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 GFF1907 PGA1_c19370 4-hydroxy-2-oxovalerate aldolase BphF
Query= SwissProt::P23522 (256 letters) >FitnessBrowser__Phaeo:GFF1907 Length = 254 Score = 205 bits (522), Expect = 6e-58 Identities = 103/248 (41%), Positives = 157/248 (63%), Gaps = 1/248 (0%) Query: 8 NKFKAALAAKQVQIGCWSALSNPISTEVLGLAGFDWLVLDGEHAPNDISTFIPQLMAL-K 66 N+FK+A+A Q+G W+ + E+LG AGF+W+++D EHA + +P L A+ + Sbjct: 6 NRFKSAIANGTRQLGVWNTIGGNTVPELLGGAGFEWVLVDCEHAAIETIEVLPALQAIGQ 65 Query: 67 GSASAPVVRVPTNEPVIIKRLLDIGFYNFLIPFVETKEEAELAVASTRYPPEGIRGVSVS 126 ++ VVRV N+ + KR+LD+G N ++P+V+T EA AV + RY P G+RG++ Sbjct: 66 NPDTSAVVRVAANDATLFKRVLDMGAQNVMVPYVQTAREAAAAVHAMRYGPHGMRGMAGM 125 Query: 127 HRANMFGTVADYFAQSNKNITILVQIESQQGVDNVDAIAATEGVDGIFVGPSDLAAALGH 186 RA +G V DYF + + ++VQ+E+Q G++N+DAIA T+GVD +F+GP+DL+A++G Sbjct: 126 TRATRYGKVDDYFDVAEDELCLIVQVETQTGLENLDAIAGTDGVDAVFIGPADLSASMGL 185 Query: 187 LGNASHPDVQKAIQHIFNRASAHGKPSGILAPVEADARRYLEWGATFVAVGSDLGVFRSA 246 G +HPDV KA+ + NR G P+G++A A RYL GATFVAV DL V A Sbjct: 186 RGQMTHPDVDKAVSNAINRLGEMGVPAGVMALDPDIADRYLALGATFVAVAVDLVVLADA 245 Query: 247 TQKLADTF 254 + + F Sbjct: 246 VSNIRNRF 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: 178 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: 254 Length adjustment: 24 Effective length of query: 232 Effective length of database: 230 Effective search space: 53360 Effective search space used: 53360 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