Align fructokinase (EC 2.7.1.4) (characterized)
to candidate WP_019867205.1 METMI_RS0115465 carbohydrate kinase
Query= BRENDA::G4T023 (295 letters) >NCBI__GCF_000384075.1:WP_019867205.1 Length = 293 Score = 330 bits (847), Expect = 2e-95 Identities = 167/294 (56%), Positives = 194/294 (65%), Gaps = 1/294 (0%) Query: 1 MNKNPITIFGEVLFDHFPDGSRVLGGAPFNVAWHLQAFRQEPHFISRVGQDATGDSVIAA 60 M I I GEVLFD FPDG ++LGGAPFNVAWHLQAF Q+P FISRVG D GD + Sbjct: 1 MTPQTIAIIGEVLFDQFPDGQQILGGAPFNVAWHLQAFGQQPCFISRVGADELGDKIRTG 60 Query: 61 MHKWGMDMSGLQRDSRHPTGVVDIVIEQGEPAYTIVPEQAYDYIDEDELQDTDRPGLLYH 120 M WGM LQ D HPTGVV I + GEPAY I+ QAYDY+ E Q G++YH Sbjct: 61 MMAWGMGTENLQTDWEHPTGVVQITVNDGEPAYQILDHQAYDYLAEPG-QAAGSTGVIYH 119 Query: 121 GTLSLRQPVSRAALDVLKDAHKGRIFMDVNLREPWWQKDQVLEWLGQADWVKLNHHELAA 180 GTL+LR P S L L H GR+F+DVNLR PWWQ V EWL ADWVKLN EL Sbjct: 120 GTLALRNPTSTQTLRKLLAQHSGRVFVDVNLRAPWWQAKTVTEWLQTADWVKLNDDELRQ 179 Query: 181 LYPVSGDLKADMRRFVELYRLQGLIVTSGKQGAFATDHQGVSCRVTPGEIAQVIDTVGAG 240 L LK ++ F++ Y+L GLIVT G+ GA A G VTP +A+V+DTVGAG Sbjct: 180 LAETKATLKETLQGFLDTYQLTGLIVTRGELGAVALTDNGEYVEVTPNALAEVVDTVGAG 239 Query: 241 DAFASVMLLGLNLDWPLQITMERAQAFASAMVGQRGATVRDPVFYEPFIAAWDL 294 DAFASV+LLGL WPL +T+ RAQ FASA+V Q+GATV+D FY PFIA W L Sbjct: 240 DAFASVLLLGLQHHWPLTLTLRRAQDFASALVTQKGATVQDMDFYLPFIAQWQL 293 Lambda K H 0.322 0.138 0.432 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: 319 Number of extensions: 14 Number of successful extensions: 2 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: 295 Length of database: 293 Length adjustment: 26 Effective length of query: 269 Effective length of database: 267 Effective search space: 71823 Effective search space used: 71823 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 (21.9 bits) S2: 48 (23.1 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