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_048191996.1 PYRFU_RS08665 fructose 1,6-bisphosphatase
Query= curated2:B6YTP6 (375 letters) >NCBI__GCF_000223395.1:WP_048191996.1 Length = 389 Score = 509 bits (1311), Expect = e-149 Identities = 251/375 (66%), Positives = 299/375 (79%), Gaps = 6/375 (1%) Query: 1 MAIGEKITISVIKADIGGWPGHSRVHPQLIEAAEEVLAKAKEEGTIIDFYVAYAGDDLQL 60 M+ K+TISVIKADIG GH +VHP + AA VLA+AK +G IIDFYV + GDDLQL Sbjct: 1 MSEERKVTISVIKADIGSIAGHHKVHPDTMAAAARVLAEAKRKGVIIDFYVTHVGDDLQL 60 Query: 61 IMTHKKGVDSPDIHGLAWKAFEEATEIAKEFGLYGAGQDLLKDAFSGNIRGMGPGIAEME 120 IMTH+KGVDSP+IH LAW AF++A E+AKE GLY AGQDLL DAFSGNIRG+GPG+AEME Sbjct: 61 IMTHRKGVDSPEIHELAWNAFKKAAEVAKELGLYAAGQDLLSDAFSGNIRGLGPGVAEME 120 Query: 121 ITLRKSEPIVTFHMDKTEPGAFNLPIFRMFADPFNTAGLVIDPNMHMGFRFEVWDIKEHK 180 I R SEPIV F DKTEPGAFNLP+FR FADPF TAGLVIDP MH GFRF++ D+ E + Sbjct: 121 IVERPSEPIVIFMADKTEPGAFNLPLFRAFADPFTTAGLVIDPRMHDGFRFQILDLYEGR 180 Query: 181 RVILNTPEEIYDLLALIGAKSRYVIKRVYPKEGHKISKDEPVAVISTEKLYEIAGEYVGK 240 + LN PEE+YD+LALIG +RYVIKR++ K +I+ AV+S+E+L IAG YVGK Sbjct: 181 MIELNAPEEMYDILALIGDPTRYVIKRIFRKTDGEIA-----AVVSSERLNLIAGRYVGK 235 Query: 241 DDPVAIVRAQSGLPALGEVLEPFAFPHLVSGWMRGSHNGPIMPVPMHQANPTRFDGPPRV 300 DDPVAI R Q G PALGE+LEPFAFPHLV GWMRGSH GP+MPV + A TRFDGPPRV Sbjct: 236 DDPVAIARVQHGFPALGEILEPFAFPHLVPGWMRGSHWGPLMPVGLRDARCTRFDGPPRV 295 Query: 301 VALGWQISPEGKLVGPVDLFDDPAFDYARQKALEITEYIRRHGPFEPHRLPLEDMEYTTL 360 +ALG+Q++ +G+L+GPVDLF+D AFD R+ A +I EY+RRHGPF PHRL E+MEYTTL Sbjct: 296 IALGFQVT-KGRLIGPVDLFEDVAFDETRRLAQQIAEYMRRHGPFMPHRLHAEEMEYTTL 354 Query: 361 PGVLKKLEERFEDIE 375 P VLKKLE R++ +E Sbjct: 355 PDVLKKLEGRWKKVE 369 Lambda K H 0.319 0.140 0.425 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: 586 Number of extensions: 29 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: 375 Length of database: 389 Length adjustment: 30 Effective length of query: 345 Effective length of database: 359 Effective search space: 123855 Effective search space used: 123855 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 (21.7 bits) S2: 50 (23.9 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