Align 6-phospho-5-dehydro-2-deoxy-D-gluconate aldolase; DKGP aldolase; EC 4.1.2.29 (uncharacterized)
to candidate H281DRAFT_01311 H281DRAFT_01311 fructose-bisphosphate aldolase
Query= curated2:Q5WKY5 (293 letters) >FitnessBrowser__Burk376:H281DRAFT_01311 Length = 345 Score = 156 bits (395), Expect = 5e-43 Identities = 112/331 (33%), Positives = 159/331 (48%), Gaps = 49/331 (14%) Query: 1 MGFVPMAPLLADAKKDSYAIGQFNINGLQWAKAILAGAESQQSPVIAAASDRLIDYLGGF 60 M F+ + LL A + Y + FN+N ++ AI+ AE SPVI AS Y G Sbjct: 1 MAFIALRQLLDHAAEHGYGVPAFNVNNMEQIHAIMQAAEETASPVILQASAGARKYAGEP 60 Query: 61 QTVVAMMGALTDELGITVPVVLHLDHGLSIERCKKAVDAGFSSVMFDGSHYPINE----- 115 ++ AL E +P+VLH DHG S C++A+ +GF+SVM DGS P + Sbjct: 61 YLRHLVLAAL--EAHPDIPLVLHQDHGASPAVCQQAIRSGFTSVMMDGSLLPDQKTPATY 118 Query: 116 --NIDMTKEVVAYAHAHNVSVEGEVGTVGGMEDGLMAEIK-------------YADVEEC 160 N+++++ VV AHA VSVEGE+G +G +E G+ E D E Sbjct: 119 DYNVEVSRRVVDAAHAVGVSVEGELGCLGSLETGMAGEEDGVGAQGQLTRDDLLTDPREA 178 Query: 161 QRFVCETNVDALAAALGSVHGKYK--GEPK---LGFNEMAAISAST-NVPLVLHGAS--- 211 Q FV T VDALA A+G+ HG YK EP L + I N LV+HG+S Sbjct: 179 QIFVESTGVDALAIAIGTSHGAYKFSREPTGDILAIGRIVEIHERIPNTHLVMHGSSSVP 238 Query: 212 ------------------GIPDEQLQRAIKLGHAKININTECMIAWSDACRTTFAEQETA 253 G+P E++QR I G K+NI+T+ +A S A R + A Sbjct: 239 QEWLAIIREFGGEIPTTYGVPVEEIQRGIAHGVRKVNIDTDIRLAMSGAMRKSLANARAE 298 Query: 254 FEPRLLLQEGLAMVQATVEKKIKQFGAANKA 284 F+PR L+ A + ++ + FG A +A Sbjct: 299 FDPRAALKAATAAARGVCVERFEAFGCAGQA 329 Lambda K H 0.317 0.132 0.378 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: 240 Number of extensions: 11 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: 293 Length of database: 345 Length adjustment: 27 Effective length of query: 266 Effective length of database: 318 Effective search space: 84588 Effective search space used: 84588 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: 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