Align N-acetylglucosamine kinase (EC 2.7.1.59) (characterized)
to candidate CA265_RS11300 CA265_RS11300 sugar kinase
Query= metacyc::MONOMER-19002 (326 letters) >FitnessBrowser__Pedo557:CA265_RS11300 Length = 313 Score = 140 bits (354), Expect = 3e-38 Identities = 91/312 (29%), Positives = 154/312 (49%), Gaps = 13/312 (4%) Query: 5 MEKPYVVGIDIGGTNTVFGIVDARGTIIASGAVKTQVYPTVEEYADEVCKNLLPLIIANG 64 ME+ Y +GID+GG++ G+V+ G I+ S V + T + + + A Sbjct: 1 MEQSYAIGIDVGGSSLKCGVVNQNGEILYSIIVSLKNAKTQGAIIALIVEAIHTC--AKK 58 Query: 65 GVDKIKGIGIGAPNGNYYTGTIEFAPNLPWKGVLPLASMFEERLGIPTALTNDANAAAVG 124 + I G+GIG P Y I A NLP L L + +E + NDAN +G Sbjct: 59 FKNPILGVGIGFPGIIYNNKIIAGADNLPGFKQLALGEILQEVTRYNIVMDNDANLMGLG 118 Query: 125 EMTYGAARGMKDFIMITLGTGVGSGIVINGQVVYGHDGFAGELGHVIVRRDGRICGCGRK 184 EMTYGAA+ D + +T+GTG+G ++I+ ++ G ELGH++V+ +G C CG + Sbjct: 119 EMTYGAAKDCSDVVFLTVGTGIGGAVMIDNKLYGGFRNRGTELGHIVVQHNGLACACGGR 178 Query: 185 GCLETYCSATGVARTAREFLAARTDASLLRNIPAESIVSKDVYDAAVQGDKLAQEIFEFT 244 GCLE Y S T + + + P E I K + + + ++ A E E Sbjct: 179 GCLEAYASVTALLNHYQS----------IHPNPPEEIDGKYMVEKYLAREEYAVEAMESH 228 Query: 245 GNILGEALADAIAFSSPEAIILFGGLAKSGDYIMKPIMKAMENNLLNIYKGKAKLLVSEL 304 + L + + SP+ I++ GG+++SG + ++ I + ++ + I G +L+V+ Sbjct: 229 FDYLATGIISFVNVFSPQKIVIGGGISESGAFYVREIERRIKTLAVPIAPGN-ELVVAAR 287 Query: 305 KDSDAAVLGASA 316 + A +LG +A Sbjct: 288 LGNKAGLLGCAA 299 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: 281 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: 313 Length adjustment: 28 Effective length of query: 298 Effective length of database: 285 Effective search space: 84930 Effective search space used: 84930 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