Align 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate 5210423 Shew_2864 3-hydroxyacyl-CoA dehydrogenase, NAD-binding (RefSeq)
Query= metacyc::MONOMER-15953 (257 letters) >FitnessBrowser__PV4:5210423 Length = 708 Score = 117 bits (294), Expect = 5e-31 Identities = 70/164 (42%), Positives = 94/164 (57%), Gaps = 3/164 (1%) Query: 16 LITLQRPEALNALNTQLLDELAAELALAEQDAETRAVVLTGSRKAFAAGADIKEMAERDL 75 +I L +P +N+L L L A+L AE D A+VL S K F GADI E + D Sbjct: 15 VIILNQPP-VNSLGLALRTHLLADLKRAEADESVDAIVLASSGKLFCGGADISEFSSDDA 73 Query: 76 VGILEDPRVAHWQRIAAFSKPLIAAVNGFCLGGGCELAMHADILIAGEDARFGQPEINLG 135 + P+V + A K ++AAVNG LGGGCEL + D IA A+ G PE+NLG Sbjct: 74 LAEPNLPQVC--DALEASPKLVVAAVNGLALGGGCELTLACDYRIALPAAKLGLPEVNLG 131 Query: 136 IMPGAGGTQRLLRAVGKSLAMQMVLSGQAIDARHAQRAGLVSEV 179 I+PGAGGTQRL R G LA++M+ SG+ + A AG++ + Sbjct: 132 ILPGAGGTQRLPRIGGVQLALEMITSGRPLGAAAMLDAGVIDNL 175 Lambda K H 0.320 0.134 0.374 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: 389 Number of extensions: 20 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: 257 Length of database: 708 Length adjustment: 32 Effective length of query: 225 Effective length of database: 676 Effective search space: 152100 Effective search space used: 152100 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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