Align tagatose-bisphosphate aldolase; EC 4.1.2.40 (characterized)
to candidate H281DRAFT_01311 H281DRAFT_01311 fructose-bisphosphate aldolase
Query= CharProtDB::CH_024465 (286 letters) >FitnessBrowser__Burk376:H281DRAFT_01311 Length = 345 Score = 163 bits (413), Expect = 4e-45 Identities = 112/328 (34%), Positives = 169/328 (51%), Gaps = 45/328 (13%) Query: 1 MSIISTKYLLQDAQANGYAVPAFNIHNAETIQAILEVCSEMRSPVILAGTPGTFKHIALE 60 M+ I+ + LL A +GY VPAFN++N E I AI++ E SPVIL + G K+ Sbjct: 1 MAFIALRQLLDHAAEHGYGVPAFNVNNMEQIHAIMQAAEETASPVILQASAGARKYAGEP 60 Query: 61 EI-YALCSAYSTTYNMPLALHLDHHESLDDIRRKVHAGVRSAMIDGSHFP-------FAE 112 + + + +A ++PL LH DH S ++ + +G S M+DGS P + Sbjct: 61 YLRHLVLAALEAHPDIPLVLHQDHGASPAVCQQAIRSGFTSVMMDGSLLPDQKTPATYDY 120 Query: 113 NVKLVKSVVDFCHSQDCSVEAELGRLGGVEDDMSVDAESA----------FLTDPQEAKR 162 NV++ + VVD H+ SVE ELG LG +E M+ + + LTDP+EA+ Sbjct: 121 NVEVSRRVVDAAHAVGVSVEGELGCLGSLETGMAGEEDGVGAQGQLTRDDLLTDPREAQI 180 Query: 163 FVELTGVDSLAVAIGTAHGLY--SKTPKID---FQRLAEIRE-VVDVPLVLHGASDVPDE 216 FVE TGVD+LA+AIGT+HG Y S+ P D R+ EI E + + LV+HG+S VP E Sbjct: 181 FVESTGVDALAIAIGTSHGAYKFSREPTGDILAIGRIVEIHERIPNTHLVMHGSSSVPQE 240 Query: 217 F---------------------VRRTIELGVTKVNVATELKIAFAGAVKAWFAENPQGND 255 + ++R I GV KVN+ T++++A +GA++ A D Sbjct: 241 WLAIIREFGGEIPTTYGVPVEEIQRGIAHGVRKVNIDTDIRLAMSGAMRKSLANARAEFD 300 Query: 256 PRYYMRVGMDAMKEVVRNKINVCGSANR 283 PR ++ A + V + G A + Sbjct: 301 PRAALKAATAAARGVCVERFEAFGCAGQ 328 Lambda K H 0.319 0.134 0.386 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: 245 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: 286 Length of database: 345 Length adjustment: 27 Effective length of query: 259 Effective length of database: 318 Effective search space: 82362 Effective search space used: 82362 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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