Align 3-oxoadipate enol-lactonase (EC 3.1.1.24); 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate H281DRAFT_02073 H281DRAFT_02073 3-oxoadipate enol-lactonase (EC 3.1.1.24)
Query= BRENDA::Q0SH24 (400 letters) >FitnessBrowser__Burk376:H281DRAFT_02073 Length = 262 Score = 163 bits (413), Expect = 5e-45 Identities = 97/242 (40%), Positives = 131/242 (54%), Gaps = 5/242 (2%) Query: 14 SGAADAPVVVLLGSLGSNRSMWDPQIAALSYECRVVAVDQRGHGESPAPDGPYSVRDLSE 73 S P + + LG + S+WD + V+ D RGHG++ P+SV DL+ Sbjct: 15 SNEGGGPWLTFIHQLGGDLSVWDQLAGYFRDDYTVLRYDVRGHGQTELSKEPFSVGDLAG 74 Query: 74 DVLALLDSLGVDAAHFVGLSMGGAIAQWLGAHAPRRVLSLSLLCTAAKFGEPQA---WIE 130 D+ ALLD+LG + H VG+SMGG IAQ RV SL++ + A P+A W + Sbjct: 75 DLAALLDALGAPSTHLVGMSMGGMIAQQFALDHSSRVDSLTIADSVAA-NPPEARATWDQ 133 Query: 131 RAAASRTDGPESLADAVVARWFSEGLAKRDPEFVRHYREMIASTSPEGYAACCDALADWD 190 RAA++R DG LA A + RW +E PE V E + T PEGYA C+AL ++D Sbjct: 134 RAASARRDGMAPLAAATLERWLTEDFRVAHPEAVEPIHEALTRTLPEGYAMACEALREFD 193 Query: 191 FTADLSRISAPTLVIAGEEDPSTPPSVMQILADGITEARFEVLSPAAHVANLEQAGAVTA 250 L I PTLV+AG D T P+ Q +AD I A FE+L AAH+A +EQ+ A Sbjct: 194 VRGKLGAIHCPTLVVAGRHDTGTRPAASQEIADAIEGAHFELLD-AAHLAPVEQSQRFAA 252 Query: 251 LL 252 LL Sbjct: 253 LL 254 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: 309 Number of extensions: 13 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: 262 Length adjustment: 28 Effective length of query: 372 Effective length of database: 234 Effective search space: 87048 Effective search space used: 87048 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: 48 (23.1 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