Align N-acetyl-D-glucosamine kinase; EC 2.7.1.59; GlcNAc kinase (uncharacterized)
to candidate 14532 b0394 possible NAGC-like transcriptional regulator (VIMSS)
Query= curated2:Q4QP08 (304 letters) >FitnessBrowser__Keio:14532 Length = 302 Score = 225 bits (574), Expect = 9e-64 Identities = 123/302 (40%), Positives = 175/302 (57%), Gaps = 4/302 (1%) Query: 1 MYYGLDIGGTKIELAVFNEELEKLYSERVPTPKTDYEEWLNTIVDLVNRADEKFGEVGTV 60 M G+D+GGTK E+ + E+LY R+PTP+ DY + + TI LV+ A++ G+ GTV Sbjct: 1 MRIGIDLGGTKTEVIALGDAGEQLYRHRLPTPRDDYRQTIETIATLVDMAEQATGQRGTV 60 Query: 61 GLGVPGFVNQQTGLAEITNIRVADNKPILRDLSVRLGREVRAENDANCFALSEAWDTENQ 120 G+G+PG ++ TG+ + N + +P +DLS RL REVR NDANC A+SEA D Sbjct: 61 GMGIPGSISPYTGVVKNANSTWLNGQPFDKDLSARLQREVRLANDANCLAVSEAVDGAAA 120 Query: 121 QYPTVLGLILGTGFGGGFVLNGKVHSGQVGMAGELGHLQLNYHALKLLGW-DNAPIYQCG 179 TV +I+GTG G G NG+ H G G AGE GH L + L + + P C Sbjct: 121 GAQTVFAVIIGTGCGAGVAFNGRAHIGGNGTAGEWGHNPLPWMDEDELRYREEVP---CY 177 Query: 180 CGNKACLDNYLSGRGFEMLYRDLKGETLSAREIIDLFYQGNESAVDFVNLFVELAAISIG 239 CG + C++ ++SG GF M YR L G L EII L + + A + + A S+ Sbjct: 178 CGKQGCIETFISGTGFAMDYRRLSGHALKGSEIIRLVEESDPVAELALRRYELRLAKSLA 237 Query: 240 NIITAFDPHMIVLGGGLSNFDYLYEALPKALPPHLMRTAKVPPIKKAKHGDSGGVRGAAA 299 +++ DP +IVLGGG+SN D LY+ + + + + P++KAKHGDS GVRGAA Sbjct: 238 HVVNILDPDVIVLGGGMSNVDRLYQTVGQLIKQFVFGGECETPVRKAKHGDSSGVRGAAW 297 Query: 300 LF 301 L+ Sbjct: 298 LW 299 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: 251 Number of extensions: 14 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: 304 Length of database: 302 Length adjustment: 27 Effective length of query: 277 Effective length of database: 275 Effective search space: 76175 Effective search space used: 76175 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