Align 3-oxoadipate enol-lactonase (EC 3.1.1.24) (characterized)
to candidate Echvi_1589 Echvi_1589 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily)
Query= BRENDA::Q13KT2 (263 letters) >FitnessBrowser__Cola:Echvi_1589 Length = 424 Score = 71.2 bits (173), Expect = 3e-17 Identities = 65/257 (25%), Positives = 110/257 (42%), Gaps = 35/257 (13%) Query: 7 NGTELHYRIDGERHGNAPWIVLSNSLGTDLSMWAPQVAALSKHFRVLRYDTRGHGHSEAP 66 NG L+Y E +G ++L + ++ + + L+KH++V+ DTRGHG S Sbjct: 196 NGVALYY----ETYGKGDPLLLLHGADMSIASFNRIIPILAKHYKVIALDTRGHGQSSED 251 Query: 67 KGPYTIEQLTGDVLGLMDTLKIARANFCGLSMGGLTGVALAARHADRIERVALCNTAARI 126 T E DV +D L + N G S GG TG+ LA H D+++ +A A Sbjct: 252 GKKLTYELYAEDVNAFLDELGLEAVNVLGWSDGGNTGLILAMNHPDKVKSLA-AMAAVLY 310 Query: 127 GSPEVWVPRAVKARTEGMHALADAVLPRWFTADYMEREPVVLAMIRDVFVHTDKEGYASN 186 P+ K ++ + AL + L TD+E ++ Sbjct: 311 NDKSSVDPQVNKILSKQIKALENGAL-------------------------TDREAFSLR 345 Query: 187 CE--AIDAADLRPEA-PGIKVPALVISGTHDLAATPAQGRELAQAIAGARYVEL-DASHI 242 + + ++ P + I PAL+++G +D A + +A I+ A V D H Sbjct: 346 VKKSLLTEPNISPSSLSKITCPALIMAGENDY-VKEAHTKLIADHISDATLVTFKDTGHN 404 Query: 243 SNIERADAFTKTVVDFL 259 + +E F++ VV+FL Sbjct: 405 APLEIPKKFSEIVVNFL 421 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: 197 Number of extensions: 14 Number of successful extensions: 1 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: 424 Length adjustment: 28 Effective length of query: 235 Effective length of database: 396 Effective search space: 93060 Effective search space used: 93060 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: 49 (23.5 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