Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate BWI76_RS01365 BWI76_RS01365 multifunctional fatty acid oxidation complex subunit alpha
Query= BRENDA::Q5SLK3 (254 letters) >FitnessBrowser__Koxy:BWI76_RS01365 Length = 729 Score = 101 bits (252), Expect = 4e-26 Identities = 73/237 (30%), Positives = 113/237 (47%), Gaps = 5/237 (2%) Query: 1 MVLKERQDGVLVLTLNRPEKLNAITGELLDALYAALKEGEEDREVRALLLTGAGRAFSAG 60 + L R+DG+ L + P +N + + +L AL E+ ++++ LLL AF G Sbjct: 8 LYLDWREDGIAELVFDAPGSVNKLDTATVASLGEALDVLEKQKDLKGLLLRSEKAAFIVG 67 Query: 61 QDLTEFGDRKPDYEAHLRRY----NRVVEALSGLEKPLVVAVNGVAAGAGMSLALWGDLR 116 D+TEF E L ++ N V L L P + AVNG A G G L D R Sbjct: 68 ADITEFLSLFLVPEEQLSQWLHFANSVFNRLEDLPVPTISAVNGYALGGGCECVLATDYR 127 Query: 117 LAAVGASFTTAFVRIGLVPDSGLSFLLPRLVGLAKAQELLLLSPRLSAEEALALGLVHRV 176 LA ++G++P G S +PR++G A E++ L AE+AL +GLV V Sbjct: 128 LATPDLRIGLPETKLGIMPGFGGSVRMPRMLGADSALEIIAAGKDLGAEQALKIGLVDGV 187 Query: 177 VPAEKLMEEALSLAKELAQGPTRAYALTKKLLLETYRLSLTEALALEAVLQGQAGQT 233 V EKL++ A+++ ++ G + ++ LE LS EA + +G QT Sbjct: 188 VKHEKLIDGAVAILRQAINGDL-DWKAKRQPKLEPLHLSKIEAAMSFTIAKGMVAQT 243 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: 339 Number of extensions: 9 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: 729 Length adjustment: 32 Effective length of query: 222 Effective length of database: 697 Effective search space: 154734 Effective search space used: 154734 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: 51 (24.3 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