Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate WP_011779227.1 MVAN_RS10025 enoyl-CoA hydratase
Query= BRENDA::Q5SLK3 (254 letters) >NCBI__GCF_000015305.1:WP_011779227.1 Length = 294 Score = 165 bits (418), Expect = 9e-46 Identities = 106/261 (40%), Positives = 150/261 (57%), Gaps = 18/261 (6%) Query: 9 GVLVLTLNRPEKLNAITGELLDALYAALKEGEEDREVRALLLTGAGRAFSAGQDLTEF-- 66 GV VLTLNRPE++N+ G L A Y + E D VR ++LTG GRAF AG D+ + Sbjct: 26 GVAVLTLNRPERMNSWGGGLAQAFYRCIDRAEADPHVRVIVLTGNGRAFCAGADMGDLDS 85 Query: 67 ----GD----RKPDYEAHLRRYN-------RVVEALSGLEKPLVVAVNGVAAGAGMSLAL 111 GD + D E+ L + R L+ L KPL+ A+NG AG G++ AL Sbjct: 86 ISAAGDTGRGERSDGESGLADTDVSQLVGERHPHFLTQLRKPLIAAINGACAGIGLTHAL 145 Query: 112 WGDLRLAAVGASFTTAFVRIGLVPDSGLSFLLPRLVGLAKAQELLLLSPRLSAEEALALG 171 D+R AA GA FTTAF R GL+ + G+S++LPR+VG + AQ+LLL AEEA LG Sbjct: 146 MCDVRFAAAGAKFTTAFARRGLIAEYGISWILPRIVGWSAAQDLLLSGRTFYAEEANELG 205 Query: 172 LVHRVVPAEKLMEEALSLAKELAQG-PTRAYALTKKLLLETYRLSLTEALALEAVLQGQA 230 LV++VV ++LM L+ A+++A+ + A+ K+ + +L++A A L ++ Sbjct: 206 LVNQVVAPDELMAHTLAYAEDMARNCAPSSLAVIKRQIYRDALRNLSDASADAEKLMHES 265 Query: 231 GQTQDHEEGVRAFREKRPPRF 251 Q D EG+ AF EKR P F Sbjct: 266 MQRPDFIEGITAFFEKRQPSF 286 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: 196 Number of extensions: 14 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: 294 Length adjustment: 25 Effective length of query: 229 Effective length of database: 269 Effective search space: 61601 Effective search space used: 61601 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