Align N-acetyl-D-glucosamine kinase; EC 2.7.1.59; GlcNAc kinase (uncharacterized)
to candidate 5208927 Shew_1428 fructokinase (RefSeq)
Query= curated2:Q4QP08 (304 letters) >FitnessBrowser__PV4:5208927 Length = 296 Score = 219 bits (559), Expect = 5e-62 Identities = 122/301 (40%), Positives = 176/301 (58%), Gaps = 6/301 (1%) Query: 1 MYYGLDIGGTKIELAVFNEELEKLYSERVPTPKTDYEEWLNTIVDLVNRADEKFGEVGTV 60 M G+D+GGTKIEL +E ++L+ +R+PTP+ +Y+ L+ I LVN A+ G+ GTV Sbjct: 2 MRMGVDLGGTKIELVALSEAGKELFRKRIPTPR-EYKATLDAIEALVNEAESTLGQKGTV 60 Query: 61 GLGVPGFVNQQTGLAEITNIRVADNKPILRDLSVRLGREVRAENDANCFALSEAWDTENQ 120 G+G+PG ++ +GL + N + P+ DL RL REVR NDANCFA+SEA D Sbjct: 61 GVGIPGVISPFSGLVKNANSTWINGHPLDLDLGARLEREVRVANDANCFAVSEAVDGAAA 120 Query: 121 QYPTVLGLILGTGFGGGFVLNGKVHSGQVGMAGELGHLQLNYHALKLLGWDNAPIYQCGC 180 V G+I+GTG GGG +NGKVH G G+ GE GH + L + D +C C Sbjct: 121 GKGLVFGVIIGTGCGGGIAINGKVHGGGNGIGGEWGH-----NPLPWMTPDEFNSTECFC 175 Query: 181 GNKACLDNYLSGRGFEMLYRDLKGETLSAREIIDLFYQGNESAVDFVNLFVELAAISIGN 240 GNK C++ ++SG GF Y+ G+ S EI QG A +++ A S+ + Sbjct: 176 GNKDCIETFISGTGFVRDYKAAGGDAPSGIEIARRMEQGEALATAAFERYIDRLARSLAH 235 Query: 241 IITAFDPHMIVLGGGLSNFDYLYEALPKALPPHLMRTAKVPPIKKAKHGDSGGVRGAAAL 300 +I DP +IVLGGG+SN + +Y LP+AL +++ P+ + +G S GVRGAA L Sbjct: 236 MINMLDPDIIVLGGGVSNIEAIYPRLPEALSKYVLGGECRTPVVQNMYGGSSGVRGAAWL 295 Query: 301 F 301 + Sbjct: 296 W 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: 250 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: 296 Length adjustment: 27 Effective length of query: 277 Effective length of database: 269 Effective search space: 74513 Effective search space used: 74513 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