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 Ac3H11_601 2-dehydro-3-deoxyphosphogalactonate aldolase (EC 4.1.2.21)
Query= SwissProt::Q6BF16 (205 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_601 Length = 219 Score = 167 bits (424), Expect = 1e-46 Identities = 92/193 (47%), Positives = 122/193 (63%) Query: 9 LIAILRGITPDEALAHVGAVIDAGFDAVEIPLNSPQWEQSIPAIVDAYGDKALIGAGTVL 68 LIAILRG+ P E +A A+ DAGF +E+PLNSP+ SI A+ DA L+GAGTVL Sbjct: 17 LIAILRGVQPHEVVAIGHALYDAGFRIIEVPLNSPEPLASIRALRDALPADCLVGAGTVL 76 Query: 69 KPEQVDALARMGCQLIVTPNIHSEVIRRAVGYGMTVCPGCATATEAFTALEAGAQALKIF 128 + V +A G Q+IV P+ +VIR A GM PG AT TEA+ AL AGA LK+F Sbjct: 77 SIDAVADVAAAGGQIIVMPHSDPDVIRAARAAGMACAPGVATLTEAYAALAAGANMLKLF 136 Query: 129 PSSAFGPQYIKALKAVLPSDIAVFAVGGVTPENLAQWIDAGCAGAGLGSDLYRAGQSVER 188 P+ A P +KA +AV+ +A+ VGG+ PE++A + AG +G GLGS LYR G Sbjct: 137 PAEALPPHVLKAWRAVITPPMALVPVGGIVPESIAPYAAAGASGFGLGSALYRPGDQAPE 196 Query: 189 TAQQAAAFVKAYR 201 A +AAAF +A++ Sbjct: 197 VAHKAAAFARAWQ 209 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: 155 Number of extensions: 9 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: 219 Length adjustment: 21 Effective length of query: 184 Effective length of database: 198 Effective search space: 36432 Effective search space used: 36432 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