Align N-acetylglucosamine kinase (EC 2.7.1.59) (characterized)
to candidate 352021 BT2493 ROK family transcriptional repressor, with glucokinase domain (NCBI ptt file)
Query= metacyc::MONOMER-19002 (326 letters) >FitnessBrowser__Btheta:352021 Length = 326 Score = 609 bits (1571), Expect = e-179 Identities = 299/326 (91%), Positives = 317/326 (97%) Query: 1 MNSSMEKPYVVGIDIGGTNTVFGIVDARGTIIASGAVKTQVYPTVEEYADEVCKNLLPLI 60 MNS+MEKPYVVGIDIGGTNTVFGIVDARGTIIAS ++KT YPT EYADEVCKNLLPLI Sbjct: 1 MNSNMEKPYVVGIDIGGTNTVFGIVDARGTIIASSSIKTAGYPTAAEYADEVCKNLLPLI 60 Query: 61 IANGGVDKIKGIGIGAPNGNYYTGTIEFAPNLPWKGVLPLASMFEERLGIPTALTNDANA 120 IANGGVDKI+GIG+GAPNGNYYTGTIEFAPNLPWKG+LPLA+MFEERLGIPTALTNDANA Sbjct: 61 IANGGVDKIRGIGVGAPNGNYYTGTIEFAPNLPWKGILPLAAMFEERLGIPTALTNDANA 120 Query: 121 AAVGEMTYGAARGMKDFIMITLGTGVGSGIVINGQVVYGHDGFAGELGHVIVRRDGRICG 180 AA+GEMTYGAARGMKDFIMITLGTGVGSGIVINGQ+VYGHDGFAGELGHVI RRDGR+CG Sbjct: 121 AAIGEMTYGAARGMKDFIMITLGTGVGSGIVINGQMVYGHDGFAGELGHVIARRDGRVCG 180 Query: 181 CGRKGCLETYCSATGVARTAREFLAARTDASLLRNIPAESIVSKDVYDAAVQGDKLAQEI 240 CGRKGCLETYCSATGVARTAREFLAARTDASLLRNIPAE+I SKDVYDAAVQGDKLAQEI Sbjct: 181 CGRKGCLETYCSATGVARTAREFLAARTDASLLRNIPAENITSKDVYDAAVQGDKLAQEI 240 Query: 241 FEFTGNILGEALADAIAFSSPEAIILFGGLAKSGDYIMKPIMKAMENNLLNIYKGKAKLL 300 FEFTGNILGEALADAIAFSSPEAI+LFGGLAKSGDYIMKPI KA+++N+LNIYKGK KLL Sbjct: 241 FEFTGNILGEALADAIAFSSPEAIVLFGGLAKSGDYIMKPIQKAIDDNILNIYKGKTKLL 300 Query: 301 VSELKDSDAAVLGASALAWELKDLRD 326 VSELKDSDAAVLGASALAWELKDL++ Sbjct: 301 VSELKDSDAAVLGASALAWELKDLKE 326 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: 519 Number of extensions: 10 Number of successful extensions: 1 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: 326 Length adjustment: 28 Effective length of query: 298 Effective length of database: 298 Effective search space: 88804 Effective search space used: 88804 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: 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