Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate CCNA_02658 CCNA_02658 3-hydroxybutyryl-CoA dehydratase
Query= BRENDA::Q5SLK3 (254 letters) >FitnessBrowser__Caulo:CCNA_02658 Length = 265 Score = 176 bits (445), Expect = 6e-49 Identities = 100/263 (38%), Positives = 155/263 (58%), Gaps = 11/263 (4%) Query: 1 MVLKERQDGVLVLTLNRPEKLNAI--TGELLDALYAALKEGEEDREVRALLLTGAGRAFS 58 ++L E++ + +LTLNRP+ +NA+ G+ D + AA + +D+++R ++LTGAG+AFS Sbjct: 3 LILTEKRGHIAILTLNRPDAMNALGAPGDG-DQVAAACEAINDDQDIRCVILTGAGKAFS 61 Query: 59 AGQDLTEFGDRKPDY--------EAHLRRYNRVVEALSGLEKPLVVAVNGVAAGAGMSLA 110 AG D+ R+ + + + + +R+V A+ GLE P + AVNG A G G +A Sbjct: 62 AGGDVKAMKAREGAFGGNGVKVRDGYRKNIHRIVRAIYGLEVPSIAAVNGAAIGLGCDVA 121 Query: 111 LWGDLRLAAVGASFTTAFVRIGLVPDSGLSFLLPRLVGLAKAQELLLLSPRLSAEEALAL 170 D+R+AA A F F+++GL+P G ++L+PR +G+++A ELL + A +A Sbjct: 122 CMTDIRIAADTARFGVTFLKLGLIPGDGGAWLMPRTIGMSRAAELLFTGDVIDAAKAAEW 181 Query: 171 GLVHRVVPAEKLMEEALSLAKELAQGPTRAYALTKKLLLETYRLSLTEALALEAVLQGQA 230 GL+ + VPA LM EAL+LA+ +AQ P A + K LL S + + A Q A Sbjct: 182 GLISKAVPAGDLMGEALALAERIAQQPPHALRMAKSLLKHGQTASYDTLMEMSAAAQAIA 241 Query: 231 GQTQDHEEGVRAFREKRPPRFQG 253 T+DH EGV A EKR P F+G Sbjct: 242 HHTEDHMEGVDAILEKRSPVFKG 264 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: 178 Number of extensions: 10 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: 265 Length adjustment: 24 Effective length of query: 230 Effective length of database: 241 Effective search space: 55430 Effective search space used: 55430 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