Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate BPHYT_RS25360 BPHYT_RS25360 enoyl-CoA hydratase
Query= reanno::WCS417:GFF2712 (367 letters) >FitnessBrowser__BFirm:BPHYT_RS25360 Length = 256 Score = 99.8 bits (247), Expect = 7e-26 Identities = 62/182 (34%), Positives = 97/182 (53%), Gaps = 5/182 (2%) Query: 23 VRNHIGHLTLNRPAGLNAITLNMVRRLASQLKAWADDPQVYAVVLRGAGEKAFCAGGDIR 82 V + +G LTL+RPA +N++ M L +QLKAW +D V +V+ G G +AFCAG D+ Sbjct: 7 VVDSVGWLTLDRPAAMNSLNREMATGLIAQLKAWRNDDAVRVLVVTGNG-RAFCAGADLI 65 Query: 83 SLYDSFKNGDTLHQDFFVEEYALDLAIHHYRKPVLALMDGFVLGGGMGLVQGADLRVVTE 142 ++ + G + VE + + + KPV+A ++G L GG+ +V D+ + E Sbjct: 66 EAAEATQPGRREFLELIVEFFD---TLRAFPKPVIAAVNGLALAGGLEVVLACDVVLAAE 122 Query: 143 RSRLAMPEVAIGYFPDVGGSYFLPR-IPGELGIYLGVTGVQIRAADALYCGLADWYLESS 201 +RL G FP GG+ LPR +P + YL TG + AA+ GL + L + Sbjct: 123 SARLGDAHSNFGVFPGAGGAAILPRKVPANVARYLLFTGDAMSAAELKGYGLVNEVLADA 182 Query: 202 KL 203 +L Sbjct: 183 EL 184 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: 210 Number of extensions: 10 Number of successful extensions: 3 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