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 3606718 Dshi_0149 dihydrodipicolinate synthase (RefSeq)
Query= SwissProt::P75682 (302 letters) >FitnessBrowser__Dino:3606718 Length = 291 Score = 129 bits (324), Expect = 8e-35 Identities = 89/288 (30%), Positives = 138/288 (47%), Gaps = 7/288 (2%) Query: 6 LFTGIIPPVSTIFTADGQLDKPGTAALIDDLIKAGVDGLFFLGSGGEFSQLGAEERKAIA 65 +F G +P + T DG +D AL++ I G GL +G+ GE L EE +A+ Sbjct: 1 MFKGSMPALVTPMK-DGAVDFATLEALVEWQIAEGSHGLVPVGTTGESPTLSHEEHEAVV 59 Query: 66 RFAIDHVDRRVPVLIGTGGTNARETIELSQHAQQAGADGIVVINPYYWKVSEANLIRYFE 125 I+ RVPV+ G G N E + +HA+ AGADG +V+ PYY K ++ +I ++ Sbjct: 60 AKVIEVAAGRVPVIAGAGSNNTVEAVRFVRHAKDAGADGALVVTPYYNKPTQGGMIAHYT 119 Query: 126 QVADSVTLPVMLYNFPALTGQDLTPALVKTLADSRSNIIGIKDTIDSVAHLRSMIHTVKG 185 +A++ +P+++YN P + D+TPA + LA + I+G+KD +A + T Sbjct: 120 ALAEAADIPIVIYNIPGRSVVDMTPATMAALA-ALPTIVGVKDATGDLARVS---QTRMA 175 Query: 186 AHPHFTVLCGYDDHLFNTLLLGGDGAISASGNFAPQVSVNLLKAWRDGDVAKAAGYHQTL 245 P F L G D GG G IS + N AP + +A GD A A L Sbjct: 176 CGPEFIQLSGEDATALGFNAHGGVGCISVTANVAPALCAQFQEATLAGDFATALALQDKL 235 Query: 246 LQIPQMYQLDTPFVNVIKEAIVLCGRPVSTHVLPPASPLDEPRKAQLK 293 + + + ++ V K A+ L G+ S V P L + K +K Sbjct: 236 MPLHEAIFVEPGLVGA-KYALSLLGK-CSEDVRLPLLGLSDGTKVLIK 281 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: 8 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: 291 Length adjustment: 26 Effective length of query: 276 Effective length of database: 265 Effective search space: 73140 Effective search space used: 73140 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