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 H281DRAFT_00509 H281DRAFT_00509 dihydrodipicolinate synthase
Query= SwissProt::P75682 (302 letters) >FitnessBrowser__Burk376:H281DRAFT_00509 Length = 308 Score = 149 bits (376), Expect = 8e-41 Identities = 96/280 (34%), Positives = 144/280 (51%), Gaps = 12/280 (4%) Query: 9 GIIPPVSTIFTADGQLDKPGTAALIDDLIKAGVDGLFFLGSGGEFSQLGAEERKAIARFA 68 G IP + T DG LD P LID + G + L +G+ GE + L EE + + A Sbjct: 20 GSIPAIITPMLEDGSLDLPAFRKLIDWHVAEGTNALVVVGTSGESATLSVEEHVLMVKTA 79 Query: 69 IDHVDRRVPVLIGTGGTNARETIELSQHAQQAGADGIVVINPYYWKVSEANLIRYFEQVA 128 ++H R+PV+ G+GG + E IEL++ A++ GAD + + PYY K ++ + R+F ++A Sbjct: 80 VEHTAGRIPVIAGSGGNSTAEAIELTRQAKEVGADATLQVVPYYNKPTQEGIYRHFAKIA 139 Query: 129 DSVTLPVMLYNFPALTGQDLTPALVKTLADSRSNIIGIKD---TIDSVAHLRSMIHTVKG 185 ++V LPV+LYN P T D++ + A IIG+K+ ID AHL +K Sbjct: 140 ETVDLPVILYNVPGRTVADMSNETILRCAQV-PGIIGVKEATGNIDRAAHL------IKS 192 Query: 186 AHPHFTVLCGYDDHLFNTLLLGGDGAISASGNFAPQVSVNLLKAWRDGDVAKAAGYHQTL 245 A HF + G D +LLGG G IS + N AP+ L KA D A H L Sbjct: 193 APAHFGIYSGDDPTAIALMLLGGHGNISVTANVAPRAMSELCKAALAADAKTAREIHLKL 252 Query: 246 LQIPQMYQLDTPFVNVIKEAIVLCGRPVSTHVLPPASPLD 285 L + + +++ + K A+ GR V + P +PLD Sbjct: 253 LSLHKNLFIESNPIPA-KWALQQLGR-VQGGIRLPLTPLD 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: 235 Number of extensions: 13 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: 308 Length adjustment: 27 Effective length of query: 275 Effective length of database: 281 Effective search space: 77275 Effective search space used: 77275 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