Align 3-oxoadipate enol-lactonase (EC 3.1.1.24); 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate AO356_04905 AO356_04905 3-oxoadipate enol-lactonase
Query= BRENDA::Q0SH24 (400 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_04905 Length = 271 Score = 204 bits (518), Expect = 3e-57 Identities = 111/236 (47%), Positives = 145/236 (61%), Gaps = 5/236 (2%) Query: 15 GAADAPVVVLLGSLGSNRSMWDPQIAALSYECRVVAVDQRGHGESPAPDGPYSVRDLSED 74 G DAPV+VL SLG++ MWD Q+AA S RV+ D RGHG+S +GPYS+ L D Sbjct: 22 GTQDAPVLVLSNSLGTDLHMWDEQVAAFSEHFRVLRFDTRGHGQSLVTEGPYSIEQLGRD 81 Query: 75 VLALLDSLGVDAAHFVGLSMGGAIAQWLGAHAPRRVLSLSLLCTAAKFGEPQAWIERAAA 134 VLA+LD L +D HF GLSMGG I QWLG +A R+ L + TAAK G+P W R Sbjct: 82 VLAMLDQLNIDKVHFCGLSMGGLIGQWLGINAGERLHKLVVCNTAAKIGDPSVWNPRIET 141 Query: 135 SRTDGPE---SLADAVVARWFSEGLAKRDPEFVRHYREMIASTSPEGYAACCDALADWDF 191 DG + +L DA +ARWF+ ++ P V+ +M+A+TSP+GYAA C A+ D DF Sbjct: 142 VLRDGKDAMVALRDASIARWFTADFSEAHPAKVKKITDMLAATSPQGYAANCAAVRDADF 201 Query: 192 TADLSRISAPTLVIAGEEDPSTPPSVMQILADGITEARFEVLSPAAHVANLEQAGA 247 LS I P LVIAG ED TPPS + + ++ A + AAH++N+ QAGA Sbjct: 202 REQLSLIRVPLLVIAGTEDAVTPPSGGHFILERVSGAEYAEFY-AAHLSNV-QAGA 255 Lambda K H 0.318 0.132 0.392 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: 293 Number of extensions: 11 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: 400 Length of database: 271 Length adjustment: 28 Effective length of query: 372 Effective length of database: 243 Effective search space: 90396 Effective search space used: 90396 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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