Align glucokinase (EC 2.7.1.2) (characterized)
to candidate WP_010631476.1 RH97_RS06160 ROK family protein
Query= BRENDA::B1VZT1 (313 letters) >NCBI__GCF_000246965.1:WP_010631476.1 Length = 297 Score = 83.2 bits (204), Expect = 7e-21 Identities = 85/322 (26%), Positives = 134/322 (41%), Gaps = 54/322 (16%) Query: 6 GVDIGGTKIAAGVVDEEGRILSTFKVATPPTAEGIVDAICAAVAGASEGHDVEAVGIGAA 65 G++ GGTK V DE G +L+ ++AT D V + ++++GI + Sbjct: 5 GIEAGGTKFVCAVGDESGNVLAKERIATKDP-----DYTMDRVIHFFKNFQIDSLGIASF 59 Query: 66 GYVD-----DKRATVLFAPNIDWRHEPLKDKVEQRVGLPVVVENDANAAAWGEYRFGAGQ 120 G +D ++ P W + P ++ + LPV D N AA GE GA + Sbjct: 60 GPIDLDPESAAYGSITSTPKPGWANYPFVGTMKDALHLPVGFTTDVNGAALGELYHGAAK 119 Query: 121 GHDDVICITLGTGLGGGIIIGNKLRRGRFGVAAEFGHI---RVVPDGLLCGCG-SQGCWE 176 G D + +T+GTG+G G++ N+L +G E GHI R D C + C E Sbjct: 120 GLDGCLYLTVGTGIGAGLVNRNQLFQGL--SHPEMGHILVRRSPKDHFEGICPYHKDCLE 177 Query: 177 QYASGRALVRYAKQRANATPENAAVLLGLGDGSVDGIEGKHISEAARQGDPVAVDSFREL 236 ASG AL K R GK SE P ++++ Sbjct: 178 GVASGPAL----KAR----------------------WGKSASEL-----PADHEAWQME 206 Query: 237 ARWAGAGLADLASLFDPSAFIVGGGVSDEGELVLDPIRKSFRRWLIGGEWRPHAQ----- 291 A + L + P I+GGGV + +L IR++ + L G P + Sbjct: 207 ADYLAQALMQYILIVSPKRIIIGGGVMKQKQL-FPMIRRNVQELLAGYIDFPEVRGGIDS 265 Query: 292 -VLAAQLGGKAGLVGAADLARQ 312 ++ +LG +G+ GA LA++ Sbjct: 266 YIVPPELGDNSGITGALILAKR 287 Lambda K H 0.319 0.140 0.427 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: 213 Number of extensions: 14 Number of successful extensions: 3 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: 313 Length of database: 297 Length adjustment: 27 Effective length of query: 286 Effective length of database: 270 Effective search space: 77220 Effective search space used: 77220 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 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