Align 2-pyrone-4,6-dicarboxylate lactonase (EC 3.1.1.57) (characterized)
to candidate PP_1699 PP_1699 2-pyrone-4,6-dicarboxylic acid hydrolase
Query= BRENDA::D1MW98 (305 letters) >FitnessBrowser__Putida:PP_1699 Length = 280 Score = 130 bits (326), Expect = 5e-35 Identities = 95/291 (32%), Positives = 142/291 (48%), Gaps = 25/291 (8%) Query: 17 PSKPQFKLPAGAVDAHCHVFGPGNEFPFAPERKYTP-CDASKAQ-LYALRDHLGFARNVV 74 P P L A +D+H HVF G A +R+Y P DA L LR H GF+ V+ Sbjct: 5 PDAPALHLTA--IDSHAHVFSRG--LNLASQRRYAPNYDAPLGDYLGQLRAH-GFSHGVL 59 Query: 75 VQATCHGADNRAMVDACKSSGGKARGVATVKRSISDAELQELHDAGVRGVRFNFVKRLVD 134 VQ + G DNR ++ A ++ G+ RGV ++R + A L E+ GVRGVR N + + + Sbjct: 60 VQPSFLGTDNRYLLSALQTVPGQLRGVVMLERDVEQATLAEMARLGVRGVRLNLMGQDMP 119 Query: 135 FTPKDELMEIAGRIAKLGWHVVIYFEAVDLPELWDFFTALPTTVVVDHMGRPDVTKGVDS 194 + + RI + GWHV ++ + D+P L +V+DH GRPD +G+ Sbjct: 120 DLTGAQWRPLLERIGEQGWHVELHRQVADIPVLVRALQPYGLDIVIDHFGRPDARRGLGQ 179 Query: 195 EEFALFLKFMREHKNVWSKVSCPERLSVSGPKALHGEQNAYQDVVPFARRVV-----EEF 249 FA L K VW KVS RL Q + ++ + FAR+ + Sbjct: 180 PGFAELLTLSGRGK-VWVKVSGIYRL-----------QGSPEENLAFARQALCALEAHYG 227 Query: 250 PERVLWGTDWPHPNLKDHMPDDGLLVDFIPHIAPTAQLQQKLLVDNPMRLY 300 ER++WG+DWPH + + G V+ + +AQL+Q LL+D L+ Sbjct: 228 AERLMWGSDWPHTQHESEV-SFGSAVEQFEALGCSAQLRQALLLDTARALF 277 Lambda K H 0.321 0.138 0.443 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: 233 Number of extensions: 16 Number of successful extensions: 4 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: 280 Length adjustment: 26 Effective length of query: 279 Effective length of database: 254 Effective search space: 70866 Effective search space used: 70866 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