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 Pf6N2E2_3203 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7)
Query= SwissProt::P75682 (302 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3203 Length = 295 Score = 128 bits (321), Expect = 2e-34 Identities = 88/293 (30%), Positives = 146/293 (49%), Gaps = 8/293 (2%) Query: 9 GIIPPVSTIFTADGQ-LDKPGTAALIDDLIKAGVDGLFFLGSGGEFSQLGAEERKAIARF 67 GII T F+ DGQ LD ID LI +GV + LGS GE + L E ++ F Sbjct: 8 GIIGYTITPFSTDGQGLDLDALGRSIDRLIDSGVHAIAPLGSTGEGAYLSDAEWDQVSEF 67 Query: 68 AIDHVDRRVPVLIGTGGTNARETIELSQHAQQAGADGIVVINPYYWKVSEANLIRYFEQV 127 +I V RVP ++ + + ++ AQ GAD ++V+ YWK+SEA ++ +++ + Sbjct: 68 SIARVAGRVPTVVSVSDLTTAKAVHRARFAQAKGADVVMVLPASYWKLSEAEILAHYQAI 127 Query: 128 ADSVTLPVMLYNFPALTGQDLTPALVKTLADSRSNIIGIKDTIDSVAHLRSMIHTVKGAH 187 S+ LP+MLYN PA +G D++ L+ + ++ N+ +K++ + + + +G Sbjct: 128 GASIDLPIMLYNNPATSGIDMSVELILRIFNTVDNVTMVKESTGDIQRMHKLQLLGEGQV 187 Query: 188 PHFTVLCGYDDHLFNTLLLGGDGAISASGNFAPQVSVNLLKAWRDGDVAKAAGYHQTLLQ 247 P + G + G G +A+ N PQ++++L A D+++A Q Sbjct: 188 PFYN---GCNPLALEAFAAGAKGWCTAAPNLIPQLNLDLYAAVLANDLSQARALFYR--Q 242 Query: 248 IPQM-YQLDTPFVNVIKEAIVLCGRPVSTHVLPPASPLDEPRKAQLKTLLQQL 299 +P + + L IK + G V L P PLDE R QL+T+L+QL Sbjct: 243 LPLLDFILKGGLPATIKAGLRTLGLEVGDPRL-PVFPLDEARNQQLQTMLKQL 294 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: 209 Number of extensions: 11 Number of successful extensions: 1 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: 295 Length adjustment: 27 Effective length of query: 275 Effective length of database: 268 Effective search space: 73700 Effective search space used: 73700 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