Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate BWI76_RS24855 BWI76_RS24855 tagatose-bisphosphate aldolase
Query= BRENDA::Q9RHA2 (305 letters) >FitnessBrowser__Koxy:BWI76_RS24855 Length = 284 Score = 237 bits (605), Expect = 2e-67 Identities = 133/304 (43%), Positives = 184/304 (60%), Gaps = 24/304 (7%) Query: 2 LVTGLEILKKAREEGYGVGAFNVNNMEFLQAVLEAAEEQRSPVILALSEGAMKYGGRA-L 60 +++ +L KA+ GY V AFN++N+E +Q V+E A E RSP+ILA + G Y G + Sbjct: 3 IISSKNMLLKAQRLGYAVPAFNIHNLETMQVVVETAAELRSPLILAGTPGTYSYAGTGNV 62 Query: 61 TLMAVELAKEARVPVAVHLDHGSSYESVLRALRAGFTSVMIDKSHEDFETNVRETRRVVE 120 +A +LAK +P+AVHLDH + R ++AG SVMID SH FE NV + VVE Sbjct: 63 VAIARDLAKIWDLPLAVHLDHHEDLADITRKVQAGIRSVMIDGSHSPFEENVALVKSVVE 122 Query: 121 AAHAVGVTVEAELGRLAGIEEHVAVDEKDALLTNPEEARIFMERTGADYLAVAIGTSHGA 180 +H +VEAELGRL G+E+ + VD KDAL TNPE+AR F+ RTG D LAVAIGT+HG Sbjct: 123 LSHRYDASVEAELGRLGGVEDDLVVDAKDALYTNPEQAREFVARTGIDSLAVAIGTAHGL 182 Query: 181 YKGKGRPFIDHARLERIARLVPAPLVLHGASAVPPELVERFRASGGEIGEAAGIHPEDIK 240 Y + P +D RL I V PLVLHGAS +P DI+ Sbjct: 183 YAAE--PKLDFDRLAAIRDRVDVPLVLHGASGLP---------------------DSDIR 219 Query: 241 KAISLGIAKINTDTDLRLAFTALIREALNKNPKEFDPRKYLGPAREAVKEVVKSRMELFG 300 +AISLG+ K+N T+L++AF+ ++ +NP DPR Y+ PA+ A+K+VV+ + + G Sbjct: 220 RAISLGVCKVNVATELKIAFSDALKHYFEENPDANDPRHYMKPAKAAMKDVVRKVIHVCG 279 Query: 301 SVGR 304 G+ Sbjct: 280 CEGQ 283 Lambda K H 0.317 0.134 0.369 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: 201 Number of extensions: 11 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: 284 Length adjustment: 26 Effective length of query: 279 Effective length of database: 258 Effective search space: 71982 Effective search space used: 71982 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 Apr 09 2024. The underlying query database was built on Apr 09 2024.
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