Align L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase (characterized)
to candidate BWI76_RS17770 BWI76_RS17770 isomerase/hydrolase
Query= reanno::Smeli:SM_b21112 (281 letters) >FitnessBrowser__Koxy:BWI76_RS17770 Length = 219 Score = 135 bits (339), Expect = 1e-36 Identities = 74/202 (36%), Positives = 111/202 (54%), Gaps = 10/202 (4%) Query: 72 KFICIGLNYSDHAAETGATVPPEPIIFMKATSAIVGPNDDLVLPRGSEKTDWEVELGIVI 131 K +C+G NY+ H E G+ P EP++F+K +A+ LVLP G EVEL ++I Sbjct: 18 KVVCVGSNYAKHIKEMGSATPEEPVLFIKPETALCDIRQPLVLPEGLGSVHHEVELAVLI 77 Query: 132 GKTAKYVSEAEALDYVAGYCTVHDVSERAFQ--TERHGQ-WTKGKSCDTFGPTGPWLVTK 188 G T + +E L +AGY D++ R Q ++ GQ W K K D P ++ Sbjct: 78 GGTLRQATEDHVLKAIAGYGVALDLTLRDLQGKLKKAGQPWEKAKGFDNACPISGFIPAA 137 Query: 189 DEVADPQDLAMWLKVNGETMQDGSTKTMVYGAAHLVSYLSQFMSLRPGDIISTGTPPGVG 248 + D Q+ + LKVNGE Q G+T M++ L++Y+S+F +L+ GD++ TGTP GVG Sbjct: 138 EFHGDAQNTPLSLKVNGEVRQQGTTADMIHKIVPLIAYMSRFFTLKAGDVVLTGTPEGVG 197 Query: 249 MGMKPPRYLKAGDVVELGIEGL 270 L +GD +E+G GL Sbjct: 198 P-------LASGDELEVGFNGL 212 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: 196 Number of extensions: 8 Number of successful extensions: 2 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: 219 Length adjustment: 24 Effective length of query: 257 Effective length of database: 195 Effective search space: 50115 Effective search space used: 50115 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: 46 (22.3 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