Align N-acetyl-D-glucosamine kinase; EC 2.7.1.59; GlcNAc kinase (uncharacterized)
to candidate 6937235 Sama_1405 fructokinase (RefSeq)
Query= curated2:Q4QP08 (304 letters) >FitnessBrowser__SB2B:6937235 Length = 310 Score = 223 bits (567), Expect = 6e-63 Identities = 123/298 (41%), Positives = 175/298 (58%), Gaps = 6/298 (2%) Query: 4 GLDIGGTKIELAVFNEELEKLYSERVPTPKTDYEEWLNTIVDLVNRADEKFGEVGTVGLG 63 G+D+GGTKIEL NE+ E+++ +RVPTPK DY L + LV+ ++++ G+V +VG+G Sbjct: 5 GIDLGGTKIELVTLNEKGEEVFRKRVPTPK-DYRATLEAVAGLVHDSEKETGQVSSVGIG 63 Query: 64 VPGFVNQQTGLAEITNIRVADNKPILRDLSVRLGREVRAENDANCFALSEAWDTENQQYP 123 +PG V+ TG + +N + +P+ +DL LGREVR NDANCFA+SE+ D Sbjct: 64 IPGVVSAVTGRVKNSNAVWLNGQPMDKDLGAMLGREVRIANDANCFAVSESVDGGGAGKT 123 Query: 124 TVLGLILGTGFGGGFVLNGKVHSGQVGMAGELGHLQLNYHALKLLGWDNAPIYQCGCGNK 183 V G ILGTG G G +N KVH G G+ GE GH + L + D +C CGN Sbjct: 124 LVFGAILGTGCGAGIAINHKVHGGGNGIGGEWGH-----NPLPWMTADEFNSTRCFCGNA 178 Query: 184 ACLDNYLSGRGFEMLYRDLKGETLSAREIIDLFYQGNESAVDFVNLFVELAAISIGNIIT 243 C++ ++SG GF +R GE S EI+ L +G A F++ A ++ ++I Sbjct: 179 DCIETFVSGTGFVRDFRAHGGEAASGIEIVALMGKGEPLAEAAFGRFIDRLARALAHVIN 238 Query: 244 AFDPHMIVLGGGLSNFDYLYEALPKALPPHLMRTAKVPPIKKAKHGDSGGVRGAAALF 301 DP +IVLGGG+SN D +YE LP LP +++ + K HG S GVRGAA L+ Sbjct: 239 LLDPDVIVLGGGVSNIDEIYEYLPALLPKYVLGGECATKVVKNHHGASSGVRGAAWLW 296 Lambda K H 0.319 0.140 0.421 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: 265 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: 304 Length of database: 310 Length adjustment: 27 Effective length of query: 277 Effective length of database: 283 Effective search space: 78391 Effective search space used: 78391 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