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_007677914.1 BN137_RS04830 bifunctional 4-hydroxy-2-oxoglutarate aldolase/2-dehydro-3-deoxy-phosphogluconate aldolase
Query= BRENDA::P0A955 (213 letters) >NCBI__GCF_000319285.1:WP_007677914.1 Length = 212 Score = 387 bits (994), Expect = e-113 Identities = 194/212 (91%), Positives = 205/212 (96%) Query: 1 MKNWKTSAESILTTGPVVPVIVVKKLEHAVPMAKALVAGGVRVLEVTLRTECAVDAIRAI 60 MKNWKTSAE IL +GPVVPVIV+ KLEHAVPMAKAL+AGGVRVLEVTLRT CA+DAIRAI Sbjct: 1 MKNWKTSAEQILKSGPVVPVIVINKLEHAVPMAKALLAGGVRVLEVTLRTPCAMDAIRAI 60 Query: 61 AKEVPEAIVGAGTVLNPQQLAEVTEAGAQFAISPGLTEPLLKAATEGTIPLIPGISTVSE 120 AKEVP+AI+GAGTVLN +QL EVTEAGAQFAISPGLTEPLLKAATEG+IPLIPGISTVSE Sbjct: 61 AKEVPDAIIGAGTVLNAEQLKEVTEAGAQFAISPGLTEPLLKAATEGSIPLIPGISTVSE 120 Query: 121 LMLGMDYGLKEFKFFPAEANGGVKALQAIAGPFSQVRFCPTGGISPANYRDYLALKSVLC 180 LMLGMDYGLKEFKFFPAEANGG KALQAIAGPFSQVRFCPTGGISPANYRDYLALKSVLC Sbjct: 121 LMLGMDYGLKEFKFFPAEANGGTKALQAIAGPFSQVRFCPTGGISPANYRDYLALKSVLC 180 Query: 181 IGGSWLVPADALEAGDYDRITKLAREAVEGAK 212 IGGSWLVPADA+EAGD+DRITKLAREAVEGA+ Sbjct: 181 IGGSWLVPADAMEAGDWDRITKLAREAVEGAQ 212 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: 295 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: 212 Length adjustment: 21 Effective length of query: 192 Effective length of database: 191 Effective search space: 36672 Effective search space used: 36672 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