Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate H281DRAFT_03491 H281DRAFT_03491 short chain enoyl-CoA hydratase (EC 4.2.1.17)/Enoyl-CoA hydratase (EC 4.2.1.17)
Query= BRENDA::Q5SLK3 (254 letters) >FitnessBrowser__Burk376:H281DRAFT_03491 Length = 266 Score = 179 bits (454), Expect = 5e-50 Identities = 106/261 (40%), Positives = 148/261 (56%), Gaps = 9/261 (3%) Query: 2 VLKERQDGVLVLTLNRPEKLNAITG-ELLDALYAALKEGEEDREVRALLLTGAGRAFSAG 60 VL E GV +TLNRPE NA+T E++DAL +L+ + D VRA++LTGAG AFS+G Sbjct: 5 VLYELDGGVATITLNRPETRNALTEMEVVDALVESLERAQADLNVRAIVLTGAGPAFSSG 64 Query: 61 QDLTEFGDRKPDY--------EAHLRRYNRVVEALSGLEKPLVVAVNGVAAGAGMSLALW 112 ++ D + E + R R+ A L+ P + AVNG A GAG LAL Sbjct: 65 GNIKHMRDEVGTFGGNSAQIRENYRRGIQRIPRAFHELDLPCIAAVNGPAHGAGCDLALM 124 Query: 113 GDLRLAAVGASFTTAFVRIGLVPDSGLSFLLPRLVGLAKAQELLLLSPRLSAEEALALGL 172 D+R+AA A F +F +IG++P G ++LLPR VGL++A E++ + A+ AL GL Sbjct: 125 CDIRIAAHSALFAESFAKIGIIPGDGGAWLLPRAVGLSRAAEMIFTGTPIDAQCALDWGL 184 Query: 173 VHRVVPAEKLMEEALSLAKELAQGPTRAYALTKKLLLETYRLSLTEALALEAVLQGQAGQ 232 V RVVP +L+ A LA +A P ++K+L+ E R+ L L L A QG + Sbjct: 185 VSRVVPDAELLSTARELAARIASNPPNVLRMSKRLIREGQRMDLPSLLELSAAFQGIVHR 244 Query: 233 TQDHEEGVRAFREKRPPRFQG 253 T DH E + A EKR P + G Sbjct: 245 TADHREALAATFEKRTPNYTG 265 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: 160 Number of extensions: 12 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: 266 Length adjustment: 24 Effective length of query: 230 Effective length of database: 242 Effective search space: 55660 Effective search space used: 55660 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