Align L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase (characterized)
to candidate 353409 BT3883 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase (NCBI ptt file)
Query= reanno::Smeli:SM_b21112 (281 letters) >FitnessBrowser__Btheta:353409 Length = 204 Score = 93.2 bits (230), Expect = 4e-24 Identities = 61/181 (33%), Positives = 91/181 (50%), Gaps = 5/181 (2%) Query: 72 KFICIGLNYSDHAAETGAT-VPPEPIIFMKATSAIVGPNDDLVLPRGSEKTDWEVELGIV 130 K I +G+NY+ H E G T V EP+IFMK SAI+ +P S + +E EL + Sbjct: 2 KIIAVGMNYALHNQELGHTSVNKEPVIFMKPDSAILKDGKPFFIPDFSNEVHYETELVVR 61 Query: 131 IGKTAKYVSEAEALDYVAGYCTVHDVSERAFQT---ERHGQWTKGKSCDTFGPTGPWLVT 187 I + K +S A Y D + R Q E W K D+ G + V Sbjct: 62 INRLGKNISPRFASRYYDALTVGIDFTARDLQRKFREAGNPWELCKGFDSSAAIGTF-VP 120 Query: 188 KDEVADPQDLAMWLKVNGETMQDGSTKTMVYGAAHLVSYLSQFMSLRPGDIISTGTPPGV 247 D D Q L L ++G+ +Q G T M++ +++Y+S+F++L+ GD++ TGTP GV Sbjct: 121 VDRYKDIQSLNFNLMIDGKEVQRGCTADMLFKVDDIIAYVSKFVTLKIGDLLFTGTPAGV 180 Query: 248 G 248 G Sbjct: 181 G 181 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: 144 Number of extensions: 7 Number of successful extensions: 3 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: 204 Length adjustment: 23 Effective length of query: 258 Effective length of database: 181 Effective search space: 46698 Effective search space used: 46698 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