Align 2-pyrone-4,6-dicarboxylate lactonase (EC 3.1.1.57) (characterized)
to candidate H281DRAFT_05953 H281DRAFT_05953 Predicted metal-dependent hydrolase, TIM-barrel fold
Query= BRENDA::D1MW98 (305 letters) >FitnessBrowser__Burk376:H281DRAFT_05953 Length = 310 Score = 201 bits (512), Expect = 1e-56 Identities = 113/288 (39%), Positives = 155/288 (53%), Gaps = 12/288 (4%) Query: 13 WYANPSKPQFKLPAGAVDAHCHVFGPGNEFPFAPERKYTPCDASKAQLYALRDHLGFARN 72 W + +P F LP GA+D H H++ + FP AP P +A+ AQ L+ LG RN Sbjct: 32 WSSGTERPAFSLPEGAIDCHMHIYD--DRFPVAPGTTLRPPNATVAQYRLLQTRLGVKRN 89 Query: 73 VVVQATCHGADNRAMVDACKSSGGKARGVATVKRSISDAELQELHDAGVRGVRFNFVKRL 132 VVV + +G DNR ++A + GG ARGVA + S++DAELQ+L G+R +RFN Sbjct: 90 VVVTPSTYGTDNRCTLEAIRQFGGNARGVAVIDSSVTDAELQDLDRGGIRAIRFNL--SY 147 Query: 133 VDFTPKDELMEIAGRIAKLGWHVVIYFEAVDLPELWDFFTALPTTVVVDHMGRPDVTKGV 192 T D L +A RIA LGWH+ + + LPEL +ALP +V+DH+ G+ Sbjct: 148 PGATTLDMLAPLATRIANLGWHIELVVQGARLPELERHLSALPCPLVIDHIAHVPEPGGL 207 Query: 193 DSEEFALFLKFMREHKNVWSKVSCPERLSVSGPKALHGEQNAYQDVVPFARRVVEEFPER 252 S+ + + E N W +S P S +G AY DV P A+ ++E PER Sbjct: 208 SSDALRTARRLV-EKGNTWITLSGPYVDSKAGAP-------AYGDVEPVAKVLIEMAPER 259 Query: 253 VLWGTDWPHPNLKDHMPDDGLLVDFIPHIAPTAQLQQKLLVDNPMRLY 300 +LWGTDWPHP K H PDD L+D I + Q + V NP +LY Sbjct: 260 MLWGTDWPHPTEKTHKPDDASLLDTIANWIGRPDWQHLIFVANPTKLY 307 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: 323 Number of extensions: 22 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: 310 Length adjustment: 27 Effective length of query: 278 Effective length of database: 283 Effective search space: 78674 Effective search space used: 78674 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