Align 3-oxoadipate enol-lactonase (EC 3.1.1.24) (characterized)
to candidate AZOBR_RS26370 AZOBR_RS26370 alpha/beta hydrolase
Query= BRENDA::Q13KT2 (263 letters) >FitnessBrowser__azobra:AZOBR_RS26370 Length = 254 Score = 120 bits (300), Expect = 4e-32 Identities = 85/247 (34%), Positives = 125/247 (50%), Gaps = 9/247 (3%) Query: 18 ERHGNAPWIVLSNSLGTDLSMWAPQVAALSKHFRVLRYDTRGHGHSEAPKGPYTIEQLTG 77 E HG ++L + LG +++ PQV ALS+ F+ +R+D G G S A +I Sbjct: 8 EVHGAGDPVILIHGLGGTSNVFTPQVGALSRFFQCVRFDLPGSGRS-AITDDVSISGFVD 66 Query: 78 DVLGLMDTLKIARANFCGLSMGGLTGVALAARHADRIERVALCNTAARIGSPEVWVP--- 134 V+ ++D+ I RA+ G S+G + LA R +R+ ++L PE P Sbjct: 67 AVVAVLDSRGIERAHVVGHSLGTVVCQHLAIRQPERVRSLSLIGPLH--APPEAARPALR 124 Query: 135 -RAVKARTEGMHALADAVLPRWFTADYMEREPVVLAMIRDVFVHTDKEGYASNCEAIDAA 193 RA KAR +GM +ADAV+ +AD P V A +R++ + D EGYA CEA+ AA Sbjct: 125 DRAAKARADGMVGIADAVVQGGTSADTKANRPEVAAFVREILMRQDPEGYARTCEALAAA 184 Query: 194 DLRPEAPGIKVPALVISGTHDLAATPAQGRELAQAIAGARYVELD-ASHISNIERADAFT 252 + + I P L+I+G D A P R LA I G+ LD H + ER A Sbjct: 185 E-PADVARIACPTLLITGDEDGTAPPPAVRALASKIPGSNLRILDRCGHWTTFERPAAVN 243 Query: 253 KTVVDFL 259 + +V+FL Sbjct: 244 EALVNFL 250 Lambda K H 0.320 0.134 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: 184 Number of extensions: 12 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: 263 Length of database: 254 Length adjustment: 24 Effective length of query: 239 Effective length of database: 230 Effective search space: 54970 Effective search space used: 54970 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 (21.8 bits) S2: 47 (22.7 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