Align 6-phospho-5-dehydro-2-deoxy-D-gluconate aldolase; DKGP aldolase; EC 4.1.2.29 (characterized)
to candidate PP_4960 PP_4960 Fructose-bisphosphate aldolase
Query= SwissProt::P42420 (290 letters) >FitnessBrowser__Putida:PP_4960 Length = 354 Score = 159 bits (403), Expect = 7e-44 Identities = 112/335 (33%), Positives = 175/335 (52%), Gaps = 53/335 (15%) Query: 1 MAFVSMKELLEDAKREQYAIGQFNINGLQWTKAILQAAQKEQSPVIAAASDRLVDYLGGF 60 MA +SM+++L+ A Y + FN+N L+ +AI++AA K SPVI AS Y G Sbjct: 1 MALISMRQMLDHAAEFGYGVPAFNVNNLEQMRAIMEAADKTDSPVIVQASAGARKYAGA- 59 Query: 61 KTIAAMVGALIEDMAITVPVVLHLDHGSSAERCRQAIDAGFSSVMIDGS-----HQPIDE 115 + ++ A IE+ +PV +H DHG+S + C+++I GFSSVM+DGS P D Sbjct: 60 PFLRHLILAAIEEFP-HIPVCMHQDHGTSPDVCQRSIQLGFSSVMMDGSLGEDGKTPTDY 118 Query: 116 --NIAMTKEVTDYAAKHGVSVEAEVGTVGGMEDGLVG--------GV-----RYADITEC 160 N+ +T++ A GVSVE E+G +G +E G+ G GV D E Sbjct: 119 EYNVRVTQQTVAMAHACGVSVEGELGCLGSLETGMAGEEDGIGAEGVLDHSQMLTDPEEA 178 Query: 161 ERIVKETNIDALAAALGSVHGKYQ-GEPNLGFKEMEAISRMTDIP-------LVLHGASG 212 VK+T +DALA A+G+ HG Y+ +P G ++ AI R+ +I LV+HG+S Sbjct: 179 ADFVKKTQVDALAIAIGTSHGAYKFTKPPTG--DVLAIDRIKEIHKRIPNTHLVMHGSSS 236 Query: 213 IPQD---------------------QIKKAITLGHAKININTECMVAWTDETRRMFQENS 251 +PQ+ +I + I G K+NI+T+ +A T RR+ +N Sbjct: 237 VPQEWLAIINQYGGDIKETYGVPVEEIVEGIKHGVRKVNIDTDLRLASTGAMRRLMAQNP 296 Query: 252 DLYEPRGYLTPGIEAVEETVRSKMREFGSAGKAAK 286 ++PR + I+A+ + ++ FG+AG A+K Sbjct: 297 SEFDPRKFFGETIKAMRDVCIARYEAFGTAGNASK 331 Lambda K H 0.316 0.132 0.372 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: 261 Number of extensions: 14 Number of successful extensions: 7 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: 290 Length of database: 354 Length adjustment: 28 Effective length of query: 262 Effective length of database: 326 Effective search space: 85412 Effective search space used: 85412 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 (21.6 bits) S2: 48 (23.1 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