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_004110704.1 RHSP_RS06210 4-hydroxy-2-oxoheptanedioate aldolase
Query= SwissProt::P23522 (256 letters) >NCBI__GCF_000359745.1:WP_004110704.1 Length = 268 Score = 246 bits (629), Expect = 3e-70 Identities = 122/250 (48%), Positives = 170/250 (68%), Gaps = 1/250 (0%) Query: 8 NKFKAALAAKQVQIGCWSALSNPISTEVLGLAGFDWLVLDGEHAPNDISTFIPQLMALKG 67 N FK AL + QIG W AL+N + E+ AG+DWL+LD EHAPND+ + QL A+KG Sbjct: 6 NLFKQALKEGRAQIGLWQALANAYTVEISAGAGYDWLLLDAEHAPNDVPLLVSQLQAMKG 65 Query: 68 SASAPVVRVPTNEPVIIKRLLDIGFYNFLIPFVETKEEAELAVASTRYPPEGIRGVSVS- 126 +AS ++R P E IIK++LDIG LIP V++KE AE V + RYPP G+RGV + Sbjct: 66 TASHAIIRPPIGETWIIKQMLDIGAQTLLIPMVDSKETAETMVKAVRYPPHGVRGVGAAL 125 Query: 127 HRANMFGTVADYFAQSNKNITILVQIESQQGVDNVDAIAATEGVDGIFVGPSDLAAALGH 186 RA+ F + DY +N I +L+Q+ES+ G++ +DAIA+T+GVDG+F+GP+DLAA +G+ Sbjct: 126 ARASAFNRIPDYLPTANDEICLLLQVESRAGLEALDAIASTDGVDGVFIGPADLAADMGY 185 Query: 187 LGNASHPDVQKAIQHIFNRASAHGKPSGILAPVEADARRYLEWGATFVAVGSDLGVFRSA 246 LG P+VQ ++ + AHGK +GIL + A+RYLE GATFVA+G+D+ + +A Sbjct: 186 LGKPGAPEVQAEVEKALAKIQAHGKAAGILIGDLSLAKRYLELGATFVAIGNDVTLLANA 245 Query: 247 TQKLADTFKK 256 T KL D FKK Sbjct: 246 TTKLLDDFKK 255 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: 208 Number of extensions: 4 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: 268 Length adjustment: 25 Effective length of query: 231 Effective length of database: 243 Effective search space: 56133 Effective search space used: 56133 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 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