Align glucokinase (EC 2.7.1.2) (characterized)
to candidate WP_012386202.1 BIND_RS16715 ROK family transcriptional regulator
Query= BRENDA::Q8RDE9 (315 letters) >NCBI__GCF_000019845.1:WP_012386202.1 Length = 428 Score = 165 bits (418), Expect = 2e-45 Identities = 90/277 (32%), Positives = 146/277 (52%), Gaps = 1/277 (0%) Query: 40 PDVVIERIEESIYQVLKDTGLEMSNLKGIGIGSPGPLNAKKGIVISPPNL-PHWSNVPIV 98 PD ++ ++E + V+ GL++ + G+GIG PG +++K GI P L P V + Sbjct: 121 PDAIVALLDEGVRSVVALAGLKLGQIAGLGIGLPGFIDSKAGISHWSPILAPEPKPVALA 180 Query: 99 EILSKRLGIEVRLENDANAAAIGEHLFGSGRGVDNFVYITVSTGIGGGVIIEGKLYSGEN 158 +++ +RLG+ V +ENDAN + E FG + DNFV + + GIG G+ ++G+LY G++ Sbjct: 181 DMVRRRLGLAVTIENDANLLTLAERWFGECQENDNFVVVMMEAGIGMGLFLDGELYRGQH 240 Query: 159 SNAAEIGHHTINFDGPRCNCGNYGCFEAYASGTAIARFAREGIEKGIKTKIKELAGEGEV 218 E GH I+ GPRC CG YGC EA+ + AI R A + I + + E E Sbjct: 241 GMGTEFGHSKIDRHGPRCRCGQYGCIEAFTADYAILREAEKIIRTPAAHEGADDTAEAET 300 Query: 219 KAEHVFEAAKLGDEFAKELVEKEAFYLGVGIANIMAFYNPRKIAIGGGVSAQWDMLYEKM 278 + V A+ G+ +++ LG+GIAN++ +P KI I G + D++ + Sbjct: 301 RVATVVRLAREGNVALRQIFATAGEILGLGIANLINIIDPAKIVISGSGTRAVDLIEPAL 360 Query: 279 METVRKKALKPNAEVCEVVKAQLGENIGVLGAAALLL 315 V L CE++ G+ + GAA+L+L Sbjct: 361 RAAVAANTLAVLQNRCEIIFHDQGDEVWARGAASLVL 397 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: 281 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: 428 Length adjustment: 30 Effective length of query: 285 Effective length of database: 398 Effective search space: 113430 Effective search space used: 113430 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