Align 3-oxoadipate enol-lactonase (EC 3.1.1.24); 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate Pf1N1B4_3238 Beta-ketoadipate enol-lactone hydrolase (EC 3.1.1.24)
Query= BRENDA::Q0SH24 (400 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3238 Length = 268 Score = 210 bits (534), Expect = 4e-59 Identities = 122/260 (46%), Positives = 157/260 (60%), Gaps = 11/260 (4%) Query: 5 LAHEISGPR-SGAADAPVVVLLGSLGSNRSMWDPQIAALSYECRVVAVDQRGHGESPAPD 63 L ++I GP+ G ADAPV+VL SLG++ MWD QI A + RV+ D RGHG+S Sbjct: 11 LHYQIQGPQLDGPADAPVLVLSNSLGTDLHMWDAQIPAFTEHFRVLRFDTRGHGQSLVTP 70 Query: 64 GPYSVRDLSEDVLALLDSLGVDAAHFVGLSMGGAIAQWLGAHAPRRVLSLSLLCTAAKFG 123 GPYS+ L DVLALLD+L ++ AHF GLSMGG I QWLG +A +R+ L + TAAK G Sbjct: 71 GPYSIEQLGRDVLALLDALHIERAHFCGLSMGGLIGQWLGINASQRLNKLIVCNTAAKIG 130 Query: 124 EPQAWIERAAASRTDGPE---SLADAVVARWFSEGLAKRDPEFVRHYREMIASTSPEGYA 180 +P W R DG +L DA +ARWF+ A+ +P V+ +M+A+TSPEGYA Sbjct: 131 DPSVWNPRIETVLRDGSAAMVALRDASIARWFTADFAEANPAAVKRITDMLAATSPEGYA 190 Query: 181 ACCDALADWDFTADLSRISAPTLVIAGEEDPSTPPSVMQILADGITEARFEVLSPAAHVA 240 A C A+ D DF LS I P LVIAG ED TPPS + + + A + AAH++ Sbjct: 191 ANCAAVRDADFRDQLSSIKVPLLVIAGTEDAVTPPSGGHFIQEHVQGAEYAEFY-AAHLS 249 Query: 241 NLEQAGA-----VTALLREH 255 N+ QAGA V A L H Sbjct: 250 NV-QAGAAFSDRVLAFLSAH 268 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: 307 Number of extensions: 11 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