Align N-acetyl-D-glucosamine kinase; GlcNAc kinase; EC 2.7.1.59 (characterized)
to candidate WP_004325323.1 C665_RS17905 ROK family protein
Query= SwissProt::Q8ZPZ9 (303 letters) >NCBI__GCF_000310185.1:WP_004325323.1 Length = 301 Score = 229 bits (584), Expect = 6e-65 Identities = 125/296 (42%), Positives = 170/296 (57%), Gaps = 4/296 (1%) Query: 4 GFDIGGTKIALGVFDSTRRLQWEKRVPTPHTSYSAFLDAVCELVEEADQRFGVKGSVGIG 63 G D+GGTKI L V D+ R +W +RVPTP Y L A+ LVEEA++ G +G+G Sbjct: 6 GIDLGGTKIELVVLDADGRERWRRRVPTPQGDYGGTLRAIAALVEEAERLTGAGARIGVG 65 Query: 64 IPGMPETEDGTLYAANVPAASGKPLRADLSARLDRDVRLDNDANCFALSEAWDDEFTQYP 123 PG P DG + AN +G+PL+ DL A L R +RL NDANC A+SEA D Sbjct: 66 TPGSPSPRDGRIRNANSTCLNGQPLQQDLEALLRRPLRLANDANCLAMSEAADGAGAGAR 125 Query: 124 LVMGLILGTGVGGGLVLNGKPITGQSYITGEFGHMRLPVDALTLMGFDFPLRRCGCGQMG 183 V ILGTGVGGG+V++ K + G + + GE+GH LP+ A D PL C CG+ G Sbjct: 126 TVFAAILGTGVGGGIVVDQKLLVGANAVAGEWGHNPLPLPAPD----DLPLPACYCGRAG 181 Query: 184 CIENYLSGRGFAWLYQHYYDQSLQAPEIIALWEQGDEQAHAHVERYLDLLAVCLGNILTI 243 CIE YLSG G A + + + L A I +G + A +ERY LA L ++ + Sbjct: 182 CIETYLSGPGLAADHLRHGGEPLDAAAIARQATEGQRASQASLERYELRLARALAGVINL 241 Query: 244 VDPDLLVIGGGLSNFTAITTQLAERLPRHLLPVARAPRIERARHGDAGGMRGAAFL 299 +DP+++V+GGGLS + + R H+ + R+ ARHGDA G+RGAA+L Sbjct: 242 LDPEVIVLGGGLSQIARLYEHVPRRWAAHVFSDTVSTRLLPARHGDASGVRGAAWL 297 Lambda K H 0.322 0.142 0.441 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: 292 Number of extensions: 17 Number of successful extensions: 2 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: 303 Length of database: 301 Length adjustment: 27 Effective length of query: 276 Effective length of database: 274 Effective search space: 75624 Effective search space used: 75624 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 (21.9 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