Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate Ac3H11_2523 Enoyl-CoA hydratase (EC 4.2.1.17) / Delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase (EC 5.3.3.8) / 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) / 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3)
Query= BRENDA::D3RXI0 (252 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2523 Length = 699 Score = 84.0 bits (206), Expect = 8e-21 Identities = 55/156 (35%), Positives = 83/156 (53%), Gaps = 11/156 (7%) Query: 14 VARIKIANPPVNVLDMETMKEIISAIDEVEG---VDVIVFSGEGKSFSAGAEIKEHFPDK 70 VA I +ANPPVN L + T + I+ + V IV +G G +FS GA+IKE DK Sbjct: 11 VAVITMANPPVNGLGLATRQGIVDGLGRANADAAVKSIVITGAGGAFSGGADIKEFGTDK 70 Query: 71 A---PEMIRWFTQLIDKVLRCKAITVAAVKGFALGGGFELAIACDFVLASKNAKLGVPEI 127 + P ++ +I + VAA+ A+GGG ELA+ C + +A+ + +PE+ Sbjct: 71 SLQEPNLL----SVIAAIENSAKPVVAAMHSVAMGGGLELALGCHYRIAAPGCSIALPEV 126 Query: 128 TLAHYPPV-AIALLPRMIGWKNAYELILTGEAITAE 162 L P LPR+IG + A LI++GE + +E Sbjct: 127 KLGLIPGAGGTQRLPRVIGVEAALNLIVSGEPVKSE 162 Lambda K H 0.318 0.136 0.382 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: 402 Number of extensions: 23 Number of successful extensions: 4 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: 252 Length of database: 699 Length adjustment: 31 Effective length of query: 221 Effective length of database: 668 Effective search space: 147628 Effective search space used: 147628 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: 50 (23.9 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