Align N-acetyl-D-glucosamine kinase; EC 2.7.1.59; GlcNAc kinase (uncharacterized)
to candidate CCNA_02549 CCNA_02549 glucokinase
Query= curated2:Q9KRV2 (302 letters) >FitnessBrowser__Caulo:CCNA_02549 Length = 296 Score = 189 bits (481), Expect = 5e-53 Identities = 114/298 (38%), Positives = 163/298 (54%), Gaps = 11/298 (3%) Query: 3 YGFDVGGTKIEFGAFNEQLERVATERVATPTDDYAKLVETIAGLVHKYDAQFGVE-GTVG 61 +G D GGTKIE A N + VA R P +Y + +E +A LV ++ G +G Sbjct: 4 FGVDFGGTKIEVAALNAAGDFVARVRKPNP-GNYDEALEVVAALVADAESMAGGSCARLG 62 Query: 62 LGIPGMEDADNGCVLTVNVPAAKGKPLRADLETKLGRAVKVENDANCFALSEAWDDELKE 121 LGIPG G + N G+P +LET+L R V++ NDANC ALSEA D Sbjct: 63 LGIPGSISPRTGLIRNANSTYLNGRPFGENLETRLARPVRIANDANCLALSEAADGAGAG 122 Query: 122 AASVMGLILGTGFGGGLVYEGKVFSGRNHVAGEIGHMRLPIDAWFHLGEKAPLLGCGCGN 181 A+ V I+GTG GGG+V +GK+ +G N + GE GH LP + E+ P C CG Sbjct: 123 ASVVFAAIVGTGCGGGVVVDGKIINGHNGIGGEWGHAPLP----WPKPEEYPGPDCWCGR 178 Query: 182 KGCMDNYLSGRGFELLYEHYYGEKKKAIDIITAQKEGESKAVEHVERFMELLAICFANIF 241 KGC++ +++G F + + + A+ I EG+ KA ++R+++ LA A + Sbjct: 179 KGCLETWIAGPAF--ARDAGFANGQAAMQAI---GEGDVKASAALDRYVDRLARSLAVVC 233 Query: 242 TANDPHVVVLGGGLSNYDLIYEEMPKRVPKHLLSVAKCPKIVKAKHGDSGGVRGAAFL 299 DP ++VLGGG+SN D +YE +P + H+ S + KA HGDS GVRGA +L Sbjct: 234 DLIDPDIIVLGGGMSNVDALYERLPAAIAPHVFSDIFETPVRKAVHGDSSGVRGAVWL 291 Lambda K H 0.319 0.140 0.422 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: 270 Number of extensions: 12 Number of successful extensions: 4 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: 302 Length of database: 296 Length adjustment: 27 Effective length of query: 275 Effective length of database: 269 Effective search space: 73975 Effective search space used: 73975 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: 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