Align 6-phospho-5-dehydro-2-deoxy-D-gluconate aldolase; DKGP aldolase; EC 4.1.2.29 (characterized)
to candidate Ac3H11_658 Fructose-bisphosphate aldolase class II (EC 4.1.2.13)
Query= SwissProt::P42420 (290 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_658 Length = 349 Score = 160 bits (405), Expect = 4e-44 Identities = 111/328 (33%), Positives = 167/328 (50%), Gaps = 49/328 (14%) Query: 6 MKELLEDAKREQYAIGQFNINGLQWTKAILQAAQKEQSPVIAAASDRLVDYLGGFKTIAA 65 M+ELL+ A Y I FN+N L+ +A++ AA + +PVI AS Y G I Sbjct: 1 MRELLDHAAANSYGIPAFNVNNLEQVQAVMAAADEVGAPVILQASAGARKYAGE-PFIKH 59 Query: 66 MVGALIEDMAITVPVVLHLDHGSSAERCRQAIDAGFSSVMIDGS-------HQPIDENIA 118 ++ A +E +P+V+H DHG+S + C AID GF SVM+DGS + N+ Sbjct: 60 LIQAAVEAFP-HIPLVMHQDHGTSPKVCAGAIDLGFGSVMMDGSLMEDGKTPSSFEYNVE 118 Query: 119 MTKEVTDYAAKHGVSVEAEVGTVG-------GMEDGLVGGVRY------ADITECERIVK 165 +T++V D A K GV+VE E+G +G G EDG+ V+ D E VK Sbjct: 119 VTRKVVDMAHKVGVTVEGELGCLGNLETGEAGEEDGIGADVKLDHSQMLTDPEEAAVFVK 178 Query: 166 ETNIDALAAALGSVHGKYQ------GEPNLGFKEMEAISRMTDIPLVLHGAS-------- 211 T +DALA A+G+ HG Y+ G+ + E R+ + LV+HG+S Sbjct: 179 ATQLDALAIAIGTSHGAYKFSRKPTGDILAISRVKEIHKRIPNTHLVMHGSSSVPAELLA 238 Query: 212 -------------GIPQDQIKKAITLGHAKININTECMVAWTDETRRMFQENSDLYEPRG 258 G+P ++I++AI G KINI+T+ +A T R+ EN D ++ R Sbjct: 239 IINQYGGKMKETYGVPVEEIQEAIKHGVRKINIDTDIRLAMTGAVRKFLAENPDKFDARE 298 Query: 259 YLTPGIEAVEETVRSKMREFGSAGKAAK 286 +L P EA ++ +++ EFG G+ AK Sbjct: 299 WLKPAREAAKQVCKARYLEFGCEGQGAK 326 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: 268 Number of extensions: 13 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: 349 Length adjustment: 27 Effective length of query: 263 Effective length of database: 322 Effective search space: 84686 Effective search space used: 84686 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