Align N-acetylglucosamine kinase (EC 2.7.1.59) (characterized)
to candidate WP_017620227.1 CDO52_RS05395 ROK family glucokinase
Query= metacyc::MONOMER-19002 (326 letters) >NCBI__GCF_002263495.1:WP_017620227.1 Length = 344 Score = 166 bits (419), Expect = 1e-45 Identities = 106/314 (33%), Positives = 167/314 (53%), Gaps = 11/314 (3%) Query: 11 VGIDIGGTNTVFGIVDARGTIIASGAVKTQVYPTVEEYADEVCKNLLPLIIANGGVDKIK 70 VGIDIGG+ G+V+ G ++A +T P + V ++ +I + Sbjct: 16 VGIDIGGSKVAAGVVNPSGRVLARRRTET---PDKSKSPKVVEDTIVSVIEELRREYPVH 72 Query: 71 GIGIGAPNG-NYYTGTIEFAPNLPWKGVLPLASMFEERLGIPTALTNDANAAAVGEMTYG 129 +G+GA + ++ FAP+L W+ PL +RL +P + NDANA+A E+ G Sbjct: 73 AVGVGAAGFVDEQRASVLFAPHLAWRKE-PLREALTQRLELPVVVENDANASAWAEVRVG 131 Query: 130 AARGMKDFIMITLGTGVGSGIVINGQVVYGHDGFAGELGHVIVRRDGRICGCGRKGCLET 189 A RG+ D +++ LGTG+G I+++G++ G G AGE GH+ V G C CG +GC E Sbjct: 132 AGRGVDDILVVNLGTGIGGAIILDGKLHRGRYGIAGEFGHMTVVPGGHRCECGNRGCWEQ 191 Query: 190 YCSATGVARTAREFLAARTDAS--LLRNIPAES--IVSKDVYDAAVQGDKLAQEIFEFTG 245 Y S V R ARE AA + + L++ + + I V D A +GD+ + E+ E G Sbjct: 192 YASGNAVTRDARELAAADSPVARGLIQAVGGDPALITGPLVSDLAREGDRASVELLEDAG 251 Query: 246 NILGEALADAIAFSSPEAIILFGGLAKSGDYIMKPIMKAMENNLLNI-YKGKAKLLVSEL 304 LG LA+ A PE I+ GG++ GD ++ P A L Y+ +A+++ +EL Sbjct: 252 GWLGIGLANLAAAFDPELFIIGGGVSDCGDLLLGPARTAFRRQLTGRGYRPEARIVRAEL 311 Query: 305 KDSDAAVLGASALA 318 ++A ++GAS LA Sbjct: 312 -GNEAGLIGASLLA 324 Lambda K H 0.318 0.138 0.399 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: 309 Number of extensions: 13 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: 326 Length of database: 344 Length adjustment: 28 Effective length of query: 298 Effective length of database: 316 Effective search space: 94168 Effective search space used: 94168 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 (21.7 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