Align 3-oxoadipate enol-lactonase (EC 3.1.1.24); 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate PfGW456L13_4585 Beta-ketoadipate enol-lactone hydrolase (EC 3.1.1.24)
Query= BRENDA::Q0SH24 (400 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4585 Length = 263 Score = 202 bits (513), Expect = 1e-56 Identities = 115/246 (46%), Positives = 149/246 (60%), Gaps = 9/246 (3%) Query: 5 LAHEISGPRSGAADAPVVVLLGSLGSNRSMWDPQIAALSYECRVVAVDQRGHGESPAPDG 64 L +++ GP DAPV+VL SLG++ MWD QI A S RV+ D RGHG+S G Sbjct: 11 LHYQLDGP----VDAPVLVLSNSLGTDLHMWDAQIPAFSKHFRVLRFDTRGHGQSLVTPG 66 Query: 65 PYSVRDLSEDVLALLDSLGVDAAHFVGLSMGGAIAQWLGAHAPRRVLSLSLLCTAAKFGE 124 PYS+ L DVLALLD+L ++ AHF GLSMGG I QWLG +A R+ L + TAAK G+ Sbjct: 67 PYSIEQLGRDVLALLDALHIERAHFCGLSMGGLIGQWLGINAGDRLNQLIVCNTAAKIGD 126 Query: 125 PQAWIERAAASRTDGPE---SLADAVVARWFSEGLAKRDPEFVRHYREMIASTSPEGYAA 181 P W R DG +L DA +ARWF+ ++ +P + +M+A+TSPEGYAA Sbjct: 127 PSVWNPRIEMVLRDGQAAMVALRDASIARWFTPDFSEANPAAAKQITDMLAATSPEGYAA 186 Query: 182 CCDALADWDFTADLSRISAPTLVIAGEEDPSTPPSVMQILADGITEARFEVLSPAAHVAN 241 C A+ D DF LS I AP LVIAG ED TPPS + + + A + AAH++N Sbjct: 187 NCAAVRDADFRDQLSSIKAPLLVIAGTEDAVTPPSGGHFIQEHVPGAEYAEFY-AAHLSN 245 Query: 242 LEQAGA 247 + QAGA Sbjct: 246 V-QAGA 250 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: 305 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: 263 Length adjustment: 28 Effective length of query: 372 Effective length of database: 235 Effective search space: 87420 Effective search space used: 87420 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