Align Fructose-bisphosphate aldolase class 1; Fructose-bisphosphate aldolase class I; FBP aldolase; EC 4.1.2.13 (characterized)
to candidate WP_013706233.1 DESAC_RS06270 fructose-bisphosphate aldolase
Query= SwissProt::P0A991 (350 letters) >NCBI__GCF_000195295.1:WP_013706233.1 Length = 350 Score = 477 bits (1227), Expect = e-139 Identities = 230/347 (66%), Positives = 285/347 (82%), Gaps = 1/347 (0%) Query: 4 IAQLLGKDADNLLQHRCMTIPSDQLYLPGHDYVDRVMIDNNRPPAVLRNMQTLYNTGRLA 63 I LLG +A++LL + C P + L+LPG D+++RVM+ +RP LR++ L+N GRLA Sbjct: 5 IHSLLGNEAESLLTYTCKGFPKETLHLPGPDFIERVMVPTDRPVKALRSLAALFNHGRLA 64 Query: 64 GTGYLSILPVDQGVEHSAGASFAANPLYFDPKNIVELAIEAGCNCVASTYGVLASVSRRY 123 GTGYLSILPVDQG+EHSAGASFA NP+YFDP+NI++LAIE GCN VAST GVLA+V+RRY Sbjct: 65 GTGYLSILPVDQGIEHSAGASFAPNPIYFDPENIIKLAIEGGCNAVASTLGVLAAVARRY 124 Query: 124 AHRIPFLVKLNHNETLSYPNTYDQTLYASVEQAFNMGAVAVGATIYFGSEESRRQIEEIS 183 A+RIPF+VK+NHNE L+YP +DQTL+A VEQAFNMGA A+GATIY+GS ESRRQI EIS Sbjct: 125 AYRIPFIVKINHNELLTYPAIHDQTLFAQVEQAFNMGATAIGATIYYGSAESRRQILEIS 184 Query: 184 AAFERAHELGMVTVLWAYLRNSAFKKDGVDYHVSADLTGQANHLAATIGADIVKQKMAEN 243 AFE+AHELG+ T+LW YLRN AFK DYHV+ADLTGQAN+L ATI ADI+KQK+ EN Sbjct: 185 DAFEQAHELGLATILWCYLRNPAFKTKEKDYHVAADLTGQANYLGATIKADIIKQKLPEN 244 Query: 244 NGGYKAINYGYTDDRVYSKLTSENPIDLVRYQLANCYMGRAGLINSGGAAGGETDLSDAV 303 NGGY A+ +G T RVYS L ++PI+L RYQ+ANC+MGR GLINSGGA+ GE DL+ A Sbjct: 245 NGGYTALKFGKTHARVYSDLAPDHPIELTRYQVANCFMGRVGLINSGGAS-GENDLAQAA 303 Query: 304 RTAVINKRAGGMGLILGRKAFKKSMADGVKLINAVQDVYLDSKITIA 350 RTAVINKRAGG GLI GRKAF++ MA+G +L++ +QDVYL ++T+A Sbjct: 304 RTAVINKRAGGTGLISGRKAFQRPMAEGAELLHTIQDVYLCPEVTVA 350 Lambda K H 0.318 0.134 0.386 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: 430 Number of extensions: 12 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: 350 Length of database: 350 Length adjustment: 29 Effective length of query: 321 Effective length of database: 321 Effective search space: 103041 Effective search space used: 103041 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 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 10 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