Align Probable enoyl-CoA hydratase; EC 4.2.1.17 (characterized)
to candidate WP_012976491.1 AZL_RS21100 3-hydroxyacyl-CoA dehydrogenase
Query= SwissProt::P94549 (258 letters) >NCBI__GCF_000010725.1:WP_012976491.1 Length = 728 Score = 139 bits (349), Expect = 2e-37 Identities = 82/194 (42%), Positives = 115/194 (59%), Gaps = 9/194 (4%) Query: 8 VDQFVAVLTIHNPPANALSSRILEELSSCLDQCETDAGVRSIIIHGEGRFFSAGADIKEF 67 +++ VAV+T+ +PP NAL+ + L + L D VR+I++ G GR F G DI EF Sbjct: 19 LNEGVAVITLDHPPVNALALALRTRLGAALHAALRDVSVRAIVLAGAGRGFCGGGDITEF 78 Query: 68 TSLKGNEDSSLLAERGQQLMERIESFPKPIIAAIHGAALGGGLELAMACHIRIAAEDAKL 127 ++ + L IE+ PKP++AA+HG ALGGGLELA+ACH R+A ++ Sbjct: 79 DLPAVCQEPTPAT-----LFSLIENSPKPVVAALHGMALGGGLELALACHARVAEARTQV 133 Query: 128 GLPELNLGIIPGFAGTQRLPRYVGTAKALELIGSGEPISGKEALDLGL---VSIGAKDEA 184 GLPE++LG++PG GTQRLPR VG AL LI G + D GL ++ G+ EA Sbjct: 134 GLPEVHLGLVPGAGGTQRLPRLVGFELALNLIVQGRTQPAQSLRDSGLFDRLTDGSPVEA 193 Query: 185 EVIEKAKALAAKFA 198 +E A ALA + A Sbjct: 194 -AVEVAMALAGELA 206 Lambda K H 0.315 0.134 0.366 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: 355 Number of extensions: 13 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: 258 Length of database: 728 Length adjustment: 32 Effective length of query: 226 Effective length of database: 696 Effective search space: 157296 Effective search space used: 157296 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: 42 (22.0 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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