Align 3-oxoadipate enol-lactonase (EC 3.1.1.24); 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate SMc04308 SMc04308 oxidoreductase
Query= BRENDA::Q0SH24 (400 letters) >FitnessBrowser__Smeli:SMc04308 Length = 271 Score = 69.3 bits (168), Expect = 1e-16 Identities = 78/247 (31%), Positives = 103/247 (41%), Gaps = 36/247 (14%) Query: 17 ADAPVVVLLGSLGSNRSMWDPQIAAL-SYECRVVAVDQRGHGESPAPDGPYSVRDLSEDV 75 A APVV+L G LG + + W Q+A L RVV +D RGHG S + PYS ++ DV Sbjct: 42 AGAPVVLLHGGLGHSGN-WGYQLAPLLDAGRRVVLIDSRGHGRSTRDERPYSYEVMASDV 100 Query: 76 LALLDSLGVDAAHFVGLSMGGAIAQWLGAHAPRRVLSLSLLC-----TAAKFGEPQAWIE 130 LA+ D L + VG S G I L AP R+ + + A E I+ Sbjct: 101 LAVADMLQLQKFAVVGWSDGACIGLVLANRAPERIAGVFFFACNMDPSGATEFEATPVID 160 Query: 131 RA-AASRTDGPESLADAVVARWFSEGLAKRDPEFVRHYREMIASTSPEGYAACCDALADW 189 R A R D E A + +FV EM+ ST P Y+A Sbjct: 161 RCFARHRKDYAELSA-----------TPDQFDDFVSAVSEMM-STQP-NYSA-------- 199 Query: 190 DFTADLSRISAPTLVIAGEEDPSTPPSVMQILADGITEARFEVLSPAAHVANLEQA---- 245 DL+ I P V+ E+D Q LA I A L +H A L++ Sbjct: 200 ---GDLAEIRVPVAVVQAEKDEFIKWEHAQYLARSIPAADLIALEHVSHFAPLQRPDVFN 256 Query: 246 GAVTALL 252 GA+ A L Sbjct: 257 GAMLAFL 263 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: 265 Number of extensions: 10 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: 271 Length adjustment: 28 Effective length of query: 372 Effective length of database: 243 Effective search space: 90396 Effective search space used: 90396 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: 49 (23.5 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