Align 2-dehydro-3-deoxy-phosphogluconate aldolase (EC 4.1.2.14) (characterized)
to candidate WP_037582103.1 BS73_RS31540 bifunctional 4-hydroxy-2-oxoglutarate aldolase/2-dehydro-3-deoxy-phosphogluconate aldolase
Query= BRENDA::D4GV57 (219 letters) >NCBI__GCF_000744815.1:WP_037582103.1 Length = 204 Score = 140 bits (354), Expect = 1e-38 Identities = 77/201 (38%), Positives = 108/201 (53%) Query: 10 MQRLADSGVVAVMRGADADTIIDVADALHEGGVTAYEITADNPDAMDLIREVSASFSDNE 69 M LA V+ V+R + AL EGG+ E+T PD +R +A ++ Sbjct: 1 MDVLAADRVLTVVRAPRIPDAAALCRALAEGGIRTVELTFTTPDLTGHLRAAAAVAAETG 60 Query: 70 AIVGAGTALDAPTANAAIQAGAEFVVGPNFDEGVVETCNRYGTLVAPGIMTPTEATDAYS 129 +GAGT L A A AA+ AGAEF+V P V G V G TPTE A Sbjct: 61 CRIGAGTVLTAGDAAAAVDAGAEFLVTPGLRPEVAAVGRERGVPVVMGAFTPTEVLTALD 120 Query: 130 AGADLVKVFPASSLGPGHLKSMKGPLPQIPMMPTGGVGLDNAADYIEAGAVVVGAGGALM 189 GA VK+FPA +LGP + K ++GPLP + ++P+GGV NA +++ GA+ V AG + Sbjct: 121 LGAAAVKIFPAHALGPRYFKDLRGPLPDVRLLPSGGVNAGNAGEFLAQGAIAVSAGTDAV 180 Query: 190 DDEAIENGDFEAITETAREFS 210 +A+ +GD+ IT AREF+ Sbjct: 181 PPQAVASGDWPEITRRAREFT 201 Lambda K H 0.314 0.133 0.374 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: 125 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: 219 Length of database: 204 Length adjustment: 21 Effective length of query: 198 Effective length of database: 183 Effective search space: 36234 Effective search space used: 36234 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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