Align 2-pyrone-4,6-dicarboxylate hydrolase; PDC hydrolase; 2-pyrone-4,6-dicarboxylate lactonase; EC 3.1.1.57 (characterized)
to candidate Ga0059261_0522 Ga0059261_0522 Predicted metal-dependent hydrolase of the TIM-barrel fold
Query= SwissProt::O87170 (293 letters) >FitnessBrowser__Korea:Ga0059261_0522 Length = 295 Score = 483 bits (1243), Expect = e-141 Identities = 223/289 (77%), Positives = 250/289 (86%), Gaps = 1/289 (0%) Query: 6 RILSWNETPSKPRYTPPPGAIDAHCHVFGPMAQFPFSPKAKYLPRDAGPDMLFALRDHLG 65 RI SW PSKPRYTPPPGA+DAHCHVFGPMAQFPFSPKAKYLP+DA PD LFALR+ LG Sbjct: 7 RIRSWTLDPSKPRYTPPPGAVDAHCHVFGPMAQFPFSPKAKYLPQDADPDALFALRERLG 66 Query: 66 FARNVIVQASCHGTDNAATLDAIARAQGKARGIAVVDPAIDEAELAALHEGGMRGIRFNF 125 FARNVIVQASCHGTDN ATL+ IA + G RG+AVVDPAI +A L LHEGG+RG+RFNF Sbjct: 67 FARNVIVQASCHGTDNRATLNGIAASNGTCRGVAVVDPAISDAGLDTLHEGGIRGVRFNF 126 Query: 126 LKRLVDDAPKDKFLEVAGRLPA-GWHVVIYFEADILEELRPFMDAIPVPIVIDHMGRPDV 184 LKRLVDDAPKDKFL++A R+ GWHVV+YFEADILEE++PF+ AIPVP+VIDHMGRPDV Sbjct: 127 LKRLVDDAPKDKFLDIARRIQRLGWHVVVYFEADILEEMKPFLAAIPVPVVIDHMGRPDV 186 Query: 185 RQGPDGADMKAFRRLLDSREDIWFKATCPDRLDPAGPPWDDFARSVAPLVADYADRVIWG 244 RQGPDGADM AFR LLDSR+DIW K TCPDRLDPAGPP+ DF RSV PLV Y DRV+WG Sbjct: 187 RQGPDGADMAAFRALLDSRDDIWTKVTCPDRLDPAGPPYADFVRSVRPLVEAYPDRVLWG 246 Query: 245 TDWPHPNMQDAIPDDGLVVDMIPRIAPTPELQHKMLVTNPMRLYWSEEM 293 TDWPHPNM++ +PDDG +VD+IP IAPT ELQHK+LV NPMRLYW E + Sbjct: 247 TDWPHPNMEEVLPDDGALVDLIPAIAPTAELQHKLLVDNPMRLYWPEAL 295 Lambda K H 0.323 0.140 0.455 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: 481 Number of extensions: 15 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: 293 Length of database: 295 Length adjustment: 26 Effective length of query: 267 Effective length of database: 269 Effective search space: 71823 Effective search space used: 71823 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