Align 3-oxoadipate enol-lactonase 2; EC 3.1.1.24; 3-oxoadipate enol-lactonase II; Beta-ketoadipate enol-lactone hydrolase II; Enol-lactone hydrolase II (uncharacterized)
to candidate AZOBR_RS05920 AZOBR_RS05920 3-oxoadipate enol-lactonase (Enol-lactone hydrolase) (Beta-ketoadipate enol-lactone hydrolase)
Query= curated2:P00632 (267 letters) >FitnessBrowser__azobra:AZOBR_RS05920 Length = 259 Score = 155 bits (393), Expect = 6e-43 Identities = 88/230 (38%), Positives = 126/230 (54%), Gaps = 2/230 (0%) Query: 23 GQADRPALIFSNSLGTNLSMWQQQIAYFQDKYFVICYDTRGHGASSTPVGPYRIDQLGTD 82 G D P ++ +SLGTN +W Q ++ VI D RGHG S P GPY ++ L D Sbjct: 16 GPQDGPPVLLLHSLGTNHHVWDPQAEVLARRFRVIRPDMRGHGLSEAPPGPYGMEDLADD 75 Query: 83 VIALLDHLQIPQATFCGISMGGLTGQWLAIHFPERFNQVIVANTAAKIGEAQAWQARAQL 142 A+LD L + + G+S+GG+ Q +A+ P R +++ +T+ W+ RA Sbjct: 76 AFAVLDALGVGRCFVGGVSIGGMIAQTMALKAPHRVGGLVLVDTSMATAVPAMWRERAGQ 135 Query: 143 VREQGLTPIAQTAATRWFTPGFIEDSPEIVEKLSHDLAQGSAEGYASCCEALAEADVRPQ 202 VR + P A RW T GF DSPE ++ L L Q +AEG+A C EALA AD+ + Sbjct: 136 VRASSVAPFADAITARWVTQGF-ADSPE-MQGLRTMLHQTAAEGFAGCAEALATADLSAR 193 Query: 203 LQRISIPVLVIAGAQDPVTTVADGQFLCEHIVHSTLEVLEASHISNVEQP 252 + I+ P LVI G QD T VA Q LC + + + + +A+HI N+EQP Sbjct: 194 VGDIAAPSLVIVGDQDQSTPVAAAQALCAALKGTLVVLPDAAHIPNLEQP 243 Lambda K H 0.321 0.134 0.405 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: 6 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: 267 Length of database: 259 Length adjustment: 25 Effective length of query: 242 Effective length of database: 234 Effective search space: 56628 Effective search space used: 56628 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: 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