Align Fructokinase (EC 2.7.1.4) (characterized)
to candidate WP_084544831.1 H566_RS22940 fructokinase
Query= reanno::Korea:Ga0059261_1776 (335 letters) >NCBI__GCF_000482785.1:WP_084544831.1 Length = 334 Score = 258 bits (660), Expect = 1e-73 Identities = 145/303 (47%), Positives = 182/303 (60%), Gaps = 13/303 (4%) Query: 16 PLLLGAVEAGGTKFLC--GIADRTGS--VLAQTRIPT-TTPAETLDAATAFFAEHVARHG 70 P LL A+EAGGTK LC G AD + L++ PT +PA L A +F A G Sbjct: 3 PPLLAALEAGGTKLLCAIGTADDAAAPRFLSRASFPTGDSPALALGAVADWFRAQQAAFG 62 Query: 71 PLSAFSVGSFGPLSLDPIAPDYGSITSTPKPGWQDVDLLGYFRQMIDA-PMALDTDVNCA 129 P++A + SFGP+ LDP +P +G IT+TPKPGW+D D+ G R + P+ DTDVN A Sbjct: 63 PIAALGIASFGPVDLDPASPGWGRITATPKPGWRDADVAGVLRAALPGIPLGFDTDVNGA 122 Query: 130 AVGERLFGSGRGLDTFCYVTVGTGIGVGLLVGGAPHGGANHPEAGHIRLPRAPGDHDFAG 189 A+GE+ +G+ RGL F Y+T+GTGIG G + GG G HPE GH+RLPR GD FAG Sbjct: 123 ALGEQRWGAARGLAEFVYITMGTGIGAGGMAGGRLLHGLVHPEMGHMRLPRLAGD-GFAG 181 Query: 190 ICPFHGDCLEGLACGPAMKARWGAAAETLPGDHPAWDIEADYLAGLCATLTYIVRPDRII 249 +C FHGDC EGL GPA+ AR G A+ LP DHP W + AD A L ++ P R+I Sbjct: 182 VCSFHGDCWEGLCSGPAIAARTGRPADELPADHPVWALLADTTALAIGNLVCVLSPRRVI 241 Query: 250 LGGGVMES-----HLMHARVRRTLVAKLAGYDASMRSLD-MDEYVVPPTAGPSAGLTGAF 303 LGG V ++ ARVR TL +LAGY A D + EY+VPP G AGL G Sbjct: 242 LGGSVRKAGGLGEAAFFARVRATLRERLAGYIAHPALADGIGEYMVPPLLGDDAGLAGTL 301 Query: 304 ALA 306 LA Sbjct: 302 VLA 304 Lambda K H 0.321 0.139 0.442 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: 421 Number of extensions: 33 Number of successful extensions: 6 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: 335 Length of database: 334 Length adjustment: 28 Effective length of query: 307 Effective length of database: 306 Effective search space: 93942 Effective search space used: 93942 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: 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