Align 3-oxoadipate enol-lactonase (EC 3.1.1.24); 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate PP_1380 PP_1380 3-oxoadipate enol-lactonase 2
Query= BRENDA::Q0SH24 (400 letters) >FitnessBrowser__Putida:PP_1380 Length = 263 Score = 197 bits (500), Expect = 4e-55 Identities = 110/242 (45%), Positives = 142/242 (58%), Gaps = 8/242 (3%) Query: 5 LAHEISGPRSGAADAPVVVLLGSLGSNRSMWDPQIAALSYECRVVAVDQRGHGESPAPDG 64 L ++I GP DAPV+VL SLG++ MWD QI S RV+ D RGHG S +G Sbjct: 11 LNYQIDGPD----DAPVLVLSNSLGTDLGMWDTQIPLWSQHFRVLRYDTRGHGASLVTEG 66 Query: 65 PYSVRDLSEDVLALLDSLGVDAAHFVGLSMGGAIAQWLGAHAPRRVLSLSLLCTAAKFGE 124 PYS+ L DVLALLD L + AHFVGLSMGG I QWLG HA R+ SL+L TAAK Sbjct: 67 PYSIEQLGRDVLALLDGLDIQKAHFVGLSMGGLIGQWLGIHAGERLHSLTLCNTAAKIAN 126 Query: 125 PQAWIERAAASRTDGPES---LADAVVARWFSEGLAKRDPEFVRHYREMIASTSPEGYAA 181 + W R G ++ L DA +ARWF+ G A+ E + +M+A TSP+GYA Sbjct: 127 DEVWNTRIDTVLKGGQQAMVDLRDASIARWFTPGFAQAQAEQAQRICQMLAQTSPQGYAG 186 Query: 182 CCDALADWDFTADLSRISAPTLVIAGEEDPSTPPSVMQILADGITEARFEVLSPAAHVAN 241 C A+ D D+ L RI P L++AG +D T P + + GI A + V PAAH++N Sbjct: 187 NCAAVRDADYREQLGRIQVPALIVAGTQDVVTTPEHGRFMQAGIQGAEY-VDFPAAHLSN 245 Query: 242 LE 243 +E Sbjct: 246 VE 247 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: 280 Number of extensions: 7 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