Align 3-oxoadipate enol-lactonase (EC 3.1.1.24) (characterized)
to candidate PP_4540 PP_4540 Hydrolase, alpha/beta fold family
Query= BRENDA::Q13KT2 (263 letters) >FitnessBrowser__Putida:PP_4540 Length = 270 Score = 109 bits (272), Expect = 7e-29 Identities = 83/271 (30%), Positives = 125/271 (46%), Gaps = 26/271 (9%) Query: 1 MPYAAVNGTELHYRIDGERHGNAPWIVLSNSLGTDLSMWAPQVAALSKHFRVLRYDTRGH 60 M Y G LHY E +G +VL + LG+ W QV S+H+RV+ D RGH Sbjct: 1 MAYFEHEGCTLHY----EEYGQGEPLVLLHGLGSSCQDWELQVPLFSRHYRVILMDIRGH 56 Query: 61 GHSEAPKGPYTIEQLTGDVLGLMDTLKIARANFCGLSMGGLTGVALAARHADRIERVALC 120 G S+ P Y I + D+L L++ L +F GLSMGG+ G A H + + + Sbjct: 57 GRSDKPADGYQIATFSADLLALLEHLHTGPVHFVGLSMGGMVGFQFAVDHPQWLRSLCIV 116 Query: 121 NTA----ARIGSPEVW------VPRAVKARTEGMHALADAVLPRWFTADYMEREPVVLAM 170 N+A R S W + R + T G LA+ + P+ AD ++ Sbjct: 117 NSAPEVKRRTRSDWAWWLKRWSLARILSVETVG-KGLAERLFPKPQQADLRQK------- 168 Query: 171 IRDVFVHTDKEGYASNCEAIDAADLRPEAPGIKVPALVISGTHDLAATPAQGRELAQA-I 229 + + DK Y + +AI ++ I P LVI+ HD TP Q +E A I Sbjct: 169 MAQRWARNDKRAYLKSFDAIVDWGVQERIGQIHCPTLVIAADHDY--TPIQLKERYVALI 226 Query: 230 AGARYVELDAS-HISNIERADAFTKTVVDFL 259 AR V +D S H + +++ + F +T++ FL Sbjct: 227 PNARLVVVDDSRHATPLDQPEVFNQTLLQFL 257 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: 190 Number of extensions: 10 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: 263 Length of database: 270 Length adjustment: 25 Effective length of query: 238 Effective length of database: 245 Effective search space: 58310 Effective search space used: 58310 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