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_047212941.1 PATSB16_RS05105 4-hydroxy-tetrahydrodipicolinate synthase
Query= SwissProt::P75682 (302 letters) >NCBI__GCF_001931675.1:WP_047212941.1 Length = 299 Score = 140 bits (353), Expect = 4e-38 Identities = 89/278 (32%), Positives = 141/278 (50%), Gaps = 6/278 (2%) Query: 21 DGQLDKPGTAALIDDLIKAGVDGLFFLGSGGEFSQLGAEERKAIARFAIDHVDRRVPVLI 80 + LD LID I G DG+ +G+ GE + EE + + A+D +RVP++ Sbjct: 23 EASLDHDALRKLIDWHIAEGTDGIVIVGTSGESPTVSVEEHCELVKLAVDQAAKRVPIIA 82 Query: 81 GTGGTNARETIELSQHAQQAGADGIVVINPYYWKVSEANLIRYFEQVADSVTLPVMLYNF 140 GTGG + E IEL+++A++ GAD + + PYY K ++ + R+F +A+ V LPV+LYN Sbjct: 83 GTGGNSTAEAIELTEYARKVGADATLQVVPYYNKPTQEGIYRHFRSIAEHVDLPVILYNV 142 Query: 141 PALTGQDLTPALVKTLADSRSNIIGIKDTIDSVAHLRSMIHTVKGAHPHFTVLCGYDDHL 200 P T D + + LA I+G+K D+ +L +K A HF V G D Sbjct: 143 PGRTVADASNETLLRLAQV-PGIVGVK---DATGNLDRGAQLIKDAPEHFAVYSGDDLTA 198 Query: 201 FNTLLLGGDGAISASGNFAPQVSVNLLKAWRDGDVAKAAGYHQTLLQIPQMYQLDTPFVN 260 +L+GG G IS + N AP+ L +A GD A H LL + + ++ P Sbjct: 199 VMLMLMGGKGNISVTANVAPRAMHELCEAAMRGDAVAARDMHFKLLNLHRAMFVE-PNPI 257 Query: 261 VIKEAIVLCGRPVSTHVLPPASPLDEPRKAQLKTLLQQ 298 +K A+ G+ + + P +PL +P + T L++ Sbjct: 258 PVKWALQQMGK-IQGGIRLPLTPLAKPYHDAVLTALRE 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: 224 Number of extensions: 12 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: 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 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