Align N-acetyl-D-glucosamine kinase; EC 2.7.1.59; GlcNAc kinase (uncharacterized)
to candidate 353126 BT3600 ROK family transcriptional repressor (NCBI ptt file)
Query= curated2:Q4QP08 (304 letters) >FitnessBrowser__Btheta:353126 Length = 298 Score = 95.9 bits (237), Expect = 1e-24 Identities = 82/314 (26%), Positives = 144/314 (45%), Gaps = 40/314 (12%) Query: 4 GLDIGGTKIELAVFN---------EELEKLYSERVPTPKTDYEEWLNTIVD-LVNRADEK 53 G+DIGGTKI+ + + E + L E P E L ++ ++ +AD Sbjct: 12 GVDIGGTKIKAGLVDINGQIIGIPESIRTLAHE----PGEMIIEQLTLLIRRMIQQADG- 66 Query: 54 FGEVGTVGLGVPGFVNQQTGLA-EITNIRVADNKPILRDLSVRLGREVRAENDANCFALS 112 E+ +G+G G ++ G+ E N+ N P+ + + G V+ +NDAN L Sbjct: 67 -AELIGIGIGSTGPLDINKGIILECNNLPTLHNYPLHKKIESTFGLPVKLDNDANAMMLG 125 Query: 113 EAWDTENQQYPTVLGLILGTGFGGGFVLNGKVHSGQVGMAGELGHLQLNYHALKLLGWDN 172 EA + ++LG+ LGTG G V+N K+ G G AGE+ W + Sbjct: 126 EALWGAGRNLNSILGITLGTGLGAAIVVNRKIIRGATGCAGEI--------------WLS 171 Query: 173 APIYQCGCGNKACLDNYLSGRGFEMLYRDLKGETLSAREIIDLFYQGNESAVDFVNLFVE 232 Y+ G +++Y+SG G LY+ + +S EI L +G+ +A+ F + Sbjct: 172 P--YKEG-----MIEDYVSGTGISNLYQRITKRKISGEEISKLAREGDINALKAWKEFTQ 224 Query: 233 LAAISIGNIITAFDPHMIVLGGG-LSNFDYLYEALPKALPPHLM-RTAKVPPIKKAKHGD 290 A ++ + DP ++++GG + + D ++++ ++ +TA +K A D Sbjct: 225 ALAYALSWTVNIVDPEVVIIGGSVMHSSDIFWDSMVSLFKKYICPQTAASIQLKPAGLKD 284 Query: 291 SGGVRGAAALFLTK 304 + G GAAAL + Sbjct: 285 NAGFMGAAALMFVE 298 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: 220 Number of extensions: 14 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: 298 Length adjustment: 27 Effective length of query: 277 Effective length of database: 271 Effective search space: 75067 Effective search space used: 75067 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