Align 6-phospho-5-dehydro-2-deoxy-D-gluconate aldolase; DKGP aldolase; EC 4.1.2.29 (characterized)
to candidate 8499233 DvMF_0013 fructose-1,6-bisphosphate aldolase, class II (RefSeq)
Query= SwissProt::P42420 (290 letters) >FitnessBrowser__Miya:8499233 Length = 307 Score = 199 bits (507), Expect = 5e-56 Identities = 120/301 (39%), Positives = 168/301 (55%), Gaps = 28/301 (9%) Query: 1 MAFVSMKELLEDAKREQYAIGQFNINGLQWTKAILQAAQKEQSPVIAAASDRLVDYLGGF 60 M K++ E A +E YAIG FN+N ++ + I+QAA +EQ+P+I S Y G Sbjct: 1 MPLTGPKQMFERAYKEGYAIGAFNVNNMEIIQGIMQAAGEEQAPLILQVSAGARKYAGQN 60 Query: 61 KTIAAMVGALIEDMAITVPVVLHLDHGSSAERCRQAIDAGFSSVMIDGSHQPIDENIAMT 120 + + AL++ +PVVLHLDHG C+ ID GF+SVM DGSH P +ENIA+T Sbjct: 61 YIVKLIEAALMDT---DLPVVLHLDHGQDFNICKDCIDGGFTSVMYDGSHLPYEENIAVT 117 Query: 121 KEVTDYAAKHGVSVEAEVGTVGGMEDGLVGGVR-YADITECERIVKETNIDALAAALGSV 179 ++V +YA GV VEAE+G + G+ED + Y D + VK T D+LA A+G+ Sbjct: 118 RQVVEYAHARGVWVEAELGQLAGVEDEVSAEHSVYTDPDQAVDFVKRTGCDSLAIAIGTS 177 Query: 180 HG--KYQGEPNLGFKEMEAI-SRMTDIPLVLHGAS---------------------GIPQ 215 HG K+ GE L F +E I S + PLVLHGAS G+P+ Sbjct: 178 HGAYKFTGEAKLDFARLEKITSMLPGYPLVLHGASSVPQEFVDMANTYGGKVGSAKGVPE 237 Query: 216 DQIKKAITLGHAKININTECMVAWTDETRRMFQENSDLYEPRGYLTPGIEAVEETVRSKM 275 D ++KA T G KINI+T+ +A T R+ F E ++PR YL P +AV+ V+ K+ Sbjct: 238 DLLRKAATYGVCKINIDTDIRLAMTATIRKHFMEKPADFDPRAYLKPARDAVKNMVQHKI 297 Query: 276 R 276 R Sbjct: 298 R 298 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: 230 Number of extensions: 11 Number of successful extensions: 6 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: 307 Length adjustment: 27 Effective length of query: 263 Effective length of database: 280 Effective search space: 73640 Effective search space used: 73640 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