Align Fructose-1,6-bisphosphate aldolase/phosphatase; FBP A/P; FBP aldolase/phosphatase; EC 3.1.3.11; EC 4.1.2.13 (characterized)
to candidate WP_048080252.1 EI99_RS01985 fructose 1,6-bisphosphatase
Query= SwissProt::D9PUH5 (365 letters) >NCBI__GCF_000746075.1:WP_048080252.1 Length = 365 Score = 630 bits (1625), Expect = 0.0 Identities = 294/365 (80%), Positives = 337/365 (92%) Query: 1 MKTTISVIKADVGSVAGHAVAHEALKKKCDEILAEARDTGILEDYYITNCGDDIDLIMTH 60 MKTTISVIKADVGSVAGH +AH AL KC+EILA+A++ +L DYY+TNCGDD +LIMTH Sbjct: 1 MKTTISVIKADVGSVAGHGIAHPALLAKCEEILAKAKEEELLTDYYVTNCGDDTELIMTH 60 Query: 61 RNGEENEEVHQTAWNAFREATEVARGLKLYGAGQDLLSDTFSGNIKGMGPGCAEMEFKER 120 + GEEN+E+H+ A+NAF EAT +A+ LKLYGAGQDLLSDTFSGNIKGMGPG AEMEFKER Sbjct: 61 KQGEENKEIHELAFNAFMEATAIAKDLKLYGAGQDLLSDTFSGNIKGMGPGVAEMEFKER 120 Query: 121 PSDPVIIFCCDKTEPGAFNLPLFRMFADPFNTAGLVIDPTLHNGYEFEVFDVVEHKKVTM 180 PSDPV++FCCDKTEPGAFNLP+FRMFADPFNTAGLVIDP+LHNGY+FE+FDV+EHKKVTM Sbjct: 121 PSDPVVVFCCDKTEPGAFNLPIFRMFADPFNTAGLVIDPSLHNGYKFEIFDVMEHKKVTM 180 Query: 181 ACPDEMYDLLALLGSISRYVIKKIHRRDDGEIAASVSTERLNLMAGKYIGKDDPVAIVRA 240 CP+EMYD LALLGSISRYVIK++ R+DD EIAA++STERLNLMAG Y+GKDDPVAIVR+ Sbjct: 181 NCPEEMYDALALLGSISRYVIKRVIRKDDNEIAAAISTERLNLMAGSYVGKDDPVAIVRS 240 Query: 241 QSGFPAAGEVVEPFAFPHLVGGWMRGSHNGPLMPVAQRDATPVRFDGPPRVIGLGFQIAD 300 QSGFPAAGEVVEPFAFPHLVGGWMRGSHNGPLMPV Q++A PVRFDGPPRV+ LGFQIAD Sbjct: 241 QSGFPAAGEVVEPFAFPHLVGGWMRGSHNGPLMPVGQKNAYPVRFDGPPRVMALGFQIAD 300 Query: 301 CKLVGPIDMFDDPSFDRSRQLASEIAEYMRRHGPFEPHRLPSDEMEYTSLPGVLEKLGDR 360 +LVGP DMFDDP++D +R+ A+EIA+YMRRHGPFEPHRLP+DEMEYTSLPGV+EKL R Sbjct: 301 GELVGPADMFDDPAYDPARKQAAEIADYMRRHGPFEPHRLPADEMEYTSLPGVMEKLEGR 360 Query: 361 FEDMD 365 FED+D Sbjct: 361 FEDID 365 Lambda K H 0.320 0.139 0.423 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: 618 Number of extensions: 19 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: 365 Length of database: 365 Length adjustment: 30 Effective length of query: 335 Effective length of database: 335 Effective search space: 112225 Effective search space used: 112225 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: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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