Align D-tagatose-1,6-bisphosphate aldolase subunit KbaY; TBPA; TagBP aldolase; D-tagatose-bisphosphate aldolase class II; Ketose 1,6-bisphosphate aldolase class II; Tagatose-bisphosphate aldolase; EC 4.1.2.40 (characterized)
to candidate 6938653 Sama_2756 fructose-1,6-bisphosphate aldolase (RefSeq)
Query= SwissProt::Q9KIP8 (286 letters) >FitnessBrowser__SB2B:6938653 Length = 355 Score = 166 bits (420), Expect = 7e-46 Identities = 110/330 (33%), Positives = 168/330 (50%), Gaps = 45/330 (13%) Query: 1 MSIISTKYLLQDAQANGYAVPAFNIHNAETIQAILEVCSEMRSPVILAGTPGTFKHIALE 60 M++IS + LL A +GY VPAFN++N E ++AI++ SPVI+ + G K+ + Sbjct: 1 MALISLRQLLDHAAEHGYGVPAFNVNNLEQMRAIMQAAEATDSPVIVQASAGARKYARPQ 60 Query: 61 EIYALCSAYSTTY-NMPLALHLDHHESLDDIRRKVHAGVRSAMIDGSHFP-------FAE 112 + L +A Y ++P+ +H DH D +R + G+ S M+DGS + Sbjct: 61 FLKYLMNAALEQYPDIPVCIHQDHGTHPDVCQRSIQLGMSSVMMDGSLMSDGKTPASYDY 120 Query: 113 NVKLVKSVVDFCHSQDCSVEAELGRLGGVEDD----------MSVDAESAFLTDPQEAKR 162 NV + + V F H+ SVE E+G LG +E + V + LT +EA R Sbjct: 121 NVDVTRKTVAFAHACGVSVEGEIGCLGSLETGTAGEEDGIGAVGVLSHDQLLTTAEEAAR 180 Query: 163 FVELTGVDSLAVAIGTAHGLY--SKTPKIDFQRLAEIREV----VDVPLVLHGASDVPD- 215 FV T VD+LA+AIGT+HG Y S+ P D R+ I+E+ + LV+HG+S VP Sbjct: 181 FVADTHVDALAIAIGTSHGAYKFSRKPTGDVLRIDRIKEIHARIPNTHLVMHGSSSVPQY 240 Query: 216 --------------------EFVRRTIELGVTKVNVATELKIAFAGAVKAWFAENPQGND 255 E + I+ GV KVN+ T+L++A GAV+ + AENP D Sbjct: 241 WLEIINQYGGEIPETYGVPLEEIVEGIKHGVRKVNIDTDLRLASTGAVRKFLAENPSEFD 300 Query: 256 PRNYMRVGMDAMKEVVRNKINVCGSANRIS 285 PR +++ M+AM ++ + G A S Sbjct: 301 PRKFLKASMEAMADICTERYEAFGCAGMAS 330 Lambda K H 0.319 0.133 0.384 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: 12 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: 286 Length of database: 355 Length adjustment: 27 Effective length of query: 259 Effective length of database: 328 Effective search space: 84952 Effective search space used: 84952 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