Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate WP_011386482.1 AMB_RS20905 enoyl-CoA hydratase/carnithine racemase
Query= BRENDA::Q5SLK3 (254 letters) >NCBI__GCF_000009985.1:WP_011386482.1 Length = 254 Score = 147 bits (370), Expect = 3e-40 Identities = 94/252 (37%), Positives = 140/252 (55%), Gaps = 6/252 (2%) Query: 1 MVLKERQDGVLVLTLNRPEKLNAITGELLDALYAALKEGEEDREVRALLLTGAGRAFSAG 60 +VL + GV V+ +NRP+K NA+ GE+ AL A +GE D +V L+ G+ FSAG Sbjct: 4 LVLSHVEGGVQVVRMNRPDKKNALIGEMYAALAEAFAKGEADDDVNVFLILGSQTDFSAG 63 Query: 61 QDLTEFGDRKPDYEAHLRRY-NRVVEALSGLEKPLVVAVNGVAAGAGMSLALWGDLRLAA 119 DL +F +EA +R + A++G KP+V AV G A G G +L DL AA Sbjct: 64 NDLPDF----LTWEALSGSVADRFIRAVAGARKPVVAAVRGAAIGIGSTLLPHCDLVYAA 119 Query: 120 VGASFTTAFVRIGLVPDSGLSFLLPRLVGLAKAQELLLLSPRLSAEEALALGLVHRVVPA 179 G F F+ +G+VP++G S +P L G +A E+L+L + A A+GL++ VVP Sbjct: 120 PGTRFHMPFINLGIVPEAGSSQTMPALAGHRRAAEMLMLGEPFGVDTAEAVGLINGVVPG 179 Query: 180 EKLMEEALSLAKELAQGPTRAYALTKKLLLETYRLSLTEALALEAVLQGQAGQTQDHEEG 239 E L E A++ A++LA P R+ + K L++T + + L EA + + + E Sbjct: 180 EDLEETAMAAARKLAAKP-RSILVQIKALMKTPAEPIMDRLTREAAVFDTCLKGEALNEA 238 Query: 240 VRAFREKRPPRF 251 V AF+EKR P F Sbjct: 239 VSAFKEKRAPDF 250 Lambda K H 0.318 0.135 0.371 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: 145 Number of extensions: 5 Number of successful extensions: 3 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: 254 Length of database: 254 Length adjustment: 24 Effective length of query: 230 Effective length of database: 230 Effective search space: 52900 Effective search space used: 52900 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 17 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