Align glucokinase (EC 2.7.1.2) (characterized)
to candidate 15241 b1119 N-acetyl-D-glucosamine kinase (NCBI)
Query= reanno::SB2B:6938110 (299 letters) >FitnessBrowser__Keio:15241 Length = 303 Score = 206 bits (524), Expect = 5e-58 Identities = 125/300 (41%), Positives = 173/300 (57%), Gaps = 7/300 (2%) Query: 2 MRMGVDLGGTKIELVALGEDGSELFRKRIATPRE-YQGTLNAVVTLVNEAEATLGTQGSL 60 M G D+GGTKI L + KR+ TPR+ Y L+AV LV EA+ G +GS+ Sbjct: 1 MYYGFDIGGTKIALGVFDSGRQLQWEKRVPTPRDSYDAFLDAVCELVAEADQRFGCKGSV 60 Query: 61 GIGIPGVISPYTGLVKNANSTWINGHPLDRDLGALLNREVRVANDANCFAVSEAVDGAAA 120 GIGIPG+ G + AN +G PL DL A L+R+VR+ NDANCFA+SEA D Sbjct: 61 GIGIPGMPETEDGTLYAANVPAASGKPLRADLSARLDRDVRLDNDANCFALSEAWDDEFT 120 Query: 121 GKRVVFGAILGTGCGAGLAFDGRVHEGGNGIGGEWGHNPLP----WMRPDEFNTTECFCG 176 +V G ILGTG G GL F+G+ G + I GE+GH LP M +F C CG Sbjct: 121 QYPLVMGLILGTGVGGGLIFNGKPITGKSYITGEFGHMRLPVDALTMMGLDFPLRRCGCG 180 Query: 177 NKDCIETFVSGTGFVRDFRNSGGTAQNGAEIMSLVDAGDELANLVFDRYLDRLARSLAHV 236 CIE ++SG GF +++ EI++L D GDE A +RYLD LA L ++ Sbjct: 181 QHGCIENYLSGRGFAWLYQHYYHQPLQAPEIIALYDQGDEQARAHVERYLDLLAVCLGNI 240 Query: 237 INMLDPDAIVLGGGMSNVQAIYARLPAILPKYVVGRECRTPVVQNL-YGCSSGVRGAAWL 295 + ++DPD +V+GGG+SN AI +L LP++++ R P ++ +G + G+RGAA+L Sbjct: 241 LTIVDPDLVVIGGGLSNFPAITTQLADRLPRHLL-PVARVPRIERARHGDAGGMRGAAFL 299 Lambda K H 0.320 0.139 0.429 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: 295 Number of extensions: 17 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: 299 Length of database: 303 Length adjustment: 27 Effective length of query: 272 Effective length of database: 276 Effective search space: 75072 Effective search space used: 75072 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 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 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