Align glucokinase (EC 2.7.1.2) (characterized)
to candidate WP_011321017.1 AVA_RS22040 ROK family protein
Query= BRENDA::B1VZT1 (313 letters) >NCBI__GCF_000204075.1:WP_011321017.1 Length = 316 Score = 179 bits (454), Expect = 8e-50 Identities = 112/317 (35%), Positives = 175/317 (55%), Gaps = 9/317 (2%) Query: 1 MGLTIGVDIGGTKIAAGVVDEEGRILSTFKVATPPT---AEGIVDAICAAVAGASEGHDV 57 M LT+ +D GGTK+AAG+V+ + R ++ P A ++ + + + +G Sbjct: 1 MKLTLALDFGGTKLAAGLVNADSRKWLRYERRFSPINGDANTDLEIMRSLIHSLLQGETP 60 Query: 58 EAVGIGAAGYVDDKRATVLFAPNID-WRHEPLKDKVEQRVGLPVVVENDANAAAWGEYRF 116 A+G+ G VD TV + ++ W + PLK +E+ G+P V+NDAN AA GE F Sbjct: 61 TAIGVSFGGPVDATTGTVRLSHHVPGWENIPLKSLLEKEFGVPTSVDNDANVAALGEQHF 120 Query: 117 GAGQGHDDVICITLGTGLGGGIIIGNKLRRGRFGVAAEFGHIRVVPDGLLCGCGSQGCWE 176 GAGQG+D + IT+ TG+GGG I+ K RG G+A E GHI V P G +C CG +GC E Sbjct: 121 GAGQGYDSLFYITISTGVGGGWILNGKPWRGAVGMAGEIGHIVVEPAGPICLCGKRGCVE 180 Query: 177 QYASGRALVRYAKQRANATP--ENAAVLLGLGDGSVDGIEGKHISEAARQGDPVAVDSFR 234 + ASG + + AK P E+ +L L +++ + G+ ISEAA +GD +A + Sbjct: 181 RLASGPYMAQNAKDILENQPEREDGQILRNLVGNNLNLLTGQLISEAATKGDNLAQAVLQ 240 Query: 235 ELARWAGAGLADLASLFDPSAFIVGGGVSDEGELVLDPIRKSFRRWLIGGEWRPHAQVLA 294 + A G G+ ++A+L +P FI+GG V+ GE+ ++++ R + +++ Sbjct: 241 KSAWALGVGIGNVANLINPQRFILGGSVTKAGEIWWTVLQETARFTALP---EVPLEIVP 297 Query: 295 AQLGGKAGLVGAADLAR 311 A L A L GA LA+ Sbjct: 298 AVLADDAPLWGAVALAQ 314 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: 278 Number of extensions: 11 Number of successful extensions: 3 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: 313 Length of database: 316 Length adjustment: 27 Effective length of query: 286 Effective length of database: 289 Effective search space: 82654 Effective search space used: 82654 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