Align Fructose-1,6-bisphosphate aldolase/phosphatase; FBP A/P; FBP aldolase/phosphatase; EC 3.1.3.11; EC 4.1.2.13 (uncharacterized)
to candidate WP_084057302.1 B9A12_RS07615 fructose 1,6-bisphosphatase
Query= curated2:Q72K02 (363 letters) >NCBI__GCF_900176285.1:WP_084057302.1 Length = 370 Score = 422 bits (1084), Expect = e-123 Identities = 217/363 (59%), Positives = 261/363 (71%) Query: 1 MKVTLSVLKADIGSVGGHTLPSRKVLAKVEEVVREEVGRLLLDAYVFHIGDDIVLLLSHT 60 MK+TL+ +KADIGS+GGH PS++VL V VR+ LL+D +V + GDDI +L +HT Sbjct: 1 MKMTLTAIKADIGSIGGHIQPSQRVLETVTGHVRQHQKGLLIDWHVSYTGDDIAILCTHT 60 Query: 61 RGVRNQEVHALAWKAFREGTEVARAEGLYGAGQDLLKDAFTGNLHGLGPQVAEMEFTERP 120 GV ++ VH LAW AF+ GT+VA+ +GLYGAGQDLLKDAF GN+ GLGP VAEMEF ER Sbjct: 61 GGVGHEGVHKLAWDAFKAGTDVAKDQGLYGAGQDLLKDAFAGNVRGLGPAVAEMEFDERT 120 Query: 121 AEPFMVLAADKTEPGAFNLPLYLAFADPMYSSGLLLSPELRPGFRFRIMDLAQTERDSYI 180 AEPF+ AADKT+PGA+NLPLY AFADPM SGLLLSP + GF F IMD++ E D I Sbjct: 121 AEPFLFFAADKTDPGAYNLPLYQAFADPMTCSGLLLSPGMFQGFSFTIMDVSHVEADRVI 180 Query: 181 ELDAPERLYDIATLLRDSHRFAIESIWSRKHGEQAAVVSTTRLRNIAGRYVGKDDPVAIV 240 L+APE LYDIA LLRD RF +ESI SR+ GEQA VSTTRL NIAG+Y GKDDP+ +V Sbjct: 181 TLNAPEDLYDIAALLRDPERFVVESIHSRQTGEQAVAVSTTRLHNIAGKYTGKDDPIMLV 240 Query: 241 RTQKIFPATEEFGPVFALAPYVAGDTRGSHHMPLMPVRANTPASTFFCVPMVCGLAFSLR 300 R Q FPAT E F L YVAG RGSH PLMPVR NT S F P+V AF + Sbjct: 241 RVQGSFPATGEVLAPFHLGAYVAGFMRGSHAGPLMPVRQNTGTSFFDGPPIVSCAAFCVH 300 Query: 301 EGRLSEPVDLFADPVWEAVRAKVVEKAQEMRRQGFYGPAMLPMEELEYTGIAERLKALER 360 GRL+ PVD FA P W+ +R ++ +KA E+RRQGF+G AMLP ELEY GI ++L LE Sbjct: 301 HGRLTSPVDAFAHPYWDRIRDRISDKATEIRRQGFFGNAMLPFSELEYGGIVKKLADLEE 360 Query: 361 EFS 363 F+ Sbjct: 361 RFT 363 Lambda K H 0.321 0.138 0.405 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: 457 Number of extensions: 18 Number of successful extensions: 1 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: 363 Length of database: 370 Length adjustment: 30 Effective length of query: 333 Effective length of database: 340 Effective search space: 113220 Effective search space used: 113220 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 (21.9 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