Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate AZOBR_RS26485 AZOBR_RS26485 enoyl-CoA hydratase
Query= reanno::psRCH2:GFF2391 (364 letters) >FitnessBrowser__azobra:AZOBR_RS26485 Length = 262 Score = 105 bits (261), Expect = 2e-27 Identities = 63/184 (34%), Positives = 101/184 (54%), Gaps = 3/184 (1%) Query: 5 ERPVLAAVRNHVGHLTLNRPAGLNAVTLEMVRLLQQQLSAWAADPQIHAVVLRANGEKAF 64 ERP+L + VG +T+NRP LNA+ + + L++ L +D +H +V+ GE+AF Sbjct: 4 ERPILTSRDGAVGLITINRPTTLNALDVPTLLELERALGELESDDGVHVIVVTGAGERAF 63 Query: 65 CAGGDIRSLYDSFQRGDTEHETFFEEEYALDQYIHAYPKPLLALMDGFVLGGGMGLVQGA 124 AGGDI L DS ++G + F E + + + KP +A ++G+ LGGG LV Sbjct: 64 VAGGDIADL-DS-RQGLAHYLDFAEVVHRVFRRFETCDKPTIAAVNGWALGGGTELVLSL 121 Query: 125 SLRVVTERVRMGMPEVGIGYFPDVGGSY-FLSRLPGELGTYMGVTGLQIRAADALHVGLA 183 +R+ + + G+PE+ +G FP GG+ L ++P + TG Q AA+A+ GL Sbjct: 122 DIRIAADTAKFGLPEINLGLFPGAGGTQRILRQIPPCRARELVFTGDQFTAAEAVAWGLV 181 Query: 184 DWCV 187 + V Sbjct: 182 NRAV 185 Lambda K H 0.321 0.136 0.412 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: 226 Number of extensions: 10 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 364 Length of database: 262 Length adjustment: 27 Effective length of query: 337 Effective length of database: 235 Effective search space: 79195 Effective search space used: 79195 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