Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate 5208024 Shew_0540 enoyl-CoA hydratase/isomerase (RefSeq)
Query= BRENDA::Q5SLK3 (254 letters) >FitnessBrowser__PV4:5208024 Length = 245 Score = 137 bits (345), Expect = 2e-37 Identities = 81/202 (40%), Positives = 119/202 (58%), Gaps = 2/202 (0%) Query: 7 QDGVLVLTLNRPEKLNAITGELLDALYAALKEGEEDREVRALLLTGAGRAFSAGQDLTEF 66 + GV ++T+NRP+K NA+ E+ L L +GE D + A LL G G F++G D+ +F Sbjct: 9 EQGVRIITINRPDKRNALNLEMYARLTEYLIQGESDNGINAFLLKGEGDCFTSGNDVADF 68 Query: 67 GDRKPDYEAHLRRYNRVVEALSGLEKPLVVAVNGVAAGAGMSLALWGDLRLAAVGASFTT 126 + H R + L L KPLV AV G A G G +L L DL A A F Sbjct: 69 LKNSDLGQNHPTV--RFLFTLLDLTKPLVAAVAGPAVGIGTTLLLHCDLVYADNTAKFQL 126 Query: 127 AFVRIGLVPDSGLSFLLPRLVGLAKAQELLLLSPRLSAEEALALGLVHRVVPAEKLMEEA 186 FV + LVP++G S LLPRLVG KA ELLLL A+ AL++GL++ ++P+++LM A Sbjct: 127 PFVNLALVPEAGASLLLPRLVGQTKASELLLLGEPFDAQSALSMGLINDLLPSDELMSHA 186 Query: 187 LSLAKELAQGPTRAYALTKKLL 208 +S + +LA+ P +A +++L+ Sbjct: 187 MSQSIKLAKKPPQALRASRRLI 208 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: 144 Number of extensions: 6 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: 245 Length adjustment: 24 Effective length of query: 230 Effective length of database: 221 Effective search space: 50830 Effective search space used: 50830 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: 46 (22.3 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