Align BadI (characterized)
to candidate WP_011423940.1 RHE_RS02885 enoyl-CoA hydratase/isomerase family protein
Query= metacyc::MONOMER-892 (260 letters) >NCBI__GCF_000092045.1:WP_011423940.1 Length = 350 Score = 62.0 bits (149), Expect = 2e-14 Identities = 47/158 (29%), Positives = 70/158 (44%), Gaps = 4/158 (2%) Query: 1 MQFEDLIYEIRNGVAWIIINRPDKMNAFRGTTCDELIKALYKAGYDKDVGAIVLAGAGDR 60 MQ ++I E R I +NRP +N+ + +AL D +V +V G G+R Sbjct: 1 MQDSEVIIERRGTAGIIRLNRPRALNSLTLAMIRTITEALDGFARDAEVATVVATGEGER 60 Query: 61 AFCTGGD-QSTHDGNYDGRGTVGLPMEE---LHTAIRDVPKPVIARVQGYAIGGGNVLAT 116 FC GGD ++ H+ G G G E L+ I PKP +A + G +GGG L++ Sbjct: 61 GFCAGGDIRALHESARAGDGLAGTFWREEFRLNHMIAVYPKPYVALMDGITMGGGVGLSS 120 Query: 117 ICDLTICSEKAIFGQVGPKMGSVDPGYGTAFLARVVGE 154 I +E+ +G V T L + GE Sbjct: 121 HGRHRIVTERTRLAMPETGIGYVPDVGATWLLPKAPGE 158 Lambda K H 0.319 0.138 0.418 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: 191 Number of extensions: 8 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: 260 Length of database: 350 Length adjustment: 27 Effective length of query: 233 Effective length of database: 323 Effective search space: 75259 Effective search space used: 75259 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 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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