Align L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase (characterized)
to candidate GFF3483 PS417_17835 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase
Query= reanno::Smeli:SM_b21112 (281 letters) >FitnessBrowser__WCS417:GFF3483 Length = 256 Score = 151 bits (381), Expect = 2e-41 Identities = 90/244 (36%), Positives = 130/244 (53%), Gaps = 21/244 (8%) Query: 38 LDPSKLDELANLDVETLPAVSGNPRLGPCVAGTGKFICIGLNYSDHAAETGATVPPEPII 97 LD +L LA VE LP +GN +GLNY+DHAAE T P EP+ Sbjct: 25 LDDGRL--LAEDQVEWLPPATGN------------MFALGLNYADHAAELAFTPPTEPLA 70 Query: 98 FMKATSAIVGPNDDLVLPRGSEKTDWEVELGIVIGKTAKYVSEAEALDYVAGYCTVHDVS 157 F+K+ G P +E EL VIGK A+ V A+ALDY+AGY +D + Sbjct: 71 FIKSVGTYTGHRHVTWRPDNVAYMHYECELVAVIGKAARNVKRADALDYLAGYTVCNDYA 130 Query: 158 ERAFQTERHGQWTKGKSCDTFGPTGPWLVTKDEVADPQDLAMWLKVNGETMQDGSTKTMV 217 R + + + K+ D P GPW+V +V DP +L + +NGE Q+GST+ M+ Sbjct: 131 IRDYLENYYRPNLRVKNRDATTPVGPWIVDVADVPDPGNLTLRTWINGELRQEGSTRDMI 190 Query: 218 YGAAHLVSYLSQFMSLRPGDIISTGTPPGVGMGMKPPRYLKAGDVVELGIEGLGSQKQRV 277 + +L+ YLS FM+L+PGD+I+TGTP G+ + GD V + +EG+G R+ Sbjct: 191 FDIPYLIEYLSSFMTLQPGDMIATGTPEGLA-------DVVPGDEVVVEVEGVGRLVNRI 243 Query: 278 RADA 281 ++A Sbjct: 244 VSEA 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: 228 Number of extensions: 5 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