Align Probable fructose-bisphosphate aldolase; FBP aldolase; FBPA; Fructose-1,6-bisphosphate aldolase; EC 4.1.2.13 (characterized)
to candidate 3607858 Dshi_1266 ketose-bisphosphate aldolase (RefSeq)
Query= SwissProt::P13243 (285 letters) >FitnessBrowser__Dino:3607858 Length = 280 Score = 164 bits (415), Expect = 2e-45 Identities = 100/258 (38%), Positives = 146/258 (56%), Gaps = 10/258 (3%) Query: 1 MPLVSMTEMLNTAKEKGYAVGQFNLNNLEFTQAILQAAEEEKSPVILGVSEGAGRYMGGF 60 M L +++E+L A E GYAVG E +A +AAE E P+IL R Sbjct: 1 MTLATLSEVLQPALEGGYAVGGLVCLGWEEMRAYTRAAEAEGVPLILQAGPSC-RAHTPL 59 Query: 61 KTVVAMVKALMEEYKVTVPVAIHLDHGSSFESCAKAIHAGFTSVMIDASHHPFEENVATT 120 + AM + L E + +VPV HLDHG SF C +A+ +GFTS+M D S P EEN+A T Sbjct: 60 PVLGAMFRHLAE--RASVPVVAHLDHGYSFAECQEALDSGFTSLMFDGSRLPLEENIAQT 117 Query: 121 AKVVELAHFHGVSVEAELGTVGGQEDDVIAEGVIYADPKECQELVERTGIDCLAPALGSV 180 A++V+LAH G+S E E+G VG E D ++G DP+E TG+D +A ++G+V Sbjct: 118 ARIVDLAHKAGISCEGEIGFVGYAEGDA-SQG---TDPEEAARFARETGVDAMAISVGNV 173 Query: 181 HGPYKGEPNLGFKEMEEIGKSTGLPLVLHGGTGIPTADIKKSISLGT--AKINVNTENQI 238 H E L + EI T +PLV+HGG+G+P A + ++ G+ K N+ TE ++ Sbjct: 174 HLQQNREGGLDEGRIAEIAARTEVPLVIHGGSGVPLAQ-RTRLARGSTICKFNIGTELRM 232 Query: 239 SSAKAVRETLAAKPDEYD 256 + A+RE + + PD +D Sbjct: 233 AFGAALREAVTSDPDRFD 250 Lambda K H 0.313 0.131 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: 235 Number of extensions: 17 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: 285 Length of database: 280 Length adjustment: 26 Effective length of query: 259 Effective length of database: 254 Effective search space: 65786 Effective search space used: 65786 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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