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_047093417.1 AAV99_RS07600 4-hydroxy-tetrahydrodipicolinate synthase
Query= SwissProt::P75682 (302 letters) >NCBI__GCF_001013305.1:WP_047093417.1 Length = 293 Score = 106 bits (265), Expect = 6e-28 Identities = 72/241 (29%), Positives = 113/241 (46%), Gaps = 6/241 (2%) Query: 6 LFTGIIPPVSTIFTADGQLDKPGTAALIDDLIKAGVDGLFFLGSGGEFSQLGAEERKAIA 65 +F+G IP ++T F + D+ ID I G GL G+ GE + L +E + Sbjct: 1 MFSGSIPALATPFRGEA-FDESAYRQFIDWQIDNGTSGLVPCGTTGESATLDNDEHHRVI 59 Query: 66 RFAIDHVDRRVPVLIGTGGTNARETIELSQHAQQAGADGIVVINPYYWKVSEANLIRYFE 125 + RVPV+ G G + R + ++ AQ AGAD ++++ PYY + S+A L+ +F Sbjct: 60 AVCAEQAAGRVPVIAGAGSNDTRTALWHAKEAQIAGADALLLVAPYYNRPSQAGLLAHFS 119 Query: 126 QVADSVTLPVMLYNFPALTGQDLTPALVKTL-ADSRSNIIGIKDTIDSVAHLRSMIHTVK 184 +A+ LP++LYN P T D+ P V L I+ +KD + S + T + Sbjct: 120 YLAERTDLPIVLYNVPGRTVTDILPETVVELHRRFPEKIVALKDASGDL----SRVVTHR 175 Query: 185 GAHPHFTVLCGYDDHLFNTLLLGGDGAISASGNFAPQVSVNLLKAWRDGDVAKAAGYHQT 244 P L G D + +G G IS + N AP++ A GD A A ++ Sbjct: 176 MGAPALCQLSGDDPLVLGGYAMGQVGCISVTANVAPKLCAEFHAAAASGDFAAAREINEK 235 Query: 245 L 245 L Sbjct: 236 L 236 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: 193 Number of extensions: 7 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: 293 Length adjustment: 26 Effective length of query: 276 Effective length of database: 267 Effective search space: 73692 Effective search space used: 73692 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 24 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