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_009141821.1 HMPREF9452_RS08955 bifunctional 4-hydroxy-2-oxoglutarate aldolase/2-dehydro-3-deoxy-phosphogluconate aldolase
Query= BRENDA::P0A955 (213 letters) >NCBI__GCF_000225705.1:WP_009141821.1 Length = 213 Score = 158 bits (400), Expect = 6e-44 Identities = 79/196 (40%), Positives = 119/196 (60%) Query: 17 VVPVIVVKKLEHAVPMAKALVAGGVRVLEVTLRTECAVDAIRAIAKEVPEAIVGAGTVLN 76 +VPV+V+ + AVPMA AL+A G+ EVT RT+ A D IRA+ + PE VGAGTVL Sbjct: 14 IVPVVVLDDVAQAVPMADALMAAGMCSAEVTFRTDAAADCIRAMREAYPEMAVGAGTVLT 73 Query: 77 PQQLAEVTEAGAQFAISPGLTEPLLKAATEGTIPLIPGISTVSELMLGMDYGLKEFKFFP 136 +Q+ + AGA+F ++P +++ + +P++PG T SE+ GL KFFP Sbjct: 74 VEQVDQAVAAGAEFIVAPNFDPEVVQHCIDIDVPVLPGTVTPSEVGAAEKMGLMVTKFFP 133 Query: 137 AEANGGVKALQAIAGPFSQVRFCPTGGISPANYRDYLALKSVLCIGGSWLVPADALEAGD 196 A GG+ ++AI PF++ RF PTGG+S AN +YL+ ++ GG+W+V A GD Sbjct: 134 AAQYGGLNTIKAICAPFTRHRFMPTGGVSLANVEEYLSCDKIIACGGTWMVKASMFADGD 193 Query: 197 YDRITKLAREAVEGAK 212 + ++ + A EA+ K Sbjct: 194 FSQVQQQAVEAINMVK 209 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: 144 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: 213 Length adjustment: 22 Effective length of query: 191 Effective length of database: 191 Effective search space: 36481 Effective search space used: 36481 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