Align Fructokinase; EC 2.7.1.4 (uncharacterized)
to candidate WP_017548855.1 C792_RS0107525 ROK family glucokinase
Query= curated2:Q03417 (301 letters) >NCBI__GCF_000330705.1:WP_017548855.1 Length = 319 Score = 73.9 bits (180), Expect = 4e-18 Identities = 88/315 (27%), Positives = 124/315 (39%), Gaps = 45/315 (14%) Query: 14 GGTKFMLALIDSDRKMLAVERVPTTTPEE---TLGKSVEFFK---KALPQYADSFASFGI 67 GGT L + D + ++ +PT EE L ++ F+ + L + G+ Sbjct: 10 GGTSCKLGVFDEELNLIEKWEIPTDISEEGSHILADVLDSFRSKEEILGFKVEECLGTGL 69 Query: 68 ASFGPLCLDRKSPKWGYITNTPKPFWPNTDVVTPFKEAFGCPVEIDTDVNGAALAENFWG 127 GP+ + K G I K + T F E G +D D N AAL E G Sbjct: 70 GMPGPVDFE-KGILNGCINLNIKG---KRSIATIFSELSGSAAIVDNDANVAALGEQSKG 125 Query: 128 ASKGTHTSVYVTVGTGFGGGVLIDGKPIHGLAHPEMGHGIPIRHPDDRDFEG---CCPYH 184 A G V +T+GTG GGGV+ +G+ IHG G G I H DF+G C Sbjct: 126 AGHGHSEVVMITLGTGVGGGVISEGRLIHGTG----GSGGEIGHITV-DFDGRFQCNCGK 180 Query: 185 GGCYEGLASGTAIRKRWGKALNEMEPAEF-------------------------EKAREI 219 GC E +AS T + G ++ E + E E Sbjct: 181 KGCLETVASATGMVNLAGYHSDDHENSVLIAAIKEGTLTSKAIVDAAMTGDPLAEFVVEE 240 Query: 220 IAFYLAHFNVTLQAFISPERIVFGGGVMHVDGMLASVRRQTAEIANSYFEGADFEKIIVL 279 A YLA ++ +P VFGGGV L ++ + + F A + IV+ Sbjct: 241 AARYLAVAMSSISVITNPGYFVFGGGVSRAGRYLTDKIKKYYD--SLIFPPAADDVEIVM 298 Query: 280 PGLGDQAGMMGAFAL 294 LG+ AGM GA L Sbjct: 299 AELGNDAGMYGAARL 313 Lambda K H 0.320 0.139 0.435 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: 227 Number of extensions: 14 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 301 Length of database: 319 Length adjustment: 27 Effective length of query: 274 Effective length of database: 292 Effective search space: 80008 Effective search space used: 80008 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 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