Align Putative 2-dehydro-3-deoxy-D-gluconate aldolase YagE; KDG aldolase YagE; Putative 2-dehydro-3-deoxy-D-pentonate aldolase YagE; EC 4.1.2.51; EC 4.1.2.28 (characterized)
to candidate WP_041099538.1 SUTH_RS12045 4-hydroxy-tetrahydrodipicolinate synthase
Query= SwissProt::P75682 (302 letters) >NCBI__GCF_000828635.1:WP_041099538.1 Length = 294 Score = 136 bits (343), Expect = 5e-37 Identities = 86/238 (36%), Positives = 126/238 (52%), Gaps = 4/238 (1%) Query: 9 GIIPPVSTIFTADGQLDKPGTAALIDDLIKAGVDGLFFLGSGGEFSQLGAEERKAIARFA 68 G IP + T DG LD G L+D I G DG+ +G+ GE + E A+ Sbjct: 6 GSIPAILTPMQDDGSLDLTGLQRLLDWHIAEGSDGVVIVGTTGESPTVDYAEHCALIETT 65 Query: 69 IDHVDRRVPVLIGTGGTNARETIELSQHAQQAGADGIVVINPYYWKVSEANLIRYFEQVA 128 + HV R+PV+ GTG + E +EL+Q A++AGAD + + PYY K ++ L R+F+ +A Sbjct: 66 VKHVAGRIPVIAGTGANSTAEAVELAQFARKAGADAHLSVVPYYNKPTQEGLFRHFKTIA 125 Query: 129 DSVTLPVMLYNFPALTGQDLTPALVKTLADSRSNIIGIKDTIDSVAHLRSMIHTVKGAHP 188 ++V LP++LYN P T DL LA I+GIK D+ A++ +K A Sbjct: 126 EAVDLPMILYNVPGRTVADLATDTTLRLAQV-PGIVGIK---DATANIERGSDLLKRAPT 181 Query: 189 HFTVLCGYDDHLFNTLLLGGDGAISASGNFAPQVSVNLLKAWRDGDVAKAAGYHQTLL 246 F+V G D +LLGG G+IS + N AP++ + A GD+A A + LL Sbjct: 182 GFSVYSGDDATAIALMLLGGKGSISVTANVAPRLMHQMCAAAIAGDLATAREINFRLL 239 Lambda K H 0.320 0.138 0.407 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: 221 Number of extensions: 11 Number of successful extensions: 2 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: 302 Length of database: 294 Length adjustment: 26 Effective length of query: 276 Effective length of database: 268 Effective search space: 73968 Effective search space used: 73968 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: 48 (23.1 bits)
This GapMind analysis is from Apr 09 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