Align 2-pyrone-4,6-dicarbaxylate hydrolase; PDC hydrolase; 2-pyrone-4,6-dicarboxylate lactonase; EC 3.1.1.57 (characterized)
to candidate Ac3H11_1186 2-pyrone-4,6-dicarboxylic acid hydrolase
Query= SwissProt::Q93PS7 (305 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1186 Length = 314 Score = 571 bits (1472), Expect = e-168 Identities = 269/302 (89%), Positives = 280/302 (92%) Query: 4 FEKTPGWLDWYANPSKPQFKLPAGAVDAHCHVFGPGNEFPFAPERKYTPCDASKAQLYAL 63 FEKTPGWLDWY PSKP+F++ AGAVDAHCHVFGPG EFP+APERKYTPCDASK QLYAL Sbjct: 9 FEKTPGWLDWYTGPSKPRFQVHAGAVDAHCHVFGPGAEFPYAPERKYTPCDASKHQLYAL 68 Query: 64 RDHLGFARNVVVQATCHGADNRAMVDACKSSGGKARGVATVKRSISDAELQQLHDAGVRG 123 RDHLGFARNVVVQATCHGADNRAMVDA SGGKARGVATVKRS+SD ELQ +HDAGVRG Sbjct: 69 RDHLGFARNVVVQATCHGADNRAMVDALVHSGGKARGVATVKRSVSDEELQAMHDAGVRG 128 Query: 124 VRFNFVKRLVDFTPKDELMEIAGRIAKLGWHVVIYFEAVDLPELWDFFTALPTTVVVDHM 183 VRFNFVKRLVDFTPKDELMEIA RI +LGWHVVIYFEAVDLPELWDFFTALPTTVVVDHM Sbjct: 129 VRFNFVKRLVDFTPKDELMEIAARIHQLGWHVVIYFEAVDLPELWDFFTALPTTVVVDHM 188 Query: 184 GRPDVTKGVDSEEFALFLKFMREHQNVWSKVSCPERLSVTGPKALNGEQNAYRDVVPFAR 243 GRPDV K VD EF LFLKFMR+H NVWSKVSCPERLSV GPKALNGEQNAY DV+PFAR Sbjct: 189 GRPDVNKPVDGPEFELFLKFMRQHPNVWSKVSCPERLSVAGPKALNGEQNAYTDVIPFAR 248 Query: 244 RVVEEFPDRVLWGTDWPHPNLKDHMPDDGLLVDFIPHIAPTAELQQKLLVDNPMRLYWPE 303 +VVEEFPDRVLWGTDWPHPNLKDHMPDDGLLVDFIPHIA T ELQ+KLLVDNPMRLYWPE Sbjct: 249 KVVEEFPDRVLWGTDWPHPNLKDHMPDDGLLVDFIPHIATTPELQKKLLVDNPMRLYWPE 308 Query: 304 EV 305 EV Sbjct: 309 EV 310 Lambda K H 0.322 0.138 0.445 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: 522 Number of extensions: 14 Number of successful extensions: 1 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: 305 Length of database: 314 Length adjustment: 27 Effective length of query: 278 Effective length of database: 287 Effective search space: 79786 Effective search space used: 79786 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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