Align 3-oxoadipate enol-lactonase (EC 3.1.1.24); 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate BPHYT_RS21430 BPHYT_RS21430 3-oxoadipate enol-lactonase
Query= BRENDA::Q0SH24 (400 letters) >FitnessBrowser__BFirm:BPHYT_RS21430 Length = 263 Score = 184 bits (466), Expect = 3e-51 Identities = 103/245 (42%), Positives = 146/245 (59%), Gaps = 3/245 (1%) Query: 5 LAHEISGPRSGAADAPVVVLLGSLGSNRSMWDPQIAALSYECRVVAVDQRGHGESPAPDG 64 L + I G R G +AP +VL SLG++ SMW Q+AALS RV+ D RGHG S AP G Sbjct: 11 LHYRIDGDRHG--NAPWIVLSNSLGTDLSMWASQVAALSKHFRVLRYDTRGHGHSEAPKG 68 Query: 65 PYSVRDLSEDVLALLDSLGVDAAHFVGLSMGGAIAQWLGAHAPRRVLSLSLLCTAAKFGE 124 PY++ L+ DVL L+D+L + A+F G+SMGG L A R + L TAA+ G Sbjct: 69 PYTIEQLTGDVLGLMDTLKIARANFCGISMGGLTGVALAARHGNRFERVVLCNTAARIGS 128 Query: 125 PQAWIERAAASRTDGPESLADAVVARWFSEGLAKRDPEFVRHYREMIASTSPEGYAACCD 184 P+ W+ RAA +R++G +LADAV+ RWF+ +R+P + R++ T EGYA+ CD Sbjct: 129 PEVWVPRAAKARSEGMLALADAVLPRWFTADYIEREPVVLALIRDVFVHTDKEGYASNCD 188 Query: 185 ALADWDFTADLSRISAPTLVIAGEEDPSTPPSVMQILADGITEARFEVLSPAAHVANLEQ 244 A+ D + I P LVI+G D + P+ + LA I AR+ L A+H++N+E+ Sbjct: 189 AIDAADLRPEAPGIKLPALVISGTHDLAATPAQGRELAQSIPGARYVELD-ASHISNIEK 247 Query: 245 AGAVT 249 A A T Sbjct: 248 ADAFT 252 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: 294 Number of extensions: 12 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: 263 Length adjustment: 28 Effective length of query: 372 Effective length of database: 235 Effective search space: 87420 Effective search space used: 87420 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