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 GFF707 PGA1_c07220 putative 6-phospho-5-dehydro-2-deoxy-D-gluconate aldolase
Query= SwissProt::Q9KIP8 (286 letters) >FitnessBrowser__Phaeo:GFF707 Length = 279 Score = 123 bits (308), Expect = 5e-33 Identities = 80/266 (30%), Positives = 129/266 (48%), Gaps = 14/266 (5%) Query: 1 MSIISTKYLLQDAQANGYAVPAFNIHNAETIQAILEVCSEMRSPVILAGTPGTFKHIALE 60 M+I + +LQ A +GYAV E ++A + PVIL P H L Sbjct: 1 MTIATLAEVLQPALRDGYAVAGLVTLGWEDMRAYVAAAEAEGVPVILQAGPSCRVHTPLP 60 Query: 61 EIYALCSAYSTTYNMPLALHLDHHESLDDIRRKVHAGVRSAMIDGSHFPFAENVKLVKSV 120 + + + ++P+ HLDH + +D R + +G S M DGS +N+ ++ Sbjct: 61 ILGKMFRHLAEGASVPVVAHLDHGYTAEDCRIAIDSGFTSVMFDGSRNALDDNIAETAAI 120 Query: 121 VDFCHSQDCSVEAELGRLGGVEDDMSVDAESAFLTDPQEAKRFVELTGVDSLAVAIGTAH 180 H+ S E E+G +G E + TDP+EA+RF + TGVD++A+++G H Sbjct: 121 AGMAHAAGVSCEGEIGFVG------YSGGEGSAGTDPEEARRFAQETGVDAMAISVGNVH 174 Query: 181 GLYSKTPKIDFQRLAEIREVVDVPLVLHGASDVPDEFVRRTI--ELGVTKVNVATELKIA 238 K +D R+ I + +VPLV+HG S VP RR + E + K N+ TEL++ Sbjct: 175 LQQDKEGGLDIDRIRAIEAITEVPLVIHGGSGVP-VAQRRMLARESRICKFNIGTELRMV 233 Query: 239 FAGAVKAWFAENPQGNDPRNYMRVGM 264 F A++ + +DP + RV + Sbjct: 234 FGAAMR-----DAVNSDPDRFDRVSI 254 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: 195 Number of extensions: 10 Number of successful extensions: 2 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: 279 Length adjustment: 26 Effective length of query: 260 Effective length of database: 253 Effective search space: 65780 Effective search space used: 65780 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: 47 (22.7 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