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 SMc00882 SMc00882 2-dehydro-3-deoxy-6-phosphogalactonate aldolase
Query= SwissProt::Q6BF16 (205 letters) >FitnessBrowser__Smeli:SMc00882 Length = 212 Score = 170 bits (431), Expect = 2e-47 Identities = 96/193 (49%), Positives = 118/193 (61%) Query: 8 PLIAILRGITPDEALAHVGAVIDAGFDAVEIPLNSPQWEQSIPAIVDAYGDKALIGAGTV 67 PLIAILRG+ P+EA VGA+I+ GF A+EIPLNSP +SI V LIGAGTV Sbjct: 12 PLIAILRGLKPEEAEGVVGALIETGFTAIEIPLNSPDPFRSIETAVKMAPAGCLIGAGTV 71 Query: 68 LKPEQVDALARMGCQLIVTPNIHSEVIRRAVGYGMTVCPGCATATEAFTALEAGAQALKI 127 L QV+ LA +G +L+V+PN+ VIR A GM PG T TEA A AGA LK Sbjct: 72 LTTAQVERLADVGGRLMVSPNVEPAVIRLAATKGMVTMPGVFTPTEALAAAAAGASGLKF 131 Query: 128 FPSSAFGPQYIKALKAVLPSDIAVFAVGGVTPENLAQWIDAGCAGAGLGSDLYRAGQSVE 187 FP+S GP I A++AVLP D+ + AVGGV+ N A + G GLGS LY+ G S Sbjct: 132 FPASVLGPSGITAIRAVLPGDLEIAAVGGVSEVNFADYAAIGIRSFGLGSSLYKPGMSAG 191 Query: 188 RTAQQAAAFVKAY 200 Q+A A + AY Sbjct: 192 DVRQRAIATLAAY 204 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: 139 Number of extensions: 4 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: 212 Length adjustment: 21 Effective length of query: 184 Effective length of database: 191 Effective search space: 35144 Effective search space used: 35144 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