Align N-acetyl-D-glucosamine kinase; EC 2.7.1.59; GlcNAc kinase (uncharacterized)
to candidate BWI76_RS27555 BWI76_RS27555 putative sugar kinase/transcriptional regulator, ATPase domain protein
Query= curated2:Q4QP08 (304 letters) >FitnessBrowser__Koxy:BWI76_RS27555 Length = 310 Score = 191 bits (486), Expect = 1e-53 Identities = 109/300 (36%), Positives = 165/300 (55%), Gaps = 6/300 (2%) Query: 2 YYGLDIGGTKIELAVFNEELEKLYSERVPTPKTDYEEWLNTIVDLVNRADEKFGEVGTVG 61 Y GLDIGG+KI V +E+ + RV T K ++++ T+V+L+ ++ + +G Sbjct: 3 YLGLDIGGSKIAAVVMDEQGHEWRRFRVETRKQTRQQFIATLVELITAIGDELAQPLAIG 62 Query: 62 LGVPGFVNQQTGLAEITNIRVADNKPILRDLSVRLGREVRAENDANCFALSEAWDTENQQ 121 + +PG ++ Q+G NI+V + + +L RLG+ V ND NCFALSEA D Sbjct: 63 IALPGSISPQSGKIRNANIQVINGCRLQDELEQRLGQSVVLANDGNCFALSEACDGAGAD 122 Query: 122 YPTVLGLILGTGFGGGFVLNGKVHSGQVGMAGELGHLQL-NYHALKLLGWDNAPIYQCGC 180 Y V G+ LGTG GGG LN ++ G G+A E GH+ L Y + ++ P +C C Sbjct: 123 YSLVFGMTLGTGCGGGIALNRQIFPGASGIAAECGHITLPGYQEV-----NDGPPARCYC 177 Query: 181 GNKACLDNYLSGRGFEMLYRDLKGETLSAREIIDLFYQGNESAVDFVNLFVELAAISIGN 240 G C+++++SG G YR L E LS++ II +G +A + V F + A ++ Sbjct: 178 GKYNCVESFISGTGLSARYRLLTQEALSSQAIIARALEGEHAACEQVLRFRQQLARTLAT 237 Query: 241 IITAFDPHMIVLGGGLSNFDYLYEALPKALPPHLMRTAKVPPIKKAKHGDSGGVRGAAAL 300 ++ DP +I+LGGGLSN L L + P + + PI A+HGDS G+RGAA L Sbjct: 238 VVNLIDPGVIILGGGLSNVALLVNDLEADVAPLVFTDHFITPIVPARHGDSSGMRGAAWL 297 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: 227 Number of extensions: 9 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: 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