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 N515DRAFT_1147 N515DRAFT_1147 4-hydroxy-tetrahydrodipicolinate synthase
Query= SwissProt::P75682 (302 letters) >FitnessBrowser__Dyella79:N515DRAFT_1147 Length = 297 Score = 131 bits (330), Expect = 2e-35 Identities = 89/291 (30%), Positives = 133/291 (45%), Gaps = 5/291 (1%) Query: 9 GIIPPVSTIFTADGQLDKPGTAALIDDLIKAGVDGLFFLGSGGEFSQLGAEERKAIARFA 68 G I ++T FT+DG LD L+D + G + GS GE L +E + + FA Sbjct: 5 GSICALATPFTSDGALDLDAFGRLLDYQVAGGTQAVVVAGSTGEAHMLEHDEYETLLSFA 64 Query: 69 IDHVDRRVPVLIGTGGTNARETIELSQHAQQAGADGIVVINPYYWKVSEANLIRYFEQVA 128 + + R+PVL GTG T+ L++ A++ GAD +V+ P+Y + ++ L R+F +VA Sbjct: 65 VKRIAGRIPVLAGTGEAGTARTVALTRRARELGADAALVVAPFYVRPTQEGLRRHFLEVA 124 Query: 129 DSVTLPVMLYNFPALTGQDLTPALVKTLADSRSNIIGIKDTIDSVAHLRSMIHTVKGAHP 188 + LPV+LYN P T DL P V L + + I+GIK+ + S +R++ A Sbjct: 125 EHGGLPVLLYNVPGRTACDLLPETVAALREHPA-IVGIKEAVGSDERIRALAEL---ARA 180 Query: 189 HFTVLCGYDDHLFNTLLLGGDGAISASGNFAPQVSVNLLKAWRDGDVAKAAGYHQTLLQI 248 F L G D +L G G IS N AP+ L A GD A L + Sbjct: 181 DFVYLSGDDPTAGKAMLAGAAGTISVVANLAPKAFRELCDAATSGDAAATTRCDDVLAPL 240 Query: 249 PQMYQLDTPFVNVIKEAIVLCGRPVSTHVLPPASPLDEPRKAQLKTLLQQL 299 Q P +K + G + LP D P + ++ L L Sbjct: 241 VQALNC-APNPIAVKAGLPALGLGSAAPRLPLVELQDGPERTRIAEALAAL 290 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: 202 Number of extensions: 10 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: 297 Length adjustment: 27 Effective length of query: 275 Effective length of database: 270 Effective search space: 74250 Effective search space used: 74250 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 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