Align N-acetylglucosamine kinase (EC 2.7.1.59) (characterized)
to candidate WP_084057691.1 B9A12_RS09725 ROK family protein
Query= metacyc::MONOMER-19002 (326 letters) >NCBI__GCF_900176285.1:WP_084057691.1 Length = 325 Score = 160 bits (406), Expect = 3e-44 Identities = 107/330 (32%), Positives = 175/330 (53%), Gaps = 14/330 (4%) Query: 5 MEKPYVVGIDIGGTNTVFGIVDARGTIIASGAVKTQVYPTVEEYADEV---CKNLLPLII 61 M+ V+G+DIGGT+ ++D +GT++A +++ E + C++LL Sbjct: 1 MKDKCVIGVDIGGTHMRCALMDRKGTVLAFRKDRSRSDEGPEALTRRLVQQCRDLL---- 56 Query: 62 ANGGVD--KIKGIGIG-APNGNYYTGTIEFAPNLPWKGVLPLASMFEERLGIPTALTNDA 118 A+GG+ ++ +G+G A + +GTI F+PNLP PLA +E L +P A+ NDA Sbjct: 57 ADGGLSNARLGAVGLGVAGKLDTASGTILFSPNLPSLAGFPLAVRVQEALQVPVAMENDA 116 Query: 119 NAAAVGEMTYGAARGMKDFIMITLGTGVGSGIVINGQVVYGHD-GFAGELGHVIVRRDGR 177 N +GE G AR + ++I +TLGTGVG NG++ G GF+GE+GH+IV G Sbjct: 117 NVFGLGEAWLGKARNVSNWIGVTLGTGVGGCFFANGRLWQGDRLGFSGEIGHMIVDPQGP 176 Query: 178 ICGCGRKGCLETYCSATGVARTAREFLAARTDAS--LLRNIPAESIVSKDVYDAAVQGDK 235 C CG+KGCLE + SAT + + R+ S L + + + + +Y AA GD Sbjct: 177 ECACGQKGCLEAHASATALVQGVRQAQKEAVPLSDLLQEALRRDQLTAHTIYRAARGGDP 236 Query: 236 LAQEIFEFTGNILGEALADAIAFSSPEAIILFGGLAKSGDYIMKPIMKAMENNLLNIYKG 295 +A+ +F G L AL++ F ++ GG++ S D ++ + + Sbjct: 237 VARRLFARMGWALAVALSNLFTFLGISTAVIGGGVSASWDQFAPAMLDYFQQVPSMLDPQ 296 Query: 296 KAKLLVSELKDSDAAVLGASALAWELKDLR 325 + +EL+D A++ GA++LAW+ D R Sbjct: 297 SIHVHRTELEDR-ASIYGAASLAWQTVDRR 325 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: 281 Number of extensions: 14 Number of successful extensions: 5 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: 325 Length adjustment: 28 Effective length of query: 298 Effective length of database: 297 Effective search space: 88506 Effective search space used: 88506 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: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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