Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate Dsui_0502 Dsui_0502 enoyl-CoA hydratase/carnithine racemase
Query= BRENDA::Q5SLK3 (254 letters) >FitnessBrowser__PS:Dsui_0502 Length = 263 Score = 165 bits (417), Expect = 1e-45 Identities = 108/258 (41%), Positives = 141/258 (54%), Gaps = 9/258 (3%) Query: 2 VLKERQDGVLVLTLNRPEKLNAITGELLDALYAALKEGEEDREVRALLLTGAGRAFSAGQ 61 VL +DGVL LTLNRPE LNA+ +++ L AA E D V A++L G G F AG Sbjct: 4 VLSHLEDGVLTLTLNRPEALNALNLAMIEDLRAATARAEHDEAVGAVVLRG-GEHFMAGG 62 Query: 62 DLTEF--------GDRKPDYEAHLRRYNRVVEALSGLEKPLVVAVNGVAAGAGMSLALWG 113 DL F +R+ +E + + + + KP+V +V+G AAG G+SL L Sbjct: 63 DLKWFHSQLALPPAERQALFEQTIAAVHATTLQVRRMGKPVVASVSGAAAGFGLSLMLAC 122 Query: 114 DLRLAAVGASFTTAFVRIGLVPDSGLSFLLPRLVGLAKAQELLLLSPRLSAEEALALGLV 173 DL +AA A FT A+ IGL PD G ++ LPR VG +A E+ LL R A +A GL+ Sbjct: 123 DLAVAADNAYFTLAYCHIGLSPDGGATWFLPRAVGAKRAAEIALLGDRFDAAQAREWGLI 182 Query: 174 HRVVPAEKLMEEALSLAKELAQGPTRAYALTKKLLLETYRLSLTEALALEAVLQGQAGQT 233 +RVVPA +L E+ LA+ LA GP +A A TK LL + SL E L E Sbjct: 183 NRVVPAAELEAESAKLARRLAAGPRQALARTKALLQASSGNSLPEQLFAEQGNFAACSVH 242 Query: 234 QDHEEGVRAFREKRPPRF 251 D EG+ AF EKR P F Sbjct: 243 PDFAEGLGAFLEKRKPAF 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: 146 Number of extensions: 7 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: 263 Length adjustment: 24 Effective length of query: 230 Effective length of database: 239 Effective search space: 54970 Effective search space used: 54970 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