Align Fructokinase-1; Fructokinase I; OsFKI; EC 2.7.1.4 (characterized)
to candidate HSERO_RS08715 HSERO_RS08715 2-dehydro-3-deoxygluconokinase
Query= SwissProt::Q0JGZ6 (323 letters) >FitnessBrowser__HerbieS:HSERO_RS08715 Length = 308 Score = 140 bits (354), Expect = 3e-38 Identities = 103/314 (32%), Positives = 153/314 (48%), Gaps = 18/314 (5%) Query: 5 SELVVSFGEMLIDFVPTVAGVSLAEAPA-FVKAPGGAPANVAIAVARLGGGAAFVGKLGD 63 S+ ++++GE +++F + +AP F++ GG +N AIA AR G +A++ +GD Sbjct: 2 SKTILAYGEAMVEFNQRI------DAPRQFLQGYGGDTSNFAIAAARQGAASAYLSAVGD 55 Query: 64 DEFGRMLAAILRDNGVDDGGVVFDAGARTALAFVTLRADGEREFMFYRNPSADMLLTHAE 123 D FG+ L A+ + VD V G T + FVT A G F + R SA Sbjct: 56 DHFGQDLLALWQREEVDVRHVAIAPGGSTGIYFVTHDAAG-HHFHYRRAGSAASAYQAKA 114 Query: 124 LNVELIKRAAVFHYGSISL-IAEPCRSAHLRAMEIAKEAGALLSYDPNLREALWPSREEA 182 L +E I A H ISL I+E A L AM A+ +G S D NLR LWP E A Sbjct: 115 LPLEAIAAAGALHLSGISLAISESACEAGLAAMAHARASGVTTSLDTNLRLRLWP-LERA 173 Query: 183 RTKILSIWDQADIVKVSEVELEFLTGIDSVEDDVVMKLWRPTMKLLLVTLGDQGCKYYAR 242 R ++ + DI S ++ LTG++ D +V +L +KL+ LG +GC Sbjct: 174 RARMEEAFRLCDICLPSWEDVSLLTGLED-RDAIVDRLLSYGVKLVAFKLGKEGCYVATS 232 Query: 243 DFRGAVPSYKVQQVDTTGAGDAFVGALLRRIVQDPSSLQDQKKLEEAIKFANACGAITAT 302 D R V Y V +D TGAGD F GA + ++ + A ++AN A++ T Sbjct: 233 DQRRMVAPYPVDSLDATGAGDCFGGAFMAELMAGRDAF-------AAARYANVAAALSTT 285 Query: 303 KKGAIPSLPTEVEV 316 GA+ +P +V Sbjct: 286 GYGAVEPIPRRAQV 299 Lambda K H 0.320 0.136 0.388 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: 238 Number of extensions: 15 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: 323 Length of database: 308 Length adjustment: 27 Effective length of query: 296 Effective length of database: 281 Effective search space: 83176 Effective search space used: 83176 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: 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