Align 3-oxoadipate enol-lactonase (EC 3.1.1.24); 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate AZOBR_RS26370 AZOBR_RS26370 alpha/beta hydrolase
Query= BRENDA::Q0SH24 (400 letters) >FitnessBrowser__azobra:AZOBR_RS26370 Length = 254 Score = 134 bits (336), Expect = 4e-36 Identities = 90/250 (36%), Positives = 127/250 (50%), Gaps = 6/250 (2%) Query: 5 LAHEISGPRSGAADAPVVVLLGSLGSNRSMWDPQIAALSYECRVVAVDQRGHGESPAPDG 64 +A ++ GA D V+L+ LG +++ PQ+ ALS + V D G G S D Sbjct: 1 MAQHLAVEVHGAGDP--VILIHGLGGTSNVFTPQVGALSRFFQCVRFDLPGSGRSAITDD 58 Query: 65 PYSVRDLSEDVLALLDSLGVDAAHFVGLSMGGAIAQWLGAHAPRRVLSLSLL--CTAAKF 122 S+ + V+A+LDS G++ AH VG S+G + Q L P RV SLSL+ A Sbjct: 59 -VSISGFVDAVVAVLDSRGIERAHVVGHSLGTVVCQHLAIRQPERVRSLSLIGPLHAPPE 117 Query: 123 GEPQAWIERAAASRTDGPESLADAVVARWFSEGLAKRDPEFVRHYREMIASTSPEGYAAC 182 A +RAA +R DG +ADAVV S PE RE++ PEGYA Sbjct: 118 AARPALRDRAAKARADGMVGIADAVVQGGTSADTKANRPEVAAFVREILMRQDPEGYART 177 Query: 183 CDALADWDFTADLSRISAPTLVIAGEEDPSTPPSVMQILADGITEARFEVLSPAAHVANL 242 C+ALA + AD++RI+ PTL+I G+ED + PP ++ LA I + +L H Sbjct: 178 CEALAAAE-PADVARIACPTLLITGDEDGTAPPPAVRALASKIPGSNLRILDRCGHWTTF 236 Query: 243 EQAGAVTALL 252 E+ AV L Sbjct: 237 ERPAAVNEAL 246 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: 272 Number of extensions: 24 Number of successful extensions: 4 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: 254 Length adjustment: 27 Effective length of query: 373 Effective length of database: 227 Effective search space: 84671 Effective search space used: 84671 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