Align Fructose-bisphosphate aldolase; FBP aldolase; FBPA; Fructose-1,6-bisphosphate aldolase; EC 4.1.2.13 (characterized)
to candidate 17210 b3137 tagatose 6-phosphate aldolase 1, kbaY subunit (NCBI)
Query= SwissProt::Q703I2 (305 letters) >FitnessBrowser__Keio:17210 Length = 286 Score = 220 bits (561), Expect = 3e-62 Identities = 126/298 (42%), Positives = 175/298 (58%), Gaps = 24/298 (8%) Query: 8 ILRKARAEGYGVGAFNTNNMEFTQAILEAAEEMKSPVILALSEGAMKYGG-RALTRMVVA 66 +L+ A+A GY V AFN +N E QAILE EM+SPVILA + G K+ + + A Sbjct: 9 LLQDAQANGYAVPAFNIHNAETIQAILEVCSEMRSPVILAGTPGTFKHIALEEIYALCSA 68 Query: 67 LAQEARVPVAVHLDHGSSYESVLKALREGFTSVMIDKSHEDFETNVRETKRVVEAAHAVG 126 + +P+A+HLDH S + + + + G S MID SH F NV+ K VV+ H+ Sbjct: 69 YSTTYNMPLALHLDHHESLDDIRRKVHAGVRSAMIDGSHFPFAENVKLVKSVVDFCHSQD 128 Query: 127 VTVEAELGRLAGIEEHVAVDEKDALLTNPEEARIFMERTGADYLAVAIGTSHGAYKGKGR 186 +VEAELGRL G+E+ ++VD + A LT+P+EA+ F+E TG D LAVAIGT+HG Y Sbjct: 129 CSVEAELGRLGGVEDDMSVDAESAFLTDPQEAKRFVELTGVDSLAVAIGTAHGLY--SKT 186 Query: 187 PFIDHPRLARIAKLVPAPLVLHGASAVPQELVERFRAAGGEIGEASGIHPEDIKKAISLG 246 P ID RLA I ++V PLVLHGAS VP E V R I LG Sbjct: 187 PKIDFQRLAEIREVVDVPLVLHGASDVPDEFVRR---------------------TIELG 225 Query: 247 IAKINTDTDLRLAFTALVRETLGKNPKEFDPRKYLGPAREAVKEVVKSRMELFGSVGR 304 + K+N T+L++AF V+ +NP+ DPR Y+ +A+KEVV++++ + GS R Sbjct: 226 VTKVNVATELKIAFAGAVKAWFAENPQGNDPRYYMRVGMDAMKEVVRNKINVCGSANR 283 Lambda K H 0.317 0.134 0.367 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: 187 Number of extensions: 6 Number of successful extensions: 4 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: 305 Length of database: 286 Length adjustment: 26 Effective length of query: 279 Effective length of database: 260 Effective search space: 72540 Effective search space used: 72540 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