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 WP_080517374.1 RSPH17029_RS18275 2-dehydro-3-deoxy-6-phosphogalactonate aldolase
Query= SwissProt::Q6BF16 (205 letters) >NCBI__GCF_000015985.1:WP_080517374.1 Length = 210 Score = 155 bits (392), Expect = 5e-43 Identities = 88/198 (44%), Positives = 115/198 (58%) Query: 6 KLPLIAILRGITPDEALAHVGAVIDAGFDAVEIPLNSPQWEQSIPAIVDAYGDKALIGAG 65 K L+AILRGI P+E + +I+AGF+A+EIPLNSP SI +IGAG Sbjct: 10 KRDLVAILRGIRPEEVEPILERLIEAGFEAIEIPLNSPDPFVSIERAARLAPASVMIGAG 69 Query: 66 TVLKPEQVDALARMGCQLIVTPNIHSEVIRRAVGYGMTVCPGCATATEAFTALEAGAQAL 125 TVL P VD LA G +L+V+PN+ V+ RA G+ PG T TEAFTAL GA L Sbjct: 70 TVLTPADVDRLAGCGGRLLVSPNVDGTVLDRAGELGLVSMPGIMTPTEAFTALRHGASGL 129 Query: 126 KIFPSSAFGPQYIKALKAVLPSDIAVFAVGGVTPENLAQWIDAGCAGAGLGSDLYRAGQS 185 K+FP+ GP I A++AVLP + AVGG+ + A + G A GLGS LYR G + Sbjct: 130 KVFPAGVLGPAGIGAVRAVLPKATVIGAVGGIDETSFAAYRAVGVAAFGLGSSLYRPGMT 189 Query: 186 VERTAQQAAAFVKAYREA 203 + A +A + A+ A Sbjct: 190 ADEVAVRAQRSIAAFDAA 207 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: 161 Number of extensions: 8 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: 210 Length adjustment: 21 Effective length of query: 184 Effective length of database: 189 Effective search space: 34776 Effective search space used: 34776 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 Apr 10 2024. 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