Align 3-oxoadipate enol-lactonase (EC 3.1.1.24); 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate AO356_02885 AO356_02885 2-succinyl-6-hydroxy-2, 4-cyclohexadiene-1-carboxylate synthase
Query= BRENDA::Q0SH24 (400 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_02885 Length = 268 Score = 99.8 bits (247), Expect = 8e-26 Identities = 85/249 (34%), Positives = 126/249 (50%), Gaps = 22/249 (8%) Query: 20 PVVVLLGSLGSNRSMWDPQIAALSYECRVVAVDQRGHGES-PAPDGPYSVRDLSEDVLAL 78 PVV+L S + SMW PQI LS + RV+A+D GHG+S P+G S+ DL+ L L Sbjct: 20 PVVLLGSSYLWDHSMWAPQIEVLSRDYRVIALDLWGHGQSGQLPEGMTSLDDLARQALTL 79 Query: 79 LDSLGVDAAHFVGLSMGGAIAQWLGAHAPRRVLSLSLLCTAAKFGEPQ-------AWIER 131 +D LG+D + VGLS+GG L AP RV +L L+ T EP+ + +R Sbjct: 80 MDHLGIDRFNLVGLSVGGMWGARLALAAPERVQTLVLMDTYVGV-EPEPTRQYYFSLFDR 138 Query: 132 AAASRTDGPESLADAVVARWFSEGLAKRDPE--FVRHYREMIASTSPEGYAACCDALADW 189 AS + PE L D VV +F G+ DP+ + +R +A+ + A L Sbjct: 139 IEASGSI-PEPLLDIVVPIFFRPGI---DPQSALYQQFRATLAALPTDRLRASIVPLGRI 194 Query: 190 DFTAD--LSRISA----PTLVIAGEEDPSTPPSVMQILADGITEARFEVLSPAAHVANLE 243 F D L R+ A T+++ G++D PPS + +A+ + ++ A H++NLE Sbjct: 195 IFGRDDILPRLHALDAKGTVIMCGDQDKPRPPSEAKEMAE-LIGCPCLLIPDAGHISNLE 253 Query: 244 QAGAVTALL 252 VT L Sbjct: 254 NPEFVTEAL 262 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: 252 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: 268 Length adjustment: 28 Effective length of query: 372 Effective length of database: 240 Effective search space: 89280 Effective search space used: 89280 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