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 AO356_25770 AO356_25770 3-oxoadipate enol-lactonase
Query= curated2:P00632 (267 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_25770 Length = 277 Score = 125 bits (314), Expect = 1e-33 Identities = 82/244 (33%), Positives = 116/244 (47%), Gaps = 7/244 (2%) Query: 18 NYATFGQADRPALIFSNSLGTNLSMWQQQIAYFQDKYFVICYDTRGHGASSTPVGPYRID 77 +Y GQ LI + +G N MW Q+ +Y VI YD GHGAS P + Sbjct: 14 SYLATGQGQPVVLI--HGVGLNKEMWGGQVVGLATQYRVIAYDMLGHGASPRPQSGTALL 71 Query: 78 QLGTDVIALLDHLQIPQATFCGISMGGLTGQWLAIHFPERFNQVIVANTAAKIGEAQ--A 135 ++ LLDHLQ+PQAT G SMGGL + A+H+P+R ++V N+ Q Sbjct: 72 GYADQLLELLDHLQLPQATVIGFSMGGLVARAFALHYPQRLQGLVVLNSVFNRSAEQRAG 131 Query: 136 WQARAQLVREQGLTPIAQTAATRWFTPGFIEDSPEIVEKLSHDLAQGSAEGYASCCEALA 195 AR E G A+ A +RWF+ + +P + L LAQ +GY + E A Sbjct: 132 VIARTAQAAEHGPDANAEAALSRWFSREYQAANPAQIAALRQTLAQNDPQGYLTTYELFA 191 Query: 196 EADV--RPQLQRISIPVLVIAGAQDPVTTVADGQFLCEHIVHSTLEVL-EASHISNVEQP 252 D+ L I +P L+ G DP +T + L E I +++ VL E H+ VE P Sbjct: 192 TQDMYRADDLGNIQVPTLIATGELDPGSTPEMARQLAERIPGASVAVLAEQRHMMPVESP 251 Query: 253 QAFN 256 + N Sbjct: 252 RLVN 255 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: 181 Number of extensions: 10 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: 267 Length of database: 277 Length adjustment: 25 Effective length of query: 242 Effective length of database: 252 Effective search space: 60984 Effective search space used: 60984 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