Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate WP_011320063.1 AVA_RS16900 enoyl-CoA hydratase/isomerase family protein
Query= BRENDA::Q5SLK3 (254 letters) >NCBI__GCF_000204075.1:WP_011320063.1 Length = 253 Score = 92.0 bits (227), Expect = 1e-23 Identities = 66/225 (29%), Positives = 109/225 (48%), Gaps = 4/225 (1%) Query: 7 QDGVLVLTLNRPEKLNAITGELLDALYAALKEGEEDREVRALLLTGAGRAFSAGQDLTEF 66 ++G+L + ++ TG+ A + DR+ R ++LTG G A+ A D Sbjct: 21 ENGILEVRMHTNNGSLVFTGKTHREFPDAFYDISRDRDNRVVILTGTGDAWMAEIDFASL 80 Query: 67 GD--RKPDYEAHLRRYNRVVEALSGLEKPLVVAVNGVAAGAGMSLALWGDLRLAAVGASF 124 GD +++ +V++ L +E P++ AVNG AA L D+ LA+ A F Sbjct: 81 GDVTNPREWDKTYWEGKKVLQNLLDIEVPVISAVNG-AALLHSEYILTTDIILASENAVF 139 Query: 125 TTA-FVRIGLVPDSGLSFLLPRLVGLAKAQELLLLSPRLSAEEALALGLVHRVVPAEKLM 183 G+VP G+ L P +GL + + LL +L+A++A L +VH V+P KLM Sbjct: 140 QDMPHFNAGIVPGDGVHILWPLALGLYRGRYFLLTQEKLTAQQAYELNVVHEVLPQSKLM 199 Query: 184 EEALSLAKELAQGPTRAYALTKKLLLETYRLSLTEALALEAVLQG 228 E A +A+ LA+ PT T+ L + + + E + L+G Sbjct: 200 ERAWEIARTLAKQPTLNLRYTRVALTQRLKRLVNEGIGYGLALEG 244 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: 141 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: 254 Length of database: 253 Length adjustment: 24 Effective length of query: 230 Effective length of database: 229 Effective search space: 52670 Effective search space used: 52670 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 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