Align L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase (characterized)
to candidate Ga0059261_1678 Ga0059261_1678 Fumarylacetoacetate (FAA) hydrolase family
Query= reanno::Smeli:SM_b21112 (281 letters) >FitnessBrowser__Korea:Ga0059261_1678 Length = 325 Score = 117 bits (293), Expect = 3e-31 Identities = 76/242 (31%), Positives = 122/242 (50%), Gaps = 7/242 (2%) Query: 40 PSKLDELANLDVETLPAVSGNPRLGPCVAGTGKFICIGLNYSDHAAETGATVPPEPIIFM 99 P+ + + AN ++ L A+ + R+ + G S A + A+ P F Sbjct: 82 PNSIRDFANFELHCLQALEASMRMRAASQPDPEAAYAGFKASG-AYDLPASWYQRPYYFK 140 Query: 100 KATSAIVGPNDDLVLPRGSEKTDWEVELGIVIGKTAKYVSEAEALDYVAGYCTVHDVSER 159 G + + PR S D+E+E VIG ++EA+A ++ GY +D S R Sbjct: 141 GNRMTCSGHDSVIQWPRFSGTMDYELEFAAVIGTRGADIAEADADAHIFGYMIYNDFSAR 200 Query: 160 AFQTE----RHGQWTKGKSCDTFGPTGPWLVTKDEVADPQDLAMWLKVNGETMQDGSTKT 215 Q R G +KGK DT GPW+VT+DE+ D +LAM ++NGE ++ Sbjct: 201 DEQVRDQQFRMGP-SKGKDFDTGNAMGPWIVTRDELPDVSNLAMTSRINGEVQGRSNSSG 259 Query: 216 MVYGAAHLVSYLSQFMSLRPGDIISTGTPPGVGMGMKPPRYLKAGDVVELGIEGLGSQKQ 275 M + A ++++S+ +L PGD+ +GT G G G + RYL+ GDV+EL +EG+G + Sbjct: 260 MQFSFAQCIAFVSRDETLYPGDVFGSGT-AGNGCGFETGRYLEPGDVIELEVEGIGVLRN 318 Query: 276 RV 277 R+ Sbjct: 319 RI 320 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: 273 Number of extensions: 15 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: 325 Length adjustment: 27 Effective length of query: 254 Effective length of database: 298 Effective search space: 75692 Effective search space used: 75692 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: 48 (23.1 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