Align N-acetyl-D-glucosamine kinase; EC 2.7.1.59; GlcNAc kinase (uncharacterized)
to candidate 200821 SO1656 ROK family protein (NCBI ptt file)
Query= curated2:Q4QP08 (304 letters) >FitnessBrowser__MR1:200821 Length = 306 Score = 209 bits (532), Expect = 6e-59 Identities = 121/306 (39%), Positives = 172/306 (56%), Gaps = 14/306 (4%) Query: 4 GLDIGGTKIELAVFNEELEKLYSERVPTPKTDYEEWLNTIVDLVNRADEKFGEVGTVGLG 63 G+D+GGTKIEL N E ++ +R+ TP+ DY+ LN IVDLVN A+ GE G+VG+G Sbjct: 5 GIDLGGTKIELVALNNEGNEVVRKRINTPR-DYQGTLNAIVDLVNEAESTLGEKGSVGVG 63 Query: 64 VPGFVNQQTGLAEITNIRVADNKPILRDLSVRLGREVRAENDANCFALSEAWDTENQQYP 123 +PG ++ +GL + N + P+ L LGREVR NDANCFALSEA D Sbjct: 64 IPGVISPYSGLVKNANSTWINGHPLDVHLGELLGREVRVANDANCFALSEAVDGAAAGKS 123 Query: 124 TVLGLILGTGFGGGFVLNGKVHSGQVGMAGELGHLQLNYHALKLLGWDNAPIYQCGCGNK 183 V G+I+GTG G G +NGKVH+G G+ GE GH + L + + +C CGN Sbjct: 124 VVFGVIIGTGCGAGVAINGKVHAGGNGIGGEWGH-----NPLPWMTKEEFNTTRCFCGNP 178 Query: 184 ACLDNYLSGRGFEMLYRDLKGETLSAR--------EIIDLFYQGNESAVDFVNLFVELAA 235 C++ ++SG GF Y + S + EI+ L G+E A+ +V+ A Sbjct: 179 DCIETFISGTGFVRDYNEALSRAASVQRVPAKSGSEIMSLVDGGDEIALAAFERYVDRLA 238 Query: 236 ISIGNIITAFDPHMIVLGGGLSNFDYLYEALPKALPPHLMRTAKVPPIKKAKHGDSGGVR 295 S+ ++I DP IVLGGG+SN + +Y LP L +++ P+ + +G S GVR Sbjct: 239 RSLAHVINLLDPDAIVLGGGMSNVEAIYPRLPALLSHYVVGRECRTPVVQNLYGCSSGVR 298 Query: 296 GAAALF 301 GAA L+ Sbjct: 299 GAAWLW 304 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: 268 Number of extensions: 13 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: 304 Length of database: 306 Length adjustment: 27 Effective length of query: 277 Effective length of database: 279 Effective search space: 77283 Effective search space used: 77283 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