Align glucokinase (EC 2.7.1.2) (characterized)
to candidate WP_013403895.1 CALHY_RS10325 ROK family protein
Query= BRENDA::Q8RDE9 (315 letters) >NCBI__GCF_000166355.1:WP_013403895.1 Length = 399 Score = 170 bits (430), Expect = 6e-47 Identities = 100/315 (31%), Positives = 168/315 (53%), Gaps = 9/315 (2%) Query: 5 LCGVDLGGTKISTGIVDENGNII----KSIKIPTMAEKGPDVVIERIEESIYQVLKDTGL 60 + G+DLG I + + G +I ++K+ EK D++ + IE +I + + Sbjct: 80 IIGIDLGVDYIHIILSNFVGEVIFEEYANMKMGEDKEKLLDLLFDLIERAINRAPQTP-- 137 Query: 61 EMSNLKGIGIGSPGPLNAKKGIVISPPNLPHWSNVPIVEILSKRLGIEVRLENDANAAAI 120 + GIGIG PG + + GIV+ PNL W NV + I+ +R + V ++N+ANA A+ Sbjct: 138 --KGILGIGIGVPGIVEKESGIVLIAPNLK-WKNVHLKSIVQQRFNLPVYIDNEANAGAL 194 Query: 121 GEHLFGSGRGVDNFVYITVSTGIGGGVIIEGKLYSGENSNAAEIGHHTINFDGPRCNCGN 180 GE FG V + +Y++V G+G G+II+ KL+ G A E+GH TINF C+CGN Sbjct: 195 GEKWFGEWGKVTDLIYLSVGIGLGAGIIIDNKLFRGAAGFAGEVGHTTINFQDDVCSCGN 254 Query: 181 YGCFEAYASGTAIARFAREGIEKGIKTKIKELAGEGEVKAEHVFEAAKLGDEFAKELVEK 240 GC E +AS A+ ++ +++G + + E+ + +AAK G + V + Sbjct: 255 IGCLENFASERALLSVIKKLVKEGAEDRYISCENVDEITPSQIIQAAKDGSRVCRMAVLE 314 Query: 241 EAFYLGVGIANIMAFYNPRKIAIGGGVSAQWDMLYEKMMETVRKKALKPNAEVCEVVKAQ 300 A + +GIAN++ +NP + IG VS D+ EK+ E V +K+ ++ ++ Sbjct: 315 VAEKMAIGIANLVNIFNPEIVIIGNKVSFFGDLFLEKLREVVNQKSFIAQFYDLKIEVSK 374 Query: 301 LGENIGVLGAAALLL 315 L + VLG A+++ Sbjct: 375 LKDRAVVLGCIAMVI 389 Lambda K H 0.316 0.138 0.398 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: 314 Number of extensions: 15 Number of successful extensions: 2 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: 315 Length of database: 399 Length adjustment: 29 Effective length of query: 286 Effective length of database: 370 Effective search space: 105820 Effective search space used: 105820 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: 49 (23.5 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