Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate CCNA_01794 CCNA_01794 enoyl-CoA hydratase/isomerase family
Query= reanno::WCS417:GFF2712 (367 letters) >FitnessBrowser__Caulo:CCNA_01794 Length = 256 Score = 73.6 bits (179), Expect = 6e-18 Identities = 59/187 (31%), Positives = 87/187 (46%), Gaps = 5/187 (2%) Query: 19 VLAEVRNHIGHLTLNRPAGLNAITLNMVRRLASQLKAWADDPQVYAVVLRGAGEKAFCAG 78 +L E R I +TLNRP +NA++ + L + DP V V+L GAG++AF AG Sbjct: 2 LLIERRGAIAIVTLNRPEAMNALSKALRLALHDAIVQLDQDPDVSVVILTGAGDRAFTAG 61 Query: 79 GDIRSL-YDSFKNGDTLHQDFFVEEYALDLAIHHYRKPVLALMDGFVLGGGMGLVQGADL 137 D++ L D G QD A+ RKPV+ ++G + GG L D+ Sbjct: 62 LDLKELGGDPAAMGAANDQDARSNPVR---AVETCRKPVIGAINGVAITGGFELALACDV 118 Query: 138 RVVTERSRLAMPEVAIGYFPDVGGSYFLPRIPGEL-GIYLGVTGVQIRAADALYCGLADW 196 + +E +R A +G P G S L R+ G L +TG + A A GL + Sbjct: 119 LLASENARFADTHARVGIMPGWGLSQKLSRLIGPYRAKELSLTGNFLDARTAADWGLVNR 178 Query: 197 YLESSKL 203 +S+L Sbjct: 179 VTTASEL 185 Lambda K H 0.322 0.138 0.419 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: 198 Number of extensions: 8 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: 367 Length of database: 256 Length adjustment: 27 Effective length of query: 340 Effective length of database: 229 Effective search space: 77860 Effective search space used: 77860 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: 48 (23.1 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