Align 2-dehydro-3-deoxy-D-gluconate-6-phosphate aldolase (EC 4.1.2.55) (characterized)
to candidate WP_019865041.1 METMI_RS0104470 ketohydroxyglutarate aldolase
Query= metacyc::MONOMER-15645 (213 letters) >NCBI__GCF_000384075.1:WP_019865041.1 Length = 216 Score = 262 bits (670), Expect = 3e-75 Identities = 131/209 (62%), Positives = 164/209 (78%) Query: 3 NWKTSAEQILTAGPVVPVIVINKLEHAVPMAKALVAGGVRVLELTLRTECAVEAIRLIAQ 62 +WK S + +L A V+PV+VI L+ AVP+A+ALVAGG+RVLE+TLRT A+EAI+LIA Sbjct: 5 HWKISPKDVLNASSVMPVMVIQNLDDAVPLAEALVAGGIRVLEITLRTPIALEAIKLIAD 64 Query: 63 EVPDAIVGAGTVTNPQQLAEVTAAGAQFAISPGLTEPLLKAATEGTIPLIPGISTVSELM 122 V DAIVGAGT+T P+QL AAGA FAISPGLT LL AA G I LIPGI+T+SELM Sbjct: 65 NVKDAIVGAGTITTPEQLQAAEAAGAVFAISPGLTPKLLAAALTGNIALIPGIATLSELM 124 Query: 123 LGMDYGLREFKFFPAEANGGVKALQAIAGPFGKIRFCPTGGISLKNYRDYLALKSVLCVG 182 GM+YGL FKFFPAEA GG+ L+AIAGP + FCPTGGIS +NY+DYLAL +V CVG Sbjct: 125 QGMEYGLDHFKFFPAEAAGGIPMLKAIAGPVPYVTFCPTGGISPENYQDYLALSNVACVG 184 Query: 183 GSWLVPADALESGDYDRITALAREAVAGA 211 GSWL PADA+++ ++ ++T LA++A+A A Sbjct: 185 GSWLAPADAVKAKNWAKVTELAQQAIANA 213 Lambda K H 0.318 0.135 0.390 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: 193 Number of extensions: 5 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: 213 Length of database: 216 Length adjustment: 22 Effective length of query: 191 Effective length of database: 194 Effective search space: 37054 Effective search space used: 37054 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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 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