Align Fructokinase; D-fructose kinase; Manno(fructo)kinase; EC 2.7.1.4 (characterized)
to candidate 7025547 Shewana3_2698 N-acetylglucosamine kinase (RefSeq)
Query= SwissProt::P23917 (302 letters) >FitnessBrowser__ANA3:7025547 Length = 308 Score = 186 bits (471), Expect = 8e-52 Identities = 108/301 (35%), Positives = 160/301 (53%), Gaps = 8/301 (2%) Query: 1 MRIGIDLGGTKTEVIALGDAGEQLYRHRLPTPRDDYRQTIETIATLVDMAEQATGQRGTV 60 M G+D+GGTK E+ + RL TP DY + T+A ++ A+Q G+RGTV Sbjct: 1 MYYGLDIGGTKIELAIFDTQLALQDKWRLSTPGQDYSAFMATLAEQIEKADQQCGERGTV 60 Query: 61 GMGIPGSISPYTGVVKNANSTWLNGQPFDKDLSARLQREVRLANDANCLAVSEAVDGAAA 120 G+ +PG + G V ++N LN + DL+ L R V + ND C A+SEAV G Sbjct: 61 GIALPGVVKA-DGTVISSNVPCLNQRRVAHDLAQLLNRTVAIGNDCRCFALSEAVLGVGR 119 Query: 121 GAQTVFAVIIGTGCGAGVAFNGRAHIGGNGTAGEWGHNPLPWMDEDELRYREEVPCY--- 177 G V +I+GTG G G+ +G+ ++G N AGE+GH + + R ++P Y Sbjct: 120 GYSRVLGMILGTGTGGGLCIDGKLYLGANRLAGEFGHQGV----SANVACRHQLPLYVCG 175 Query: 178 CGKQGCIETFISGTGFAMDYRRLSGHALKGSEIIRLVEESDPVAELALRRYELRLAKSLA 237 CG +GC ET++SGTG Y+ ++G + + +DP+A Y L +A Sbjct: 176 CGLEGCAETYVSGTGLGRLYQDIAGQTADTFAWLNALRCNDPLAIKTFDTYMDILGSLMA 235 Query: 238 HVVNILDPDVIVLGGGMSNVDRLYQTVGQLIKQFVFGGECETPVRKAKHGDSSGVRGAAW 297 +V +DPD+IVLGGG+S V+ + + Q K +F G + A G +SGVRGAA Sbjct: 236 SLVLAMDPDIIVLGGGLSEVEEILAALPQATKAHLFDGVTLPQFKLADFGSASGVRGAAL 295 Query: 298 L 298 L Sbjct: 296 L 296 Lambda K H 0.318 0.137 0.418 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: 330 Number of extensions: 18 Number of successful extensions: 4 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: 302 Length of database: 308 Length adjustment: 27 Effective length of query: 275 Effective length of database: 281 Effective search space: 77275 Effective search space used: 77275 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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