Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate BPHYT_RS03235 BPHYT_RS03235 enoyl-CoA hydratase
Query= BRENDA::Q5SLK3 (254 letters) >FitnessBrowser__BFirm:BPHYT_RS03235 Length = 256 Score = 155 bits (393), Expect = 6e-43 Identities = 100/251 (39%), Positives = 137/251 (54%), Gaps = 2/251 (0%) Query: 2 VLKERQDGVLVLTLNRPEKLNAITGELLDALYAALKEGEEDREVRALLLTGAGRAFSAGQ 61 +L ER DGVL + NRP+K NAIT + + AL E + D VRA+L+ G+ FSAG Sbjct: 5 ILVERADGVLTIAFNRPDKKNAITAAMYQTMADALVEAQGDAAVRAILIRGSAGIFSAGN 64 Query: 62 DLTEFGDRKPDYEAHLRRYNRVVEALSGLEKPLVVAVNGVAAGAGMSLALWGDLRLAAVG 121 DL +F P E H + + + A+S EKP+V +V G A G G +L L DL AA Sbjct: 65 DLEDFMKTPPMGE-HAPVF-QFLRAISSAEKPVVASVAGAAVGIGTTLLLHCDLVYAADT 122 Query: 122 ASFTTAFVRIGLVPDSGLSFLLPRLVGLAKAQELLLLSPRLSAEEALALGLVHRVVPAEK 181 ASF+ F ++GL P++ S LLPR G A E LLL A EA +G V+RV+PA + Sbjct: 123 ASFSLPFTQLGLCPEAASSLLLPRAAGYQAAAEKLLLGEAFDAAEAQRMGFVNRVLPASE 182 Query: 182 LMEEALSLAKELAQGPTRAYALTKKLLLETYRLSLTEALALEAVLQGQAGQTQDHEEGVR 241 + A S A +LA P + +TK L+ L ++ EAV G+ + E + Sbjct: 183 VDAFAASQAAKLAALPASSLRVTKSLMKRASHQELQTQMSEEAVHFGKMLLAPEAREAFK 242 Query: 242 AFREKRPPRFQ 252 AF EKR P F+ Sbjct: 243 AFFEKRKPDFR 253 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: 145 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: 256 Length adjustment: 24 Effective length of query: 230 Effective length of database: 232 Effective search space: 53360 Effective search space used: 53360 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 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