Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate WP_005816058.1 DHAF_RS14270 crotonase
Query= BRENDA::Q5SLK3 (254 letters) >NCBI__GCF_000021925.1:WP_005816058.1 Length = 260 Score = 147 bits (370), Expect = 3e-40 Identities = 87/255 (34%), Positives = 144/255 (56%), Gaps = 2/255 (0%) Query: 2 VLKERQDGVLVLTLNRPEKLNAITGELLDALYAALKEGEEDREVRALLLTGAG-RAFSAG 60 +L + Q+ + ++T++RP+ LNA+ L L +++ + VR ++LTG+G +AF AG Sbjct: 6 ILVDYQEQIALVTIDRPKALNALNTLTLQELSQVVEDLANNSSVRVVILTGSGEKAFVAG 65 Query: 61 QDLTEFGDRKP-DYEAHLRRYNRVVEALSGLEKPLVVAVNGVAAGAGMSLALWGDLRLAA 119 D+ E + P + + +++ + L +P++ A+NG A G G+ LA+ D+RLA+ Sbjct: 66 ADIAEMNMKTPLEARTFSQLGQKLMNQIESLPQPVIAAINGFALGGGLELAMACDIRLAS 125 Query: 120 VGASFTTAFVRIGLVPDSGLSFLLPRLVGLAKAQELLLLSPRLSAEEALALGLVHRVVPA 179 A F V +G+ G + LPRLVG +A E+LL + A+EA +GLV+RV P Sbjct: 126 EKARFGQPEVNLGIPAGFGGTQRLPRLVGSGRASEILLTAELFDAQEAFRMGLVNRVYPK 185 Query: 180 EKLMEEALSLAKELAQGPTRAYALTKKLLLETYRLSLTEALALEAVLQGQAGQTQDHEEG 239 E+L E+AL++A+++A A LTK + + + L EA + A T+D + G Sbjct: 186 EELQEQALAMARKIAAKAPVAIQLTKSAIYKGANMDLISGQDYEAEVFALAFHTEDRKAG 245 Query: 240 VRAFREKRPPRFQGR 254 +AF EK FQGR Sbjct: 246 FKAFLEKSQTEFQGR 260 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: 137 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: 260 Length adjustment: 24 Effective length of query: 230 Effective length of database: 236 Effective search space: 54280 Effective search space used: 54280 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