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 Ac3H11_2083 4-Hydroxy-2-oxoglutarate aldolase (EC 4.1.3.16) @ 2-dehydro-3-deoxyphosphogluconate aldolase (EC 4.1.2.14)
Query= BRENDA::P0A955 (213 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2083 Length = 209 Score = 214 bits (545), Expect = 9e-61 Identities = 106/195 (54%), Positives = 140/195 (71%) Query: 11 ILTTGPVVPVIVVKKLEHAVPMAKALVAGGVRVLEVTLRTECAVDAIRAIAKEVPEAIVG 70 I + GPV+PVIV+ ++E A+P+A+AL+AGGV+VLEVTLRT + AI AIA+ +PEA+VG Sbjct: 6 IASHGPVIPVIVIDRVEDALPLAEALLAGGVKVLEVTLRTAAGLPAIEAIARHLPEAVVG 65 Query: 71 AGTVLNPQQLAEVTEAGAQFAISPGLTEPLLKAATEGTIPLIPGISTVSELMLGMDYGLK 130 GTVLN +EAGA+FA+SPG T + A +PL+PG++T SE+M + G Sbjct: 66 VGTVLNADDARRASEAGARFAVSPGYTSEVGSACKGLNLPLLPGVATSSEIMTALADGFS 125 Query: 131 EFKFFPAEANGGVKALQAIAGPFSQVRFCPTGGISPANYRDYLALKSVLCIGGSWLVPAD 190 K FPAEA GG+ L++ A PF QV FCPTGGI+ A +YLAL +V C+GGSWL P D Sbjct: 126 FLKLFPAEAVGGIPLLKSWASPFGQVSFCPTGGITNATAPNYLALPNVRCVGGSWLTPTD 185 Query: 191 ALEAGDYDRITKLAR 205 A+ AGD+ RIT+LAR Sbjct: 186 AVRAGDWARITELAR 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: 202 Number of extensions: 4 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 17 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