Align fructokinase (EC 2.7.1.4) (characterized)
to candidate 351285 BT1757 fructokinase (NCBI ptt file)
Query= BRENDA::C4M2I2 (294 letters) >FitnessBrowser__Btheta:351285 Length = 295 Score = 239 bits (611), Expect = 4e-68 Identities = 130/282 (46%), Positives = 179/282 (63%), Gaps = 4/282 (1%) Query: 8 VAGIGEVVWDCFGDVKKQGGAPCNFAMHMAQFGFESYAFIAVGNDELGKRSLEIIHSFGV 67 + G+GE +WD + KK GGAP NFA H++QFGF+S AVGNDELG +E+ + Sbjct: 5 IVGMGEALWDVLPEGKKIGGAPANFAYHVSQFGFDSRVVSAVGNDELGDEIMEVFKEKQL 64 Query: 68 QTIDPVVDYETSTVIITLHN-GIPSYNVKLNVAWDHLKLTDSIIEKAKELDAVCFGTIAQ 126 + VDY T TV +TL + G+P Y +K VAWD++ TD + A AVCFG++AQ Sbjct: 65 KNQIERVDYPTGTVQVTLDDEGVPCYEIKEGVAWDNIPFTDELKRLALNTRAVCFGSLAQ 124 Query: 127 RSEETRKSIIQFLKLMKP--NSFKVFDVNLRQHFYNDDIIQESLSLSNIVKMSDEEIQEV 184 R+E +R +I +FL M K+FD+NLRQ FY ++++ES NI+K++DEE+ + Sbjct: 125 RNEVSRATINRFLDTMPDIDGQLKIFDINLRQDFYTKEVLRESFKRCNILKINDEELVTI 184 Query: 185 GKACGFQGNDLEILKQIH-HQYHLKYSLLTLGEKGSYVYDGTNEIFCEPTKVNVVNTVGA 243 + G+ G DL+ I +Y+LK +LT G GSYV+ F E KV V +TVGA Sbjct: 185 SRMFGYPGIDLQDKCWILLAKYNLKMLILTCGINGSYVFTPGVVSFQETPKVPVADTVGA 244 Query: 244 GDSFTAIFVGSILKGKSIEQAQKLASKVASYVCTQDSAMPKL 285 GDSFTA F SIL GKS+ +A KLA +V++YVCTQ AMP+L Sbjct: 245 GDSFTAAFCASILNGKSVPEAHKLAVEVSAYVCTQSGAMPEL 286 Lambda K H 0.318 0.135 0.389 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: 251 Number of extensions: 9 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: 294 Length of database: 295 Length adjustment: 26 Effective length of query: 268 Effective length of database: 269 Effective search space: 72092 Effective search space used: 72092 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: 48 (23.1 bits)
This GapMind analysis is from Sep 17 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