Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate WP_086511718.1 BZY95_RS20370 hypothetical protein
Query= reanno::WCS417:GFF2712 (367 letters) >NCBI__GCF_002151265.1:WP_086511718.1 Length = 292 Score = 76.6 bits (187), Expect = 8e-19 Identities = 58/167 (34%), Positives = 86/167 (51%), Gaps = 12/167 (7%) Query: 30 LTLNRPAGLNAITLNMVRRLASQLKAWADDPQVYAVVLRGAGEKAFCAGGDIRSLYDSFK 89 +TL P +NA+T + +L L +DP+V ++L+ AG + F AG D+ L Sbjct: 16 ITLFNPP-VNALTQRLRSQLRQALVEAENDPKVRWILLK-AGGRCFSAGADMGEL----- 68 Query: 90 NGDTLHQDFFVEEYALDLAIHHYRKPVLALMDGFVLGGGMGLVQGADLRVVTERSRLAMP 149 D LH+ + E L LAI KP +A + G VLGGG+ L R+ RL +P Sbjct: 69 --DRLHEAPSLPE--LTLAIESGTKPCVAWLHGAVLGGGLELAMACHYRLGPPELRLGLP 124 Query: 150 EVAIGYFPDVGGSYFLPRIPG-ELGIYLGVTGVQIRAADALYCGLAD 195 ++A+G P GG+ LPR+ G ++L ++G I A A GL D Sbjct: 125 QIALGLIPCAGGTQRLPRLMGLAAALHLLLSGETIGATQARRLGLID 171 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: 324 Number of extensions: 25 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: 292 Length adjustment: 28 Effective length of query: 339 Effective length of database: 264 Effective search space: 89496 Effective search space used: 89496 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 24 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