Align Fructokinase (EC 2.7.1.4) (characterized)
to candidate CCNA_01192 CCNA_01192 sugar kinase
Query= reanno::Korea:Ga0059261_1776 (335 letters) >FitnessBrowser__Caulo:CCNA_01192 Length = 307 Score = 261 bits (668), Expect = 1e-74 Identities = 142/291 (48%), Positives = 172/291 (59%), Gaps = 4/291 (1%) Query: 19 LGAVEAGGTKFLCGIADRTGSVLAQTRIPTTTPAETLDAATAFFAEHVARHGPLSAFSVG 78 + A+E GGTK + + RIPTTTPAETL A A G A V Sbjct: 9 IAAIELGGTKVMVAFGSGPDDLSPPLRIPTTTPAETLARIEDALA---AEQGRFDAIGVA 65 Query: 79 SFGPLSLDPIAPDYGSITSTPKPGWQDVDLLGYFRQMIDAPMALDTDVNCAAVGERLFGS 138 SFGP+ LDP APD+G I TPKPGW D+ + D P+ALDTDVN AAV E L+G+ Sbjct: 66 SFGPIRLDPAAPDWGHILKTPKPGWSHADVAARLVRRFDRPLALDTDVNGAAVAEGLWGA 125 Query: 139 GRGLDTFCYVTVGTGIGVGLLVGGAPHGGANHPEAGHIRLPRAPGDHDFAGICPFHGDCL 198 +GL + YVTVGTG+GVGL+V GAP G HPEAGHI + R F G CPFHGDCL Sbjct: 126 AKGLGDYAYVTVGTGVGVGLVVNGAPTHGLLHPEAGHILVRRDAALDPFTGSCPFHGDCL 185 Query: 199 EGLACGPAMKARWGAAAETLPGDHPAWDIEADYLAGLCATLTYIVRPDRIILGGGVMESH 258 EGL GPA+ AR GA E+L D P W + ADYLA L A L I P R+I+GGGV + Sbjct: 186 EGLISGPALAARTGAPGESLSKDDPVWALVADYLAQLVANLALIASPRRVIIGGGVGGNP 245 Query: 259 LMHARVRRTLVAKLAGYDASM-RSLDMDEYVVPPTAGPSAGLTGAFALAYR 308 + + R L LAGY A + + D+D +V P G ++GL GA AL R Sbjct: 246 QLLEQTRTRLQTHLAGYLAPLEQRSDIDAFVAAPGLGANSGLLGAVALGLR 296 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: 351 Number of extensions: 20 Number of successful extensions: 3 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: 307 Length adjustment: 28 Effective length of query: 307 Effective length of database: 279 Effective search space: 85653 Effective search space used: 85653 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