Align 4-hydroxy-2-oxo-heptane-1,7-dioate aldolase; 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase; HHED aldolase; 4-hydroxy-2-ketoheptane-1,7-dioate aldolase; HKHD aldolase; EC 4.1.2.52 (characterized)
to candidate 3608243 Dshi_1647 2-dehydro-3-deoxyglucarate aldolase (RefSeq)
Query= SwissProt::Q47098 (262 letters) >FitnessBrowser__Dino:3608243 Length = 260 Score = 241 bits (614), Expect = 1e-68 Identities = 125/255 (49%), Positives = 170/255 (66%) Query: 2 ENSFKAALKAGRPQIGLWLGLSSSYSAELLAGAGFDWLLIDGEHAPNNVQTVLTQLQAIA 61 EN K AL AG QIG+WLG + AEL AG GFDW L+DGEH+PN+ ++ QL+A+ Sbjct: 5 ENQLKQALLAGDVQIGIWLGFGAPAVAELAAGCGFDWCLVDGEHSPNDPAQMIDQLRAMV 64 Query: 62 PYPSQPVVRPSWNDPVQIKQLLDVGTQTLLVPMVQNADEAREAVRATRYPPAGIRGVGSA 121 + P+VR + +K+ LD+G QT++VPMV+ A +A++ VRA RYPP G+RGVG+A Sbjct: 65 GQGAMPIVRVPVGEDWVLKRALDLGVQTIMVPMVETAAQAQQIVRAMRYPPDGVRGVGAA 124 Query: 122 LARASRWNRIPDYLQKANDQMCVLVQIETREAMKNLPQILDVEGVDGVFIGPADLSADMG 181 LARAS ++ +Y+ AN Q+C +VQIE+ A++ +P+I VEGVD +FIGPADL+ADMG Sbjct: 125 LARASGYSLDAEYVTTANAQICTIVQIESHAAVRAIPEIAAVEGVDVLFIGPADLAADMG 184 Query: 182 YAGNPQHPEVQAAIEQAIVQIRESGKAPGILIANEQLAKRYLELGALFVAVGVDTTLLAR 241 Y G PEV A I A+ +I SGK PG+L +E A R+ GA FV VG D T LA Sbjct: 185 YPGRADAPEVDAVICAALGEIARSGKVPGVLAFSETDAVRFAAAGARFVGVGADVTSLAV 244 Query: 242 AAEALAARFGAQATA 256 A L+A A+ ++ Sbjct: 245 ALRGLSASSRARLSS 259 Lambda K H 0.317 0.133 0.387 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: 229 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: 262 Length of database: 260 Length adjustment: 25 Effective length of query: 237 Effective length of database: 235 Effective search space: 55695 Effective search space used: 55695 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: 41 (21.7 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