Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate WP_086509214.1 BZY95_RS06820 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase
Query= BRENDA::P77467 (262 letters) >NCBI__GCF_002151265.1:WP_086509214.1 Length = 263 Score = 340 bits (872), Expect = 2e-98 Identities = 167/258 (64%), Positives = 201/258 (77%) Query: 5 ILSHVEKGVMTLTLNRPERLNSFNDEMHAQLAECLKQVERDDTIRCLLLTGAGRGFCAGQ 64 +L VE GV LTLNRP+ LNSFN E+H + + LK V +D ++R LLLTG+GRGFCAGQ Sbjct: 6 LLYSVEDGVARLTLNRPDSLNSFNAELHTAMRQALKAVRQDGSVRALLLTGSGRGFCAGQ 65 Query: 65 DLNDRNVDPTGPAPDLGMSVERFYNPLVRRLAKLPKPVICAVNGVAAGAGATLALGGDIV 124 DL+DRNV P PDLG S+E+ YNP++R L LP P ICAVNGVAAGAGA +AL DIV Sbjct: 66 DLSDRNVAPGAETPDLGESLEKRYNPMLRALRDLPFPTICAVNGVAAGAGANIALACDIV 125 Query: 125 IAARSAKFVMAFSKLGLIPDCGGTWLLPRVAGRARAMGLALLGNQLSAEQAHEWGMIWQV 184 +AARSA F+ AF K+GL+PD GGTW LPR+ G ARA GL +LG++LSAEQA WGMIW+V Sbjct: 126 LAARSASFIQAFCKIGLLPDSGGTWTLPRLVGMARAKGLTMLGDKLSAEQAERWGMIWKV 185 Query: 185 VDDETLADTAQQLARHLATQPTFGLGLIKQAINSAETNTLDTQLDLERDYQRLAGRSADY 244 VDDE L D A LARHLATQPT GL LIK+A++++ N+ D QLDLERD QRLAGR+ADY Sbjct: 186 VDDEALQDEALTLARHLATQPTRGLALIKRALHASADNSFDQQLDLERDLQRLAGRTADY 245 Query: 245 REGVSAFLAKRSPQFTGK 262 REGV+AF+ KR P F G+ Sbjct: 246 REGVAAFMEKRQPSFKGE 263 Lambda K H 0.321 0.136 0.403 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: 197 Number of extensions: 2 Number of successful extensions: 1 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: 262 Length of database: 263 Length adjustment: 25 Effective length of query: 237 Effective length of database: 238 Effective search space: 56406 Effective search space used: 56406 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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