Align KHG/KDPG aldolase; EC 4.1.3.16; EC 4.1.2.14 (characterized)
to candidate Synpcc7942_0017 Synpcc7942_0017 keto-hydroxyglutarate-aldolase/keto-deoxy- phosphogluconate aldolase
Query= SwissProt::P50846 (196 letters) >FitnessBrowser__SynE:Synpcc7942_0017 Length = 187 Score = 116 bits (291), Expect = 2e-31 Identities = 68/175 (38%), Positives = 102/175 (58%), Gaps = 2/175 (1%) Query: 10 LKEAKLIAVIRSKDKQEACQQIESLLDKGIRAVEVTYTTPGASDIIESFRNR-EDILIGA 68 L++A+++AV+RS D + E+ + +G+R +EVT+T+ ++++ R++ D GA Sbjct: 9 LQQARIVAVLRSPDLTQGFAMAETAIARGLRWLEVTWTSDRPAELLSQLRDKYPDCCWGA 68 Query: 69 GTVISAQQAGEAAKAGAQFIVSPGFSADLAEHLSFVKTHYIPGVLTPSEIMEALTFGFTT 128 G+++S EA AGAQF VSP S L E ++PG LTP+EIM A G Sbjct: 69 GSLLSLTDLEEAIAAGAQFGVSPILSLPLLERAQARDLPFLPGALTPTEIMTAHAAGAAV 128 Query: 129 LKLFPSGVFGIP-FMKNLAGPFPQVTFIPTGGIHPSEVPDWLRAGAGAVGVGSQL 182 +KLFP+ G P ++++L P GGIHP V +L AGA AVG+GSQL Sbjct: 129 VKLFPASSAGGPAYVRSLQQPLNHPKLFACGGIHPDAVQSYLDAGAIAVGLGSQL 183 Lambda K H 0.318 0.135 0.386 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: 108 Number of extensions: 8 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: 196 Length of database: 187 Length adjustment: 20 Effective length of query: 176 Effective length of database: 167 Effective search space: 29392 Effective search space used: 29392 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: 44 (21.6 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