Align 2-dehydro-3-deoxy-6-phosphogalactonate aldolase; 2-oxo-3-deoxygalactonate 6-phosphate aldolase; 6-phospho-2-dehydro-3-deoxygalactonate aldolase; 6-phospho-2-keto-3-deoxygalactonate aldolase; KDPGal; EC 4.1.2.21 (characterized)
to candidate Ga0059261_1625 Ga0059261_1625 2-keto-3-deoxy-6-phosphogluconate aldolase
Query= SwissProt::Q6BF16 (205 letters) >FitnessBrowser__Korea:Ga0059261_1625 Length = 208 Score = 180 bits (457), Expect = 1e-50 Identities = 95/192 (49%), Positives = 123/192 (64%) Query: 8 PLIAILRGITPDEALAHVGAVIDAGFDAVEIPLNSPQWEQSIPAIVDAYGDKALIGAGTV 67 PLIAILRG+ P E A A+ DAGF +E+PLNSP +SI + GD+A++G GTV Sbjct: 15 PLIAILRGVKPGEVEAIGDALADAGFTLIEVPLNSPDPFESITRLARRLGDRAMVGGGTV 74 Query: 68 LKPEQVDALARMGCQLIVTPNIHSEVIRRAVGYGMTVCPGCATATEAFTALEAGAQALKI 127 L+ +V A+A +LIV+PN VI +G+ PG AT TEAF AL+AGA ALK+ Sbjct: 75 LREAEVTAVAESAGRLIVSPNASPAVIAATAAHGLISLPGIATPTEAFAALDAGATALKL 134 Query: 128 FPSSAFGPQYIKALKAVLPSDIAVFAVGGVTPENLAQWIDAGCAGAGLGSDLYRAGQSVE 187 FP+ A P +KA++AVLP V VGG+TP+ + W DAG +G GLGS LYR G S Sbjct: 135 FPAEAASPVALKAMRAVLPVATRVLPVGGITPDTIQPWRDAGASGFGLGSALYRPGFSAA 194 Query: 188 RTAQQAAAFVKA 199 +AAAFV+A Sbjct: 195 EVGARAAAFVRA 206 Lambda K H 0.319 0.134 0.399 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: 164 Number of extensions: 7 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: 205 Length of database: 208 Length adjustment: 21 Effective length of query: 184 Effective length of database: 187 Effective search space: 34408 Effective search space used: 34408 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 45 (21.9 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