Align fructokinase; EC 2.7.1.4 (characterized)
to candidate SMc02164 SMc02164 fructokinase
Query= CharProtDB::CH_006620 (326 letters) >FitnessBrowser__Smeli:SMc02164 Length = 308 Score = 419 bits (1077), Expect = e-122 Identities = 203/279 (72%), Positives = 234/279 (83%) Query: 1 MILCCGEALIDMLPRDTTLGEKGFAPYAGGAIFNTAIALGRLGIPTAFFTGIADDMMGEI 60 MI+CCGEALIDMLPR+TT GE FAPYAGGAIFNTA+ALGRLG+PT FFTG++DDM G+I Sbjct: 1 MIVCCGEALIDMLPRETTAGESAFAPYAGGAIFNTAVALGRLGVPTGFFTGLSDDMFGDI 60 Query: 61 LLETLKASNVDYSPCAITPRPSTIAFVKLVNGQATYAFYDEGTAGRMITTADLPDLGDDC 120 L TLKA+NVD++PCA P +T+AFVKLV+G A+YAF+DE TAGRMIT LP LGD C Sbjct: 61 LRATLKAANVDFAPCATLPLHTTLAFVKLVDGHASYAFFDENTAGRMITAEHLPALGDFC 120 Query: 121 EALHFGAISLIPSPCGETYEALLDREAASRVISLDPNIRPGFIKDKPSHMARIKRMAAKS 180 EALHFGAISLIP PCG TYEAL+ RE RVIS DPNIRPGFIKD+ +H+ R+ RMAA S Sbjct: 121 EALHFGAISLIPEPCGSTYEALMAREHEKRVISFDPNIRPGFIKDREAHVGRMNRMAAMS 180 Query: 181 DIVKFSDEDLDWFGLQGDHDALAAHWLNHGAKLVVITKGAEGASGYTKDRKVTVPSERVT 240 DIVKFSDEDL WFG++G HDALAA WL G KLV+IT+GA+GA GYT KV V SERV Sbjct: 181 DIVKFSDEDLAWFGMEGSHDALAAEWLKRGPKLVLITRGADGAVGYTNGHKVEVASERVE 240 Query: 241 VVDTVGAGDTFDAGILASLKMDNLLTKRQVASLDEQALR 279 VVDTVGAGDTFDAG+LASLK +NLLTK +VASL ++A+R Sbjct: 241 VVDTVGAGDTFDAGVLASLKFNNLLTKERVASLTDEAIR 279 Lambda K H 0.319 0.137 0.410 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: 341 Number of extensions: 7 Number of successful extensions: 1 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: 326 Length of database: 308 Length adjustment: 27 Effective length of query: 299 Effective length of database: 281 Effective search space: 84019 Effective search space used: 84019 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