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_017549000.1 C792_RS0108265 4-hydroxy-tetrahydrodipicolinate synthase
Query= SwissProt::P75682 (302 letters) >NCBI__GCF_000330705.1:WP_017549000.1 Length = 297 Score = 135 bits (340), Expect = 1e-36 Identities = 80/245 (32%), Positives = 135/245 (55%), Gaps = 4/245 (1%) Query: 4 SALFTGIIPPVSTIFTADGQLDKPGTAALIDDLIKAGVDGLFFLGSGGEFSQLGAEERKA 63 + +F GI ++T F D +D I+ LI+ L G+ GE L AEE + Sbjct: 3 TVIFEGIGVAMTTPFRND-VIDYGAFRNHIEYLIENDAQALIINGTTGESPTLRAEEIRE 61 Query: 64 IARFAIDHVDRRVPVLIGTGGTNARETIELSQHAQQAGADGIVVINPYYWKVSEANLIRY 123 + R ++ VD RVPV+ GTG + +IEL+++A++ GAD I++I PYY K ++ LIR+ Sbjct: 62 LLRVGVETVDGRVPVIAGTGTNSTSASIELTKYAEKIGADAIMLITPYYNKSNQRGLIRH 121 Query: 124 FEQVADSVTLPVMLYNFPALTGQDLTPALVKTLADSRSNIIGIKDTIDSVAHLRSMIHTV 183 F +AD+ LP +LYN P TG + P V+ L+ R NI+ +KD + + + R ++ Sbjct: 122 FTAIADNTELPAVLYNVPGRTGMTIEPETVRELSTHR-NIVALKDAVGDLEYTREVLALT 180 Query: 184 KGAHPHFTVLCGYDDHLFNTLLLGGDGAISASGNFAPQVSVNLLKAWRDGDVAKAAGYHQ 243 + + F + G DD++ + + LGG G IS GN P ++ + ++GD + +++ Sbjct: 181 E--NQDFVLYSGNDDNMHDFVKLGGKGLISVVGNIIPGELQDVYERIQNGDASAQDRFNR 238 Query: 244 TLLQI 248 + I Sbjct: 239 VMPMI 243 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: 189 Number of extensions: 10 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: 297 Length adjustment: 27 Effective length of query: 275 Effective length of database: 270 Effective search space: 74250 Effective search space used: 74250 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