Align L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase (characterized)
to candidate Pf6N2E2_1308 5-carboxymethyl-2-oxo-hex-3- ene-1,7-dioate decarboxylase (EC 4.1.1.68) / 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase (EC 5.3.3.-)
Query= reanno::Smeli:SM_b21112 (281 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1308 Length = 256 Score = 147 bits (372), Expect = 2e-40 Identities = 79/212 (37%), Positives = 118/212 (55%), Gaps = 7/212 (3%) Query: 70 TGKFICIGLNYSDHAAETGATVPPEPIIFMKATSAIVGPNDDLVLPRGSEKTDWEVELGI 129 TG +GLNY+DHAAE P EP+ F+K+ G N P +E EL Sbjct: 43 TGSMFALGLNYADHAAELAFKPPTEPLAFIKSPGTYTGHNQATWRPDNVAYMHYECELVA 102 Query: 130 VIGKTAKYVSEAEALDYVAGYCTVHDVSERAFQTERHGQWTKGKSCDTFGPTGPWLVTKD 189 VIGK A+ V +AL+Y+AGY +D + R + + + K+ D P GPW+V Sbjct: 103 VIGKAARNVKREDALEYLAGYTVCNDYAIRDYLENYYRPNLRVKNRDATTPVGPWIVDVA 162 Query: 190 EVADPQDLAMWLKVNGETMQDGSTKTMVYGAAHLVSYLSQFMSLRPGDIISTGTPPGVGM 249 +V DP +L + +NG+ Q+GSTK M++ +L+ YLS FM+L+PGD+I+TGTP G+ Sbjct: 163 DVPDPSNLKLRTWINGQLRQEGSTKDMIFDIPYLIEYLSSFMTLQPGDMIATGTPEGLA- 221 Query: 250 GMKPPRYLKAGDVVELGIEGLGSQKQRVRADA 281 + GD V + +EG+G R+ ++A Sbjct: 222 ------DVVPGDEVVVEVEGVGRLVNRIVSEA 247 Lambda K H 0.315 0.136 0.408 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: 7 Number of successful extensions: 1 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: 281 Length of database: 256 Length adjustment: 25 Effective length of query: 256 Effective length of database: 231 Effective search space: 59136 Effective search space used: 59136 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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