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_013707055.1 DESAC_RS10530 fructose 1,6-bisphosphatase
Query= curated2:B6YTP6 (375 letters) >NCBI__GCF_000195295.1:WP_013707055.1 Length = 367 Score = 476 bits (1226), Expect = e-139 Identities = 222/373 (59%), Positives = 290/373 (77%), Gaps = 7/373 (1%) Query: 3 IGEKITISVIKADIGGWPGHSRVHPQLIEAAEEVLAKAKEEGTIIDFYVAYAGDDLQLIM 62 + +KIT+SVIKAD+GG+ GH +H +LI A L A+ +G ++D++V GDDL+LIM Sbjct: 1 MADKITLSVIKADVGGYVGHCAMHGELILEASRHLDDARSQGVLVDYHVTACGDDLELIM 60 Query: 63 THKKGVDSPDIHGLAWKAFEEATEIAKEFGLYGAGQDLLKDAFSGNIRGMGPGIAEMEIT 122 TH GVD+ D+H LAW+ FE TE+AK+ LYGAGQDLL AFSGN+RGMGPG+AEME Sbjct: 61 THSHGVDNRDVHHLAWEVFEACTEVAKKLKLYGAGQDLLSHAFSGNVRGMGPGVAEMEFV 120 Query: 123 LRKSEPIVTFHMDKTEPGAFNLPIFRMFADPFNTAGLVIDPNMHMGFRFEVWDIKEHKRV 182 R+SEPIV F DKT GA+NLP++++FADPFNTAGLVI P +H GFR+EV D+K H+++ Sbjct: 121 ERESEPIVIFMADKTSAGAWNLPLYKIFADPFNTAGLVIAPTLHAGFRYEVHDVKGHQKI 180 Query: 183 ILNTPEEIYDLLALIGAKSRYVIKRVYPKEGHKISKDEPVAVISTEKLYEIAGEYVGKDD 242 + +TPEE+YDLL IGA RY++K VY K+G E AV STE+L IAG+YVGKDD Sbjct: 181 LFSTPEELYDLLVFIGATGRYLVKAVYTKDG------EIAAVSSTERLALIAGKYVGKDD 234 Query: 243 PVAIVRAQSGLPALGEVLEPFAFPHLVSGWMRGSHNGPIMPVPMHQANPTRFDGPPRVVA 302 PV +VR Q PA+GEV+EPF+ PH+V GWMRGSH GP+MPVP+ QA PTRFDGPPRV+ Sbjct: 235 PVCVVRCQGKFPAVGEVVEPFSMPHIVEGWMRGSHYGPLMPVPLSQARPTRFDGPPRVIC 294 Query: 303 LGWQISPEGKLVGPVDLFDDPAFDYARQKALEITEYIRRHGPFEPHRLPLEDMEYTTLPG 362 LG+Q++ G LVGP D+FDDP+F+ AR+ I +++RRHGPFEPHRLP+++MEYTTLP Sbjct: 295 LGFQLA-NGHLVGPCDIFDDPSFNEARRLCNVIADHLRRHGPFEPHRLPMDEMEYTTLPQ 353 Query: 363 VLKKLEERFEDIE 375 V+ KL++R++ +E Sbjct: 354 VMAKLQDRWQPLE 366 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: 507 Number of extensions: 20 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: 367 Length adjustment: 30 Effective length of query: 345 Effective length of database: 337 Effective search space: 116265 Effective search space used: 116265 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: 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