Align L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase (characterized)
to candidate WP_011383249.1 AMB_RS04120 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase
Query= reanno::Smeli:SM_b21112 (281 letters) >NCBI__GCF_000009985.1:WP_011383249.1 Length = 254 Score = 139 bits (351), Expect = 5e-38 Identities = 77/201 (38%), Positives = 111/201 (55%), Gaps = 7/201 (3%) Query: 71 GKFICIGLNYSDHAAETGATVPPEPIIFMKATSAIVGPNDDLVLPRGSEKTDWEVELGIV 130 G + +NY+DHA E P +P+ F+K VG P + +E EL +V Sbjct: 45 GTTFALAINYADHAKELAFKAPEKPLAFLKGPGTFVGHRAVTRKPADAGFMHYECELAVV 104 Query: 131 IGKTAKYVSEAEALDYVAGYCTVHDVSERAFQTERHGQWTKGKSCDTFGPTGPWLVTKDE 190 IG+TA+ V +A D+VAGY +D + R F + + K+ D GPW+V +D+ Sbjct: 105 IGRTARDVKAKDAYDFVAGYTVANDYAIRNFLQNYYRPNLRTKNRDGCTVLGPWMVDRDD 164 Query: 191 VADPQDLAMWLKVNGETMQDGSTKTMVYGAAHLVSYLSQFMSLRPGDIISTGTPPGVGMG 250 VADP L + VNG +Q G+T+ MV+G L+ YLS FM+L PGD+I TGTP G+ + Sbjct: 165 VADPMSLDISTFVNGARVQSGNTRDMVFGVPALIEYLSSFMTLSPGDLILTGTPDGI-VD 223 Query: 251 MKPPRYLKAGDVVELGIEGLG 271 +KP GD V +EG+G Sbjct: 224 VKP------GDEVVTEVEGVG 238 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: 252 Number of extensions: 9 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: 254 Length adjustment: 25 Effective length of query: 256 Effective length of database: 229 Effective search space: 58624 Effective search space used: 58624 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