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 PfGW456L13_3931 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase (EC 4.1.2.n4)
Query= SwissProt::Q47098 (262 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3931 Length = 266 Score = 278 bits (712), Expect = 6e-80 Identities = 137/257 (53%), Positives = 180/257 (70%) Query: 3 NSFKAALKAGRPQIGLWLGLSSSYSAELLAGAGFDWLLIDGEHAPNNVQTVLTQLQAIAP 62 N+FKAAL + Q G+W G ++ Y+AE++A G+DW+LIDGEHAPN V VL QLQA+AP Sbjct: 6 NAFKAALNSSGTQYGIWAGFATGYAAEIVATTGYDWMLIDGEHAPNTVPGVLAQLQAVAP 65 Query: 63 YPSQPVVRPSWNDPVQIKQLLDVGTQTLLVPMVQNADEAREAVRATRYPPAGIRGVGSAL 122 Y + PVVR D IKQLLD+G QTL++PMV+ A +A+ VRA RYPP GIRGVG L Sbjct: 66 YSTAPVVRAVNGDANLIKQLLDIGAQTLMIPMVETAAQAQALVRAMRYPPHGIRGVGGGL 125 Query: 123 ARASRWNRIPDYLQKANDQMCVLVQIETREAMKNLPQILDVEGVDGVFIGPADLSADMGY 182 RA+RW+ +PDYL A++Q+C++VQ+E+R ++N+ I VEGVD VFIGPADLS +G+ Sbjct: 126 TRATRWDDVPDYLNTAHEQLCLIVQVESRTGVENVAAIAAVEGVDAVFIGPADLSIGLGH 185 Query: 183 AGNPQHPEVQAAIEQAIVQIRESGKAPGILIANEQLAKRYLELGALFVAVGVDTTLLARA 242 AGNP HPEVQ I+ A+ +GKA GIL NE+ A+RY G F+AV +D +LL + Sbjct: 186 AGNPGHPEVQERIQYAVNATLAAGKACGILAPNEEDARRYQRWGCQFIAVAIDISLLRQG 245 Query: 243 AEALAARFGAQATAVKP 259 A A AR+ A P Sbjct: 246 AMASLARYREPAATQAP 262 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: 213 Number of extensions: 5 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: 266 Length adjustment: 25 Effective length of query: 237 Effective length of database: 241 Effective search space: 57117 Effective search space used: 57117 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