Align N-acetylglucosamine kinase (EC 2.7.1.59) (characterized)
to candidate AZOBR_RS27950 AZOBR_RS27950 transcriptional regulator
Query= metacyc::MONOMER-19002 (326 letters) >FitnessBrowser__azobra:AZOBR_RS27950 Length = 392 Score = 152 bits (385), Expect = 1e-41 Identities = 89/250 (35%), Positives = 136/250 (54%), Gaps = 15/250 (6%) Query: 71 GIGIGAPNGNYYTGTIEFAPNLPWKGVLPLASMFEERLGIPTALTNDANAAAVGEMTYGA 130 GIG+G P G + APNL W+ P+ + EE LG P + ND AAA+ E +GA Sbjct: 148 GIGVGIPALMDREGRLVLAPNLGWRDT-PIRPLLEEALGAPVHVDNDTKAAAMAERLFGA 206 Query: 131 ARGMKDFIMITLGTGVGSGIVINGQVVYGHDGFAGELGHVIVRRDGRICGCGRKGCLETY 190 RG++DF+ +T +GVG G+ G++ G GFAGE+GH+ + GR CGCG++GCLETY Sbjct: 207 CRGVEDFVYLTGHSGVGGGLFFGGRLYRGAQGFAGEIGHLTIVPGGRACGCGKRGCLETY 266 Query: 191 CSATGVARTAREFLAARTDASLLRNIPAESIVSKDVYDAAVQGDKLAQEIFEFTGNILGE 250 S T + A E L ++ A + ++D GD + + + E G+ LG Sbjct: 267 VSETSILAQAAE------RGRALPDLWAAAAAARD-------GDPVVRTLLEEAGSHLGF 313 Query: 251 ALADAIAFSSPEAIILFGGLAKSGDYIMKPIMKAMENNLLNIYKGKAKLLVSELKDSDAA 310 AL+ + ++P ++L G LA ++I+ + A+ + L + +LLVS L DA Sbjct: 314 ALSHLVNLANPGLVVLGGNLAIVAEFILPALNAALGEHALEPLRRDLRLLVSPL-GPDAV 372 Query: 311 VLGASALAWE 320 +G ALA + Sbjct: 373 PMGGIALAMD 382 Lambda K H 0.318 0.138 0.399 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: 306 Number of extensions: 12 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: 326 Length of database: 392 Length adjustment: 29 Effective length of query: 297 Effective length of database: 363 Effective search space: 107811 Effective search space used: 107811 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 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