Align 3-oxoadipate enol-lactonase (EC 3.1.1.24); 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate RR42_RS21850 RR42_RS21850 3-oxoadipate enol-lactonase
Query= BRENDA::Q0SH24 (400 letters) >FitnessBrowser__Cup4G11:RR42_RS21850 Length = 262 Score = 177 bits (448), Expect = 4e-49 Identities = 102/245 (41%), Positives = 137/245 (55%), Gaps = 8/245 (3%) Query: 3 VALAHEISGPRSGAADAPVVVLLGSLGSNRSMWDPQIAALSYECRVVAVDQRGHGESPAP 62 +AL +EI G A +APV+V+ SLG++ MW PQ+ +L RV+ D RGHG S P Sbjct: 9 IALHYEIEG----APNAPVLVMSNSLGTDMQMWAPQMDSLLPRFRVLRYDTRGHGGSGLP 64 Query: 63 D---GPYSVRDLSEDVLALLDSLGVDAAHFVGLSMGGAIAQWLGAHAPRRVLSLSLLCTA 119 P+ +L +DVLA++D G+ AHF GLSMGG WL A+ P R L TA Sbjct: 65 SPAAAPFGFAELGQDVLAIMDHAGIQRAHFCGLSMGGMTGMWLAANHPERFDRFVLANTA 124 Query: 120 AKFGEPQAWIERAAASRTDGPESLADAVVARWFSEGLAKRDPEFVRHYREMIASTSPEGY 179 A G W R R+ G ++ DAV+ARWFS + + R+M+ SPEGY Sbjct: 125 ALIGPASGWDTRIQTVRSQGMAAIVDAVLARWFSAAWLAGNAARIAPVRQMLLDASPEGY 184 Query: 180 AACCDALADWDFTADLSRISAPTLVIAGEEDPSTPPSVMQILADGITEARFEVLSPAAHV 239 A C A+ D D A L RI++P LVIAG D +T P+ + +A GI AR+ L AH+ Sbjct: 185 TANCAAVRDADLRAQLQRIASPVLVIAGTHDLATTPAQGREVAQGIAGARYVELD-GAHL 243 Query: 240 ANLEQ 244 +N EQ Sbjct: 244 SNWEQ 248 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: 311 Number of extensions: 17 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