Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate 3608199 Dshi_1604 Enoyl-CoA hydratase/isomerase (RefSeq)
Query= BRENDA::Q5SLK3 (254 letters) >FitnessBrowser__Dino:3608199 Length = 264 Score = 142 bits (358), Expect = 7e-39 Identities = 93/261 (35%), Positives = 137/261 (52%), Gaps = 14/261 (5%) Query: 1 MVLKERQDGVLVLTLNRPEKLNAITGELLDALYAALKEGEEDREVRALLLTGAGRAFSAG 60 ++L+ DG+ LTLN P+ LN ++ +L AL A + EDR R ++L GAGRAF AG Sbjct: 5 LLLRSDADGIATLTLNAPQSLNVLSDAMLAALQAQIDTLAEDRTTRVVVLRGAGRAFCAG 64 Query: 61 QDLTEFGDRKPDYEAHLRRYN-------RVVEALSGLEKPLVVAVNGVAAGAGMSLALWG 113 DL E + + + R++ L L +P++ V+G+A AG L Sbjct: 65 HDLKEMTAARQSEDGGAAAFKDLFDRCARMMMGLQALPQPVIAQVHGIATAAGCQLVATA 124 Query: 114 DLRLAAVGASFTTAFVRIGL---VPDSGLSFLLPRLVGLAKAQELLLLSPRLSAEEALAL 170 D+ +AA GA F V IGL P LS +PR +A ELL + A++A AL Sbjct: 125 DMAVAAEGARFGVNGVNIGLFCSTPMVALSRNIPR----KQAFELLTTGEMIEAQKAQAL 180 Query: 171 GLVHRVVPAEKLMEEALSLAKELAQGPTRAYALTKKLLLETYRLSLTEALALEAVLQGQA 230 GLV+RVVP E L E +LA ++A+ A+ K+ E ++SL +A A + + Sbjct: 181 GLVNRVVPTEDLEAETNALATKVAEKRGAVVAIGKRAFYEQSQMSLADAYAFTGNVMVKN 240 Query: 231 GQTQDHEEGVRAFREKRPPRF 251 +D EEG+ AF +KRPP + Sbjct: 241 MALRDTEEGIAAFLDKRPPNW 261 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: 143 Number of extensions: 8 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: 264 Length adjustment: 24 Effective length of query: 230 Effective length of database: 240 Effective search space: 55200 Effective search space used: 55200 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