Align 2-pyrone-4,6-dicarboxylate lactonase (EC 3.1.1.57) (characterized)
to candidate Ac3H11_139 putative 2-pyrone-4,6-dicarboxylic acid hydrolase
Query= BRENDA::D1MW98 (305 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_139 Length = 300 Score = 159 bits (401), Expect = 1e-43 Identities = 102/291 (35%), Positives = 148/291 (50%), Gaps = 21/291 (7%) Query: 18 SKPQFKLPAGAVDAHCHVFGPGNEFPFAPERKY--TPCDASKAQLYALRDHLGFARNVVV 75 ++PQ LP GA D+H H+F + FAP + TP DA A + L+ LG R VVV Sbjct: 17 NRPQRLLPPGACDSHMHIF----DARFAPSAHWPRTPPDAPVAAYWQLQQRLGSTRTVVV 72 Query: 76 QATCHGADNRAMVDACKSSGGKARGVATVKRSISDAELQELHDAGVRGVRFNFVK-RLVD 134 + +G DN +DA G ARGVA V +SDAEL L V G+R NFV + Sbjct: 73 TPSTYGTDNACTLDALDQLGDDARGVAVVDPRVSDAELARLAARRVCGLRVNFVSPQSWG 132 Query: 135 FTPKDELMEIAGRIAK----LGWHVVIYFEAVDLPELWDFFTALPTTVVVDHMGRPDVTK 190 T L +AG++A+ GWH+ ++ + L ALP +V+DH+GR D + Sbjct: 133 TTTAQMLTTLAGKVAQHADCAGWHIQVFAHPEQIVALAHVLQALPVPLVIDHLGRIDPAE 192 Query: 191 GVDSEEFALFLKFMREHKNVWSKVS-CPERLSVSGPKALHGEQNAYQDVVPFARRVVEEF 249 G ++ F + L+ + + N W K+S R +V GP +Y D +P + +V Sbjct: 193 GPSAQAFGV-LRRLLDGGNTWVKLSGAYMRSAVQGP--------SYADTLPLGQALVRAA 243 Query: 250 PERVLWGTDWPHPNLKDHMPDDGLLVDFIPHIAPTAQLQQKLLVDNPMRLY 300 P ++WG+DWPH +D LVD + A + ++LVDNP RLY Sbjct: 244 PSHLVWGSDWPHTTEAPGTVNDADLVDLLRAWAGSDAAMDRILVDNPARLY 294 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: 305 Number of extensions: 14 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: 300 Length adjustment: 27 Effective length of query: 278 Effective length of database: 273 Effective search space: 75894 Effective search space used: 75894 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