Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate 3610445 Dshi_3826 3-hydroxyacyl-CoA dehydrogenase NAD-binding (RefSeq)
Query= BRENDA::O87873 (258 letters) >FitnessBrowser__Dino:3610445 Length = 673 Score = 70.9 bits (172), Expect = 7e-17 Identities = 50/178 (28%), Positives = 78/178 (43%), Gaps = 7/178 (3%) Query: 12 LERDGSLLRLRLARPKANIVDAAMIAAMRQALGEHLQAPALRAVLLDAEGPHFSFGASVD 71 ++ D L + + P N A+ + A+ + R +L G F G + Sbjct: 9 VDTDTGLAWVTVDNPPVNATSTAVRQGLLDAV---TRVQGARLAILRCAGRTFIAGGDMR 65 Query: 72 EHMPDQCAQMLKSLHGLVREMLDSPVPILVALRGQCLGGGLEVAAAGNLLFAAPDAKFGQ 131 E L +V + S P + ++G LGGGLE+A AAP +FG Sbjct: 66 EF---DAPPQPPDLPDVVDAIEASATPFVAVMQGTVLGGGLEIAMGCAYRIAAPGTRFGL 122 Query: 132 PEIRLGVFAPAASCLLPPRV-GQACAEDLLWSGRSIDGAEGHRIGLIDVLAEDPEAAA 188 PE+ +G+ A PR+ G A D+ +G+ + E H G +D +A+DPEAAA Sbjct: 123 PEVTVGLIPGAGGTQRAPRLFGWDAAIDMACAGKLLSAQEAHARGALDAIADDPEAAA 180 Lambda K H 0.321 0.135 0.402 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: 478 Number of extensions: 27 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: 673 Length adjustment: 31 Effective length of query: 227 Effective length of database: 642 Effective search space: 145734 Effective search space used: 145734 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 (21.9 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