Align 2-dehydro-3-deoxy-D-gluconate/2-dehydro-3-deoxy-phosphogluconate aldolase; 2-dehydro-3-deoxy-galactonate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase; EC 4.1.2.14; EC 4.1.2.51; EC 4.1.2.-; EC 4.1.2.21 (characterized)
to candidate Echvi_1276 Echvi_1276 Dihydrodipicolinate synthase/N-acetylneuraminate lyase
Query= SwissProt::Q6KZI8 (266 letters) >FitnessBrowser__Cola:Echvi_1276 Length = 308 Score = 103 bits (257), Expect = 4e-27 Identities = 68/213 (31%), Positives = 112/213 (52%), Gaps = 7/213 (3%) Query: 1 MITPLDAHGNIDYNATNILIKYLEGINVDYLFPMGSTGVFPYFTLKERKDFLKFVRE--N 58 MITPL +D LI ++ V LF +G+TG + R + +K N Sbjct: 18 MITPLADENQLDIPGLERLINHIIAGGVHGLFILGTTGESTSLSYDIRHELVKRTCAIVN 77 Query: 59 SKKPIMAGVGSSSINEVNELMKFSMDIGIEAAVLMPPYYIKLNQEAIYHYYKEILSSNDM 118 + P++ G+ ++ E L + G A V PPYY L Q + YY+ ++ + Sbjct: 78 GRVPVLVGITDTAATESLRLADTAAKEGAAAVVAAPPYYFSLGQPELIEYYEYLVERLSL 137 Query: 119 DLLIYNIPQFTN-KIDPETVKNLKSEFSSVKGVKDSSADIRGFMEMLSLSDD--DFAVFQ 175 L +YN+P T I+P+TVK L S++ ++ G+KDSSA+ F ++++ D DF++F Sbjct: 138 PLFLYNMPSHTKIVIEPDTVKTL-SQYDNIVGLKDSSANNAYFNKVMAKMKDRQDFSLFV 196 Query: 176 GQDDLLFTSLELGASGGVCGTTN-FSDGIVRLY 207 G ++++ ++ LGA GGV G N F + V+LY Sbjct: 197 GPEEIMAETVLLGAHGGVNGGANMFPELYVKLY 229 Lambda K H 0.319 0.139 0.400 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: 235 Number of extensions: 12 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: 266 Length of database: 308 Length adjustment: 26 Effective length of query: 240 Effective length of database: 282 Effective search space: 67680 Effective search space used: 67680 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 (21.7 bits) S2: 47 (22.7 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