Align N-acetylglucosamine kinase (EC 2.7.1.59) (characterized)
to candidate WP_017548855.1 C792_RS0107525 ROK family glucokinase
Query= metacyc::MONOMER-19002 (326 letters) >NCBI__GCF_000330705.1:WP_017548855.1 Length = 319 Score = 165 bits (417), Expect = 2e-45 Identities = 100/315 (31%), Positives = 164/315 (52%), Gaps = 12/315 (3%) Query: 10 VVGIDIGGTNTVFGIVDARGTIIASGAVKTQVYPTVEEYADEVCKNLLPLI-----IANG 64 ++ DIGGT+ G+ D +I + T + E + ++L I Sbjct: 4 ILAADIGGTSCKLGVFDEELNLIEKWEIPTDI----SEEGSHILADVLDSFRSKEEILGF 59 Query: 65 GVDKIKGIGIGAPNG-NYYTGTIEFAPNLPWKGVLPLASMFEERLGIPTALTNDANAAAV 123 V++ G G+G P ++ G + NL KG +A++F E G + NDAN AA+ Sbjct: 60 KVEECLGTGLGMPGPVDFEKGILNGCINLNIKGKRSIATIFSELSGSAAIVDNDANVAAL 119 Query: 124 GEMTYGAARGMKDFIMITLGTGVGSGIVINGQVVYGHDGFAGELGHVIVRRDGRI-CGCG 182 GE + GA G + +MITLGTGVG G++ G++++G G GE+GH+ V DGR C CG Sbjct: 120 GEQSKGAGHGHSEVVMITLGTGVGGGVISEGRLIHGTGGSGGEIGHITVDFDGRFQCNCG 179 Query: 183 RKGCLETYCSATGVARTAREFLAARTDASLLRNIPAESIVSKDVYDAAVQGDKLAQEIFE 242 +KGCLET SATG+ A ++ L+ I ++ SK + DAA+ GD LA+ + E Sbjct: 180 KKGCLETVASATGMVNLAGYHSDDHENSVLIAAIKEGTLTSKAIVDAAMTGDPLAEFVVE 239 Query: 243 FTGNILGEALADAIAFSSPEAIILFGGLAKSGDYIMKPIMKAMENNLLNIYKGKAKLLVS 302 L A++ ++P + GG++++G Y+ I K ++ + +++++ Sbjct: 240 EAARYLAVAMSSISVITNPGYFVFGGGVSRAGRYLTDKIKKYYDSLIFPPAADDVEIVMA 299 Query: 303 ELKDSDAAVLGASAL 317 EL +DA + GA+ L Sbjct: 300 EL-GNDAGMYGAARL 313 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: 286 Number of extensions: 16 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: 326 Length of database: 319 Length adjustment: 28 Effective length of query: 298 Effective length of database: 291 Effective search space: 86718 Effective search space used: 86718 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 24 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