Align 2-pyrone-4,6-dicarboxylate hydrolase; PDC hydrolase; 2-pyrone-4,6-dicarboxylate lactonase; EC 3.1.1.57 (characterized)
to candidate RR42_RS15075 RR42_RS15075 hypothetical protein
Query= SwissProt::O87170 (293 letters) >FitnessBrowser__Cup4G11:RR42_RS15075 Length = 240 Score = 90.5 bits (223), Expect = 3e-23 Identities = 65/196 (33%), Positives = 96/196 (48%), Gaps = 23/196 (11%) Query: 65 GFARNVIVQASCHGTDNAATLDAIARAQGKARGIAVVDPAIDEAELAALHEGGMRGIRFN 124 G V+VQ S G DN+ L+A A RG+ VV P ELA LH G+RG+R+N Sbjct: 21 GVRAGVVVQPSFFGCDNSE-LEAALAASPALRGVCVVGPEASAGELARLHGLGVRGLRWN 79 Query: 125 FLKRLVD----DAPKDKFLEVAGRLPAGWHVVIYFEADILEELRPFMDAIPVPIVIDHMG 180 + R D DA LE A L GWH+ ++ + L ELR ++ A+P+ +V+DH G Sbjct: 80 MVGRHDDASWRDARWPALLEAAHAL--GWHLELHTDPGRLNELRAWLPAVPIALVLDHFG 137 Query: 181 RPDVRQGPDGADMKAFRRLLDSREDIWFKATCPDRLDPAGPPWDDFARSVAPLVADY--- 237 +P D A M A + +++ K + P R+ A +A +VA + Sbjct: 138 KPAPGAQAD-APMLACAAHWRGQREVYVKLSAPYRV----------AADLAGVVAGWHHC 186 Query: 238 --ADRVIWGTDWPHPN 251 ++WG+DWP N Sbjct: 187 LGEQGLLWGSDWPWTN 202 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: 242 Number of extensions: 15 Number of successful extensions: 3 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: 240 Length adjustment: 25 Effective length of query: 268 Effective length of database: 215 Effective search space: 57620 Effective search space used: 57620 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: 47 (22.7 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