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_011383244.1 AMB_RS04095 4-hydroxy-2-oxoheptanedioate aldolase
Query= SwissProt::P23522 (256 letters) >NCBI__GCF_000009985.1:WP_011383244.1 Length = 267 Score = 232 bits (592), Expect = 5e-66 Identities = 120/249 (48%), Positives = 161/249 (64%), Gaps = 1/249 (0%) Query: 8 NKFKAALAAKQVQIGCWSALSNPISTEVLGLAGFDWLVLDGEHAPNDISTFIPQLMALKG 67 N FK ALA + QIG W L+NP + E+ AGFDWL++DGEHAPND+ + QL A+ Sbjct: 6 NPFKRALAEGRPQIGLWVGLANPYTAEICAGAGFDWLLIDGEHAPNDVPGLLAQLQAVAP 65 Query: 68 SASAPVVRVPTNEPVIIKRLLDIGFYNFLIPFVETKEEAELAVASTRYPPEGIRGVSVS- 126 S P+VR + +IK+LLDIG L+P ++T E+A VA+ YPP G+RGV + Sbjct: 66 YPSHPIVRPVIGDTALIKQLLDIGAQTLLVPMIDTPEQAAATVAAMHYPPRGVRGVGAAL 125 Query: 127 HRANMFGTVADYFAQSNKNITILVQIESQQGVDNVDAIAATEGVDGIFVGPSDLAAALGH 186 RA+ +G + DY ++ + +L+QIE+ G+ N++AIA T+GVDGIF+GP+DLAA+LGH Sbjct: 126 ARASRWGRIGDYLKTASDELCLLLQIETVTGLRNLEAIATTDGVDGIFIGPADLAASLGH 185 Query: 187 LGNASHPDVQKAIQHIFNRASAHGKPSGILAPVEADARRYLEWGATFVAVGSDLGVFRSA 246 LG SHP+VQ I+ G PSGILA E AR++L GATFVAVG D V A Sbjct: 186 LGAPSHPEVQAEIEKALAMLKRLGVPSGILAADETLARKFLAAGATFVAVGIDTMVLSRA 245 Query: 247 TQKLADTFK 255 LA T+K Sbjct: 246 LSALAATYK 254 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: 212 Number of extensions: 7 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: 267 Length adjustment: 25 Effective length of query: 231 Effective length of database: 242 Effective search space: 55902 Effective search space used: 55902 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 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