Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate WP_058929110.1 AU252_RS00885 enoyl-CoA hydratase/isomerase family protein
Query= BRENDA::Q5SLK3 (254 letters) >NCBI__GCF_001484605.1:WP_058929110.1 Length = 258 Score = 138 bits (348), Expect = 1e-37 Identities = 82/249 (32%), Positives = 137/249 (55%), Gaps = 2/249 (0%) Query: 8 DGVLVLTLNRPEKLNAITGELLDALYAALKEGEEDREVRALLLTGAG-RAFSAGQDLTEF 66 DG+ + +NRPE++NA E L +D +R ++TGAG +AFSAG DL + Sbjct: 10 DGIATIVMNRPERMNAFDAEAYKQLSEVWIRVRDDHAIRVAVITGAGEKAFSAGADLKDL 69 Query: 67 GDRKPD-YEAHLRRYNRVVEALSGLEKPLVVAVNGVAAGAGMSLALWGDLRLAAVGASFT 125 P+ ++ L + ++++ + KP++ AVNG G G+++ D+R+A A+F Sbjct: 70 VPAPPELHDLWLTQKDQLLNRGLEIWKPVIAAVNGYCLGGGLTMLFATDIRIACHDATFG 129 Query: 126 TAFVRIGLVPDSGLSFLLPRLVGLAKAQELLLLSPRLSAEEALALGLVHRVVPAEKLMEE 185 + V+ G++P +G + + V +A E+LL + A +AL GL++ VV +LME Sbjct: 130 LSEVKRGVLPGNGATQRVIDNVSYPRAMEMLLTGEPIDASKALEWGLINEVVDRARLMER 189 Query: 186 ALSLAKELAQGPTRAYALTKKLLLETYRLSLTEALALEAVLQGQAGQTQDHEEGVRAFRE 245 +L +A+++A A TK+L + + + L L LE VLQ ++D EG +AF E Sbjct: 190 SLEIARQIAANAPLAVQATKELAVRSRSMDLASGLRLEQVLQRILQTSEDAVEGPKAFAE 249 Query: 246 KRPPRFQGR 254 +RP F GR Sbjct: 250 RRPAVFGGR 258 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: 143 Number of extensions: 8 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: 258 Length adjustment: 24 Effective length of query: 230 Effective length of database: 234 Effective search space: 53820 Effective search space used: 53820 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 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