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 H281DRAFT_02229 H281DRAFT_02229 2-dehydro-3-deoxyglucarate aldolase
Query= SwissProt::Q47098 (262 letters) >FitnessBrowser__Burk376:H281DRAFT_02229 Length = 260 Score = 186 bits (472), Expect = 4e-52 Identities = 103/246 (41%), Positives = 154/246 (62%), Gaps = 7/246 (2%) Query: 3 NSFKAALKAGRPQIGLWLGLSSSYSAELLAGAGFDWLLIDGEHAPNNVQTVLTQLQAIAP 62 N K L+ P GLWL L S +AE LA AGFDWLLID EHAPN+ V +QL+AIA Sbjct: 6 NPLKQRLRDADPLFGLWLSLGSDSAAEALAHAGFDWLLIDMEHAPNDSGDVTSQLRAIAA 65 Query: 63 --YPSQPVVRPSWNDPVQIKQLLDVGTQTLLVPMVQNADEAREAVRATRYPPA----GIR 116 PS+PVVR N+ +K+++D G +TL+ P +++A+EA AVR T+YP A G+R Sbjct: 66 AHLPSEPVVRVPANEGWLVKRVMDAGARTLMFPNIESAEEAAHAVRLTQYPSAEALDGLR 125 Query: 117 GVGSALARASRWNRIPDYLQKANDQMCVLVQIETREAMKNLPQILDVEGVDGVFIGPADL 176 GV + + RA+ + DY+Q AN Q+ +VQIE+ A+ + +I GVD +F+GPADL Sbjct: 126 GV-AGVVRAAAYGMRRDYVQTANAQIATIVQIESARALDEVDKIAATPGVDCLFVGPADL 184 Query: 177 SADMGYAGNPQHPEVQAAIEQAIVQIRESGKAPGILIANEQLAKRYLELGALFVAVGVDT 236 +A +G+ G+ +H +VQAA+ + + ++G A GI + A+++ + G F+A+ D Sbjct: 185 AASLGHLGDSKHADVQAAMARIVSAADKAGIAAGIFSMDVASARQHRDAGFRFIALAADV 244 Query: 237 TLLARA 242 + RA Sbjct: 245 MWMLRA 250 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: 179 Number of extensions: 12 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: 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