Align 5-keto-4-deoxy-D-glucarate aldolase; KDGluc aldolase; KDGlucA; 2-dehydro-3-deoxy-D-glucarate aldolase; 2-keto-3-deoxy-D-glucarate aldolase; 5-dehydro-4-deoxy-D-glucarate aldolase; Alpha-keto-beta-deoxy-D-glucarate aldolase; EC 4.1.2.20 (characterized)
to candidate WP_041100875.1 SUTH_RS16720 aldolase/citrate lyase family protein
Query= SwissProt::P23522 (256 letters) >NCBI__GCF_000828635.1:WP_041100875.1 Length = 253 Score = 130 bits (327), Expect = 3e-35 Identities = 77/254 (30%), Positives = 125/254 (49%), Gaps = 3/254 (1%) Query: 1 MNNDVFPNKFKAALAAKQVQIGCWSALSNPISTEVLGLAGFDWLVLDGEHAPNDISTFIP 60 MN + +A L + IG W + +P E++G G+DW+ +D EH I Sbjct: 1 MNRLKAVREIRAQLKSGGHSIGSWMQIPHPAIAEIMGQGGYDWVAVDMEHGAVAIHQLPD 60 Query: 61 QLMALKGSASAPVVRVPTNEPVIIKRLLDIGFYNFLIPFVETKEEAELAVASTRYPPEGI 120 AL+ + P+VR+ +P K+ LD G ++P +E+ E+ + R+PP G Sbjct: 61 LFRALELGGTLPLVRLAHGQPKDCKQALDAGAGGVIVPMIESAEQLAGVRDACRWPPAGT 120 Query: 121 RGVSVSHRANMFGTVADYFAQSNKNITILVQIESQQGVDNVDAIAATEGVDGIFVGPSDL 180 RGV S RAN+FG D + + + ++ IE + V N++ I A +G+D I +GP DL Sbjct: 121 RGVGFS-RANLFGKHFDAYREEAQAPLLVAMIEHHRAVANLEGILAVDGLDAILIGPYDL 179 Query: 181 AAALGHLGNASHPDVQKAIQHIFNRASAHGKPSG--ILAPVEADARRYLEWGATFVAVGS 238 +A++G HP+ ++ I A AH P+G ++AP + R L+ G F+A Sbjct: 180 SASMGLTAQFDHPEFCAVMEKIRALAEAHAVPAGLHVVAPSRDELNRRLDEGYRFLAYSI 239 Query: 239 DLGVFRSATQKLAD 252 D + S D Sbjct: 240 DAVMLNSVVSHGVD 253 Lambda K H 0.318 0.134 0.392 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: 156 Number of extensions: 6 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: 256 Length of database: 253 Length adjustment: 24 Effective length of query: 232 Effective length of database: 229 Effective search space: 53128 Effective search space used: 53128 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: 47 (22.7 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