Align 3-oxoadipate enol-lactonase (EC 3.1.1.24); 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate BWI76_RS16125 BWI76_RS16125 3-oxoadipate enol-lactonase
Query= BRENDA::Q0SH24 (400 letters) >FitnessBrowser__Koxy:BWI76_RS16125 Length = 255 Score = 179 bits (455), Expect = 6e-50 Identities = 99/257 (38%), Positives = 145/257 (56%), Gaps = 6/257 (2%) Query: 7 HEISGPRSGAADAPVVVLLGSLGSNRSMWDPQIAALSYECRVVAVDQRGHGESPAPDGPY 66 ++I GP+ DAPV+VL SLG+ R+MW PQ+ AL+ RV+ D GHG + +G Sbjct: 5 YQIDGPQ----DAPVIVLSNSLGTTRAMWQPQLEALTQHFRVLRYDTHGHGAT-RKNGKV 59 Query: 67 SVRDLSEDVLALLDSLGVDAAHFVGLSMGGAIAQWLGAHAPRRVLSLSLLCTAAKFGEPQ 126 ++ L EDV+ALLD L + A F G+SMGG WLG AP R L + TAA+ G+ Sbjct: 60 TLAQLGEDVVALLDHLNIAKAWFCGISMGGLTGLWLGRFAPERFYGLVVANTAARIGDQA 119 Query: 127 AWIERAAASRTDGPESLADAVVARWFSEGLAKRDPEFVRHYREMIASTSPEGYAACCDAL 186 +W+ RA A R +G + +A RWF+ ++ PE V + EGYAACC+AL Sbjct: 120 SWLSRARAVRQEGMDVVAAGAADRWFTHAFRQKTPEVVAALCHQLTHIDAEGYAACCEAL 179 Query: 187 ADWDFTADLSRISAPTLVIAGEEDPSTPPSVMQILADGITEARFEVLSPAAHVANLEQAG 246 A D A++++I P L++AGE DP T + L I + VL+ A+H++N+E Sbjct: 180 AAADLRAEVAQIPIPVLIVAGESDPVTTVADADFLHQQIPVSEVVVLA-ASHLSNIEAPK 238 Query: 247 AVTALLREHIVGAGYAR 263 A ++ L + G + R Sbjct: 239 AFSSALLGFVQGEKHGR 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: 282 Number of extensions: 14 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: 255 Length adjustment: 27 Effective length of query: 373 Effective length of database: 228 Effective search space: 85044 Effective search space used: 85044 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