Align Fructokinase-1; Fructokinase I; OsFKI; EC 2.7.1.4 (characterized)
to candidate PP_3378 PP_3378 putative 2-ketogluconokinase
Query= SwissProt::Q0JGZ6 (323 letters) >FitnessBrowser__Putida:PP_3378 Length = 316 Score = 126 bits (317), Expect = 6e-34 Identities = 101/320 (31%), Positives = 153/320 (47%), Gaps = 13/320 (4%) Query: 8 VVSFGEMLIDFVPTVAGVSLAEAPAFVKAPGGAPANVAIAVARLGGGAAFVGKLGDDEFG 67 V+ FGE + FV AG LA F K GA +NVAI +ARLG ++ ++GDD G Sbjct: 6 VLCFGETMAMFVAEQAG-DLAGVGQFGKRIAGADSNVAIGLARLGFKVRWLSRVGDDSLG 64 Query: 68 RMLAAILRDNGVDDGGVVFDAGARTALAFVTLRADG-EREFMFYRNPSADMLLTHAELNV 126 R + LR G+D GV DA T DG + ++R SA L+ A ++ Sbjct: 65 RFVLDSLRCEGLDCSGVEVDANYPTGFQLKARSEDGSDPAVEYFRRGSAASRLSAAMVSP 124 Query: 127 ELIKRAAVFHYGSISLIAEPCRSAHLRAMEIAKEAGALLSYDPNLREALWPSREEARTKI 186 ++ V G +++ CR+ ++ + AG +S+DPNLR +LWP + +I Sbjct: 125 VWLQARHVHATGIPLALSDSCRALSHALLDGMRAAGRSISFDPNLRPSLWPDQSSMVREI 184 Query: 187 LSIWDQADIVKVSEVELEFLTGIDSVEDDVVMKLWRPTMKLLLVTLGDQGCKYYARDFRG 246 ++ +AD V E LTG + D L ++L+++ LGD G + + G Sbjct: 185 NALAAKADWVLPGLEEGRLLTGQHTPADIAAFYL-DQGVELVVIKLGDAGAYFRSAKGEG 243 Query: 247 AVPSYKVQQ-VDTTGAGDAFVGALLRRIVQDPSSLQDQKKLEEAIKFANACGAITATKKG 305 V V + VDT GAGDAF +L S+L + + + EA+ N CG+ +G Sbjct: 244 QVAPVPVSRVVDTVGAGDAFAVGVL-------SALLEGRPVAEAVARGNWCGSRAVQSRG 296 Query: 306 AIPSLPT--EVEVLKLMESA 323 + LP E+E L SA Sbjct: 297 DMEGLPLRHELEAYDLRRSA 316 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: 237 Number of extensions: 12 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: 316 Length adjustment: 28 Effective length of query: 295 Effective length of database: 288 Effective search space: 84960 Effective search space used: 84960 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