Align 3-oxoadipate enol-lactonase (EC 3.1.1.24); 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate RR42_RS10690 RR42_RS10690 3-oxoadipate enol-lactonase
Query= BRENDA::Q0SH24 (400 letters) >FitnessBrowser__Cup4G11:RR42_RS10690 Length = 259 Score = 190 bits (482), Expect = 5e-53 Identities = 107/237 (45%), Positives = 139/237 (58%), Gaps = 1/237 (0%) Query: 20 PVVVLLGSLGSNRSMWDPQIAALSYECRVVAVDQRGHGESPAPDGPYSVRDLSEDVLALL 79 PV+VL SLG+N MW+PQI A + RV+ D RGHG+S GPY++ L EDV+ALL Sbjct: 22 PVLVLANSLGTNLDMWNPQIEAFAKHFRVLRYDTRGHGQSSVTPGPYTIPQLGEDVIALL 81 Query: 80 DSLGVDAAHFVGLSMGGAIAQWLGAHAPRRVLSLSLLCTAAKFGEPQAWIERAAASRTDG 139 D+L +D AHF GLSMGG WL + R + L TAA G + W RAAA DG Sbjct: 82 DALKIDRAHFCGLSMGGITGMWLALNHAGRFDKVVLCNTAAYIGPAENWTNRAAAVERDG 141 Query: 140 PESLADAVVARWFSEGLAKRDPEFVRHYREMIASTSPEGYAACCDALADWDFTADLSRIS 199 S+A+AVV +W + G A P V+ + M+++T GYAA C A+ D D ++ I+ Sbjct: 142 VGSIANAVVDKWLTPGYAAGQPALVQLLQAMLSATDAAGYAANCRAVRDSDLRDAVAGIT 201 Query: 200 APTLVIAGEEDPSTPPSVMQILADGITEARFEVLSPAAHVANLEQAGAVTALLREHI 256 PTLVIAG D TPP Q LA I AR+ L AAH++NLEQ T + E + Sbjct: 202 RPTLVIAGSGDIPTPPHDGQYLAQKIPGARYAELD-AAHLSNLEQVEGFTDAVLEFL 257 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: 297 Number of extensions: 19 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: 259 Length adjustment: 28 Effective length of query: 372 Effective length of database: 231 Effective search space: 85932 Effective search space used: 85932 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