Align glucokinase (EC 2.7.1.2) (characterized)
to candidate WP_009762999.1 MICLODRAFT_RS16860 ROK family transcriptional regulator
Query= BRENDA::B1VZT1 (313 letters) >NCBI__GCF_000262405.1:WP_009762999.1 Length = 405 Score = 125 bits (315), Expect = 1e-33 Identities = 95/302 (31%), Positives = 150/302 (49%), Gaps = 21/302 (6%) Query: 1 MGLTIGVDIGGTKIAAGVVDEEGRILSTFKVATPPT---AEGIVDAICAAVAGASEG--- 54 +G IGV G +I +VD GR ++ + P A ++D + + ++G Sbjct: 85 LGSVIGVWTGFNRIELRLVDSAGRNRASRHIERPLRNLGANELMDVLAETITAFAQGTGA 144 Query: 55 HDVEAVGIGAAGYVDDKRATVLFAPNIDWRHEPLKDKVEQRVGLPVVVENDANAAAWGEY 114 HDV+A+G+ GYVD + V ++P + R PL + +R+GLPV++ENDA+A A+ Sbjct: 145 HDVKAIGLACQGYVDTRDGIVAWSPVLGTRDLPLASGLGERLGLPVLMENDASAMAFAIT 204 Query: 115 RFGAGQGHDDVICITLGTGLGGGIIIGNKLRRG-RFGVAAEFGHIRVVPDGLLCGCGSQG 173 + + C+ +G G+G G +I +L RG RFG +EFGH+R+ G C CG +G Sbjct: 205 QRNSDLRSGRTACLMVGDGVGLGFLIQGELYRGARFG-GSEFGHVRLRRGGPQCRCGGRG 263 Query: 174 CWEQYASGRALVRYAKQRANATPENAAVLLGLGDGSVDGIEGKHISEAARQGDPVAVDSF 233 C E Y + AL R A Q + P A LL G+ +++ I E AR GDP ++ F Sbjct: 264 CIEAYLADYALHRDA-QLIDHRP--APTLLLPGEDAMES-----IVEQARAGDPALLNLF 315 Query: 234 RELARWAGAGLADLASLFDPSAFIVGGGVSDEGELVLDPIRKSFRRWLIGGEWRPHAQVL 293 + G + L +P ++ G G +D +R SF + + P + L Sbjct: 316 QAAGEVLGDAVGILIQTLEPDHIVLCG----PGTRAMDLLRPSFEA-ALESQTIPELRAL 370 Query: 294 AA 295 AA Sbjct: 371 AA 372 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: 315 Number of extensions: 20 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: 405 Length adjustment: 29 Effective length of query: 284 Effective length of database: 376 Effective search space: 106784 Effective search space used: 106784 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: 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