Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate N515DRAFT_1256 N515DRAFT_1256 glucokinase
Query= curated2:Q21LZ9 (321 letters) >FitnessBrowser__Dyella79:N515DRAFT_1256 Length = 330 Score = 206 bits (523), Expect = 8e-58 Identities = 114/317 (35%), Positives = 175/317 (55%), Gaps = 5/317 (1%) Query: 5 PYIVADIGGTNARFALVT-GKKGNAFNLEQIQILNGSEFPRLQDAMQHYIDTLGGEKPKA 63 P++ AD+GGT+AR AL+ G +G ++ +I E ++ ++D LG +P+ Sbjct: 9 PFLAADVGGTHARLALMAPGNRGGGPVVQAYRIFRCGEHASFAAIVRAFLDGLGS-RPRE 67 Query: 64 ACVAIAGPIDGDNARMTNLNWEFSQAAVKAEFGFDKYDTLNDFGALAVATSSLQADN--L 121 +A G +L W AA+ AE D+ LNDF AL A + L Sbjct: 68 LVLACTGCAHEGVLINESLPWRIEPAALAAELRLDEVHLLNDFVALTHAAPYIDTARSPL 127 Query: 122 IEIKAGTMDPKGNKAILGPGTGLGVAGLACAGDSWLPIPSEGGHVNVAPATQLECEVIRA 181 + A G ++GPGTGLG A + G + +PSE G + +A E +V+R Sbjct: 128 LHAPARAASAPGPIVVVGPGTGLGAA-VRLPGSPSVVLPSEAGQMQLAARVGREQDVMRL 186 Query: 182 AMAEHGHVSAETFISGPGLVRLYRALATVRGETPKNYEPKDITAGALDGTDDLCKETLDL 241 H+S E +SGPG++R+Y AL +G+ P EP +TA A++G+D +ETLDL Sbjct: 187 LAGRDTHISYEAVLSGPGVLRVYEALCREQGKVPACAEPAAVTAAAIEGSDPRARETLDL 246 Query: 242 FCSFIGSLSGNLALTYGAKGGVYLAGGVLPRFIDYFKSSDFVKRFSEKGVMSHYVENIPV 301 FC ++GS +G+LA+ Y A GG+YLAGG L R Y + S F++RF +KGVM +++N+PV Sbjct: 247 FCGWLGSFAGDLAMLYQATGGIYLAGGFLSRLAGYVRGSSFLERFLDKGVMRPFLDNVPV 306 Query: 302 NLISYEYTAFVGAAAWL 318 ++ + +GAA+WL Sbjct: 307 RVVDHGQLGVIGAASWL 323 Lambda K H 0.319 0.137 0.410 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: 311 Number of extensions: 12 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: 321 Length of database: 330 Length adjustment: 28 Effective length of query: 293 Effective length of database: 302 Effective search space: 88486 Effective search space used: 88486 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 (21.7 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