Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate WP_040480287.1 C943_RS09665 ROK family protein
Query= curated2:Q9KCZ4 (330 letters) >NCBI__GCF_000330725.2:WP_040480287.1 Length = 294 Score = 111 bits (277), Expect = 3e-29 Identities = 94/318 (29%), Positives = 143/318 (44%), Gaps = 40/318 (12%) Query: 2 SDRWYVGVDVGGTTIKMAFLTTAGEIVDKWEIPTNKQDGGALITTNIADALDKRLSGHHK 61 ++R +G+D+GGT IK L E+VD I T Q+ I IAD + L HH Sbjct: 4 TERPILGLDIGGTNIKAGVLV-GSELVDIRMIETPSQESQEYILETIADLIGTYL--HH- 59 Query: 62 SKSDLIGIGLGAPGFIEMDTGFIYHAVNI-GWRDFPLKDKLEEETKLPVIVDNDANIAAL 120 D IG+G PG I+ D G + + NI ++ L++ LE PV ++NDAN AL Sbjct: 60 ---DFFAIGVGIPGLIDTDLGIVLNLENIPSFKRVHLREFLELRFGKPVYINNDANCFAL 116 Query: 121 GEMWKGAGDGAKNMLLITLGTGVGGGIVANGNILHGVNGMAGEIGHITVIPEGGAPCNCG 180 GE GA K+++ ITLGTG+G GI+ANG++ G N AGE + + Sbjct: 117 GEYKFGAAKIYKHVVGITLGTGLGAGIIANGHLYCGFNCAAGEWCSAPYLDQDFEFYCSS 176 Query: 181 KTGCLETVASATGIARIATEGVTEHKESQLALDYDKHGVLTAKDVFSAADASDAFALSVV 240 K + A A +++ A +G D AL Sbjct: 177 KFFYAKYHAKAKSLSKRAKDG-------------------------------DKEALRAY 205 Query: 241 DHIAYYLGFAIANLANALNPEKIVIGGGVSKAGDTLLKPIKQHFEAYALPRVADGAEFRI 300 ++LG I N+ L P+ IV+GG + KA + + + + P V+ + I Sbjct: 206 AEYGHHLGELIKNILYTLAPQAIVLGGSIRKAYPFFRESMLANIATFKYPSVSANLKILI 265 Query: 301 ATLGNDAGVIGGGWLVKQ 318 + L ++ G+ G LV + Sbjct: 266 SEL-DETGIHGAVALVDE 282 Lambda K H 0.316 0.137 0.405 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: 243 Number of extensions: 12 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 330 Length of database: 294 Length adjustment: 27 Effective length of query: 303 Effective length of database: 267 Effective search space: 80901 Effective search space used: 80901 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 (21.6 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