Align 2-dehydro-3-deoxy-phosphogluconate aldolase (EC 4.1.2.14); 4-Hydroxy-2-oxoglutarate aldolase (EC 4.1.3.16); (4S)-4-hydroxy-2-oxoglutarate aldolase (EC 4.1.3.42) (characterized)
to candidate WP_008486142.1 B3C1_RS16160 bifunctional 4-hydroxy-2-oxoglutarate aldolase/2-dehydro-3-deoxy-phosphogluconate aldolase
Query= BRENDA::P0A955 (213 letters) >NCBI__GCF_000299915.1:WP_008486142.1 Length = 209 Score = 157 bits (398), Expect = 1e-43 Identities = 83/199 (41%), Positives = 121/199 (60%) Query: 6 TSAESILTTGPVVPVIVVKKLEHAVPMAKALVAGGVRVLEVTLRTECAVDAIRAIAKEVP 65 T +L +VP+I AV A+A+ GG+ +EV LR A+D I+AI EVP Sbjct: 2 TLLTDLLDQSRLVPIIQADSAAAAVAAARAIHQGGIGQVEVVLRNAQALDCIKAIRSEVP 61 Query: 66 EAIVGAGTVLNPQQLAEVTEAGAQFAISPGLTEPLLKAATEGTIPLIPGISTVSELMLGM 125 E VGAGTVL+ +Q V EAGAQF ++P T+ LL A + +P PG+S++S++ + Sbjct: 62 EVRVGAGTVLSGEQARAVREAGAQFIVTPTTTDTLLAALMDTGLPFAPGVSSLSDIGRMV 121 Query: 126 DYGLKEFKFFPAEANGGVKALQAIAGPFSQVRFCPTGGISPANYRDYLALKSVLCIGGSW 185 + G ++ K FPAE +GGV L+AI+ F V FCPTGG++ N YLAL +V +GGSW Sbjct: 122 EAGCQQLKLFPAELSGGVALLKAISSIFPGVTFCPTGGVAENNLASYLALGNVFAVGGSW 181 Query: 186 LVPADALEAGDYDRITKLA 204 + P + G++ I++ A Sbjct: 182 IAPNKLVAEGNWQGISQRA 200 Lambda K H 0.317 0.135 0.387 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: 141 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: 209 Length adjustment: 21 Effective length of query: 192 Effective length of database: 188 Effective search space: 36096 Effective search space used: 36096 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