Align 2-dehydro-3-deoxy-phosphogluconate aldolase (EC 4.1.2.14) (characterized)
to candidate WP_078429241.1 BK574_RS15640 bifunctional 4-hydroxy-2-oxoglutarate aldolase/2-dehydro-3-deoxy-phosphogluconate aldolase
Query= BRENDA::D4GV57 (219 letters) >NCBI__GCF_002019605.1:WP_078429241.1 Length = 214 Score = 176 bits (447), Expect = 2e-49 Identities = 90/201 (44%), Positives = 130/201 (64%), Gaps = 1/201 (0%) Query: 13 LADSGVVAVMRGADADTIIDVADALHEGGVTAYEITADNPDAMDLIREVSASFSDNEAIV 72 L + +VA++RG + + + VADA+H GGV E+T + DA +I ++ S S+ + + Sbjct: 7 LKEYRLVAIIRGIETSSAVPVADAIHAGGVHLIEVTMNTDDAPQMISKLVDS-SNGKMYI 65 Query: 73 GAGTALDAPTANAAIQAGAEFVVGPNFDEGVVETCNRYGTLVAPGIMTPTEATDAYSAGA 132 GAGT L+ A AI AGA++++ PN DE V++ G V PG+MTPTE AY+AGA Sbjct: 66 GAGTVLNKEMAKEAIAAGAQYLITPNVDEDVIKFGLERGIDVLPGVMTPTEIVKAYNAGA 125 Query: 133 DLVKVFPASSLGPGHLKSMKGPLPQIPMMPTGGVGLDNAADYIEAGAVVVGAGGALMDDE 192 +VKVFP+SSLG HLK ++GPL IPM+ GGV +DN + +AGAV VG G +L+ E Sbjct: 126 KMVKVFPSSSLGVSHLKELQGPLGHIPMVAVGGVNIDNVKSFFKAGAVAVGVGSSLIKKE 185 Query: 193 AIENGDFEAITETAREFSNII 213 AI G+F+ +T++A F I Sbjct: 186 AITQGNFDLLTQSANAFMQTI 206 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: 147 Number of extensions: 8 Number of successful extensions: 2 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: 214 Length adjustment: 22 Effective length of query: 197 Effective length of database: 192 Effective search space: 37824 Effective search space used: 37824 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 Apr 09 2024. 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