Align fructokinase (EC 2.7.1.4) (characterized)
to candidate WP_013402581.1 CALHY_RS03245 carbohydrate kinase
Query= BRENDA::O04897 (347 letters) >NCBI__GCF_000166355.1:WP_013402581.1 Length = 312 Score = 200 bits (509), Expect = 4e-56 Identities = 123/316 (38%), Positives = 180/316 (56%), Gaps = 16/316 (5%) Query: 28 VVCFGEMLIDFIPTVAGVSLAEAPAFEKAPGGAPANVAVCISKLGGSSAFIGKVGDDEFG 87 VVC+GE+LIDF+ + FE PGGAPANVA ++K GG S I +VG+D FG Sbjct: 3 VVCYGEVLIDFLNVKENL-------FEANPGGAPANVAAAVAKFGGKSYLISQVGNDMFG 55 Query: 88 RMLADILKQNNVDNSGMRFDHDARTALAFITLTAEGEREFVFFRNPSADMLLRESELDVD 147 RM+ D L VD S ++ + T LAF+ L + GER F F R AD+ L+ ++D++ Sbjct: 56 RMIIDSLSDCGVDISNVKVTDEYFTTLAFVKLDSRGERSFSFSRKYGADVYLKLEDIDMN 115 Query: 148 LIKKATIFHYGSISLIDEPCRSTHLAAMDIAKRSGSILSYDPNLRLPLWPSEDAARSGIM 207 ++K A IFH+GS+S+ E + T L + IA++SGS +SYDPN R LW S+ A ++ Sbjct: 116 IVKSADIFHFGSLSMTYEQNKRTTLELLKIARQSGSTISYDPNYRSSLWESQKKALDTMI 175 Query: 208 S-VWN-LADIIKISEDEISFLTGADDPNDDEVVLKRLFHPNLKLLLVTEGSAGCRYYTKE 265 V N DI+K+SE+E+ L D N+ +K +K+ LVT G+ G + + KE Sbjct: 176 EPVENGFVDILKMSEEEV--LLYEKDVNNFYNRIK----DKVKIFLVTFGAKGSKVFFKE 229 Query: 266 FKGRVNSIKVKAVDTTGAGDAFTGGVLKCLASDASLYQ-DEKRLREAIFFANVCAALTVT 324 V++I+V VDTTG GD F G VL ++ + E + + AN+ AL T Sbjct: 230 KSYFVDTIEVNVVDTTGCGDCFVGMVLHEISKSLPIENISENDIINIVKKANIAGALCAT 289 Query: 325 GRGGIPSLPTQDAVRQ 340 +G IP++P V + Sbjct: 290 KKGAIPAIPEYGEVME 305 Lambda K H 0.319 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: 248 Number of extensions: 13 Number of successful extensions: 3 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: 347 Length of database: 312 Length adjustment: 28 Effective length of query: 319 Effective length of database: 284 Effective search space: 90596 Effective search space used: 90596 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 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