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 SM_b20299 SM_b20299 N-acetylneuraminate lyase
Query= SwissProt::P75682 (302 letters) >FitnessBrowser__Smeli:SM_b20299 Length = 299 Score = 113 bits (283), Expect = 5e-30 Identities = 72/230 (31%), Positives = 110/230 (47%), Gaps = 6/230 (2%) Query: 9 GIIPPVSTIFTADGQLDKPGTAALIDDLIKAGVDGLFFLGSGGEFSQLGAEERKAIARFA 68 GI + T F+ D +D+ AL+D ++ G+DG++ GS GE +ER Sbjct: 5 GIYSALLTPFSEDESIDRQAIGALVDFQVRLGIDGVYVGGSSGEAMLQSLDERADYLSDV 64 Query: 69 IDHVDRRVPVLIGTGGTNARETIELSQHAQQAGADGIVVINPYYWKVSEANLIRYFEQVA 128 R+ ++ G R+ + LSQHA ++G I I P+Y+ S ++ ++ ++A Sbjct: 65 AAAASGRLTLIAHVGTIATRDALRLSQHAAKSGYQAISAIPPFYYDFSRPEVMAHYRELA 124 Query: 129 DSVTLPVMLYNFPALTGQDLTPALVKTLADSRSNIIGIKDTIDSVAHLRSMIHTVKGAHP 188 D LP+++YNFPA T P LV+ L S NIIGIK T + L + H V P Sbjct: 125 DVSALPLIVYNFPARTSGFTLPELVELL--SHPNIIGIKHTSSDMFQLERIRHAV----P 178 Query: 189 HFTVLCGYDDHLFNTLLLGGDGAISASGNFAPQVSVNLLKAWRDGDVAKA 238 V GYD+ +G GAI + NF + V L G + +A Sbjct: 179 DAIVYNGYDEMCLAGFAMGAQGAIGTTYNFMGDLFVALRDCAAAGRIEEA 228 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: 187 Number of extensions: 11 Number of successful extensions: 4 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: 299 Length adjustment: 27 Effective length of query: 275 Effective length of database: 272 Effective search space: 74800 Effective search space used: 74800 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