Align 4-hydroxy-2-oxoglutarate aldolase (EC 4.1.3.16; EC 4.1.2.55) (characterized)
to candidate Echvi_3630 Echvi_3630 Entner-Doudoroff aldolase
Query= metacyc::MONOMER-4906 (205 letters) >FitnessBrowser__Cola:Echvi_3630 Length = 222 Score = 125 bits (313), Expect = 8e-34 Identities = 71/199 (35%), Positives = 113/199 (56%), Gaps = 6/199 (3%) Query: 5 ELFKKHKIVAVLRANSVEEAKEKALAVFEGGVHLIEITFTVPDADTVIKELSFL--KEKG 62 E +K ++ V + +E AK A + GGV + E T +A V +EL + KG Sbjct: 10 EAMEKTGMIPVFNHSDLEVAKNVMDASYNGGVRVFEFTNRGENALEVFRELKAYSSRHKG 69 Query: 63 AIIGAGTVTSVEQCRKAVESGAEFIVSPHLDEEISQFCKEKGVFYMPGVMTPTELVKAMK 122 ++G GT+ + ++ +E+GA+FIVSP L ++ ++PG T TE+ A + Sbjct: 70 LMLGIGTIFTPKEVEDFIEAGADFIVSPALIPNVAVTATRNDTLWIPGCGTVTEIFNARE 129 Query: 123 LGHTILKLFPGEVVGPQFVKAMKGPFPNVKFVPTGGV--NLDNVCEWFKAGVLAVGVGSA 180 +G ++K FPG V+GP F+ A+K P++K +PTGGV +N+ +WFKAGV VG+GS Sbjct: 130 MGAQVIKAFPGNVLGPSFISAVKAVLPSLKIMPTGGVEPTEENLGQWFKAGVTCVGMGSQ 189 Query: 181 LVKGTPDEVREKAKAFVEK 199 L K D +++K +EK Sbjct: 190 LFK--KDWIKQKKFDALEK 206 Lambda K H 0.318 0.136 0.393 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: 119 Number of extensions: 9 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: 205 Length of database: 222 Length adjustment: 22 Effective length of query: 183 Effective length of database: 200 Effective search space: 36600 Effective search space used: 36600 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 (21.7 bits) S2: 45 (21.9 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