Align L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase (characterized)
to candidate WP_012102723.1 CKL_RS11645 FAA hydrolase family protein
Query= reanno::Smeli:SM_b21112 (281 letters) >NCBI__GCF_000016505.1:WP_012102723.1 Length = 301 Score = 166 bits (420), Expect = 6e-46 Identities = 90/205 (43%), Positives = 124/205 (60%), Gaps = 8/205 (3%) Query: 75 CIGLNYSDHAAE------TGATVPPEPIIFMKATSAIVGPNDDLVLPRG-SEKTDWEVEL 127 C+G NY +HA E TG +P PI F K S +G D + + + D+EVEL Sbjct: 88 CLGKNYEEHAREIKLTRITGNEIPKVPIYFTKVASPAIGNGDSIEFSSEVTNQVDYEVEL 147 Query: 128 GIVIGKTAKYVSEAEALDYVAGYCTVHDVSERAFQTERHGQWTKGKSCDTFGPTGPWLVT 187 G+VIGK K + + EA Y+ GY ++D+S R Q H QW KGKS DTF P GP +V Sbjct: 148 GVVIGKNGKNIKKEEAEKYIFGYTIINDISARDLQGS-HIQWFKGKSLDTFCPMGPCIVH 206 Query: 188 KDEVADPQDLAMWLKVNGETMQDGSTKTMVYGAAHLVSYLSQFMSLRPGDIISTGTPPGV 247 K+E+ P +L + VN E QD +TK +++ +++S LS+ +SL+ GDII+TGTP GV Sbjct: 207 KNEIPFPINLDIKCWVNEELRQDSNTKNLIFDIPYIISDLSKGVSLKAGDIIATGTPSGV 266 Query: 248 GMGMKPPRYLKAGDVVELGIEGLGS 272 GMG P + LK GD +E IE +GS Sbjct: 267 GMGFSPIKVLKQGDSIECYIEKIGS 291 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: 226 Number of extensions: 17 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: 301 Length adjustment: 26 Effective length of query: 255 Effective length of database: 275 Effective search space: 70125 Effective search space used: 70125 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 24 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