Align methylmuconolactone isomerase monomer (EC 5.3.3.4) (characterized)
to candidate WP_083491884.1 ABB28_RS17645 EthD family reductase
Query= metacyc::MONOMER-14656 (91 letters) >NCBI__GCF_001431535.1:WP_083491884.1 Length = 219 Score = 68.2 bits (165), Expect = 5e-17 Identities = 33/88 (37%), Positives = 52/88 (59%) Query: 1 MLYCVQMEVNIPDSLPADRAEAIKTAERARAIEIQKAGKWPHLWRVAGRYANISVFDVDS 60 M++ + + V ++ DR + T E A A E AG+ H+WR + N S+++VD Sbjct: 1 MIFLLNIVVRFDATVDQDRRLDLLTKEHAIAKEHMAAGRLRHIWRTPAQQGNWSIWEVDH 60 Query: 61 HDELHELLSSLPLFPYMNIQVTPLARHP 88 ELH+++SSLPL+P+M + V LA HP Sbjct: 61 PTELHDIVSSLPLYPWMTLSVHALADHP 88 Lambda K H 0.321 0.134 0.411 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: 37 Number of extensions: 3 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: 91 Length of database: 219 Length adjustment: 15 Effective length of query: 76 Effective length of database: 204 Effective search space: 15504 Effective search space used: 15504 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 42 (20.8 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