: 93 Length adjustment: 9 Effective length of query: 79 Effective length of database: 84 Effective search space: 6636 Effective search space used: 6636 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