Align N-acetylglucosamine kinase (EC 2.7.1.59) (characterized)
to candidate WP_009153825.1 SACMADRAFT_RS10680 ROK family protein
Query= metacyc::MONOMER-19002 (326 letters) >NCBI__GCF_000244955.1:WP_009153825.1 Length = 317 Score = 165 bits (417), Expect = 2e-45 Identities = 105/315 (33%), Positives = 170/315 (53%), Gaps = 12/315 (3%) Query: 11 VGIDIGGTNTVFGIVDARGTIIASGAVKTQVYPTVEEYADEVCKNLLPLIIANGGVDKIK 70 +G+D+GGT+ G+VD +G ++ + V T P+ E ++ ++ + V + Sbjct: 4 IGVDVGGTSVRAGVVDEQGALLDTARVGT---PSDELALEDAVAGVIDELRNRHEVGAV- 59 Query: 71 GIGIGAPNGNYYTGTIEFAPNLPWKGVLPLASMFEERLGIPTALTNDANAAAVGEMTYGA 130 G+ + A + ++ FAP+LPW+G P+A +R+G+P L +DANAAAV E +GA Sbjct: 60 GLAVAAFVRSDRR-SVMFAPHLPWRGA-PVADRVSKRVGLPVTLEHDANAAAVAEHRFGA 117 Query: 131 ARGMKDFIMITLGTGVGSGIVINGQVVYGHDGFAGELGHVIVRRDGRICGCGRKGCLETY 190 ARG + ++ +GTG+G+G++++G++ G G A ELGH+ V GR C CG+ GC E Y Sbjct: 118 ARGARVAALVAIGTGIGAGLLLDGRLFRGAHGVAPELGHLCVVPGGRACPCGKHGCWERY 177 Query: 191 CSATGVARTAREFLAARTDASLLRNIPAE----SIVSKDVYDAAVQGDKLAQEIFEFTGN 246 CS T +A TA E LA S + SI + V AA GD +AQ Sbjct: 178 CSGTALAATAVELLARHPGRSTVLAWETAGDPGSITGRRVAGAARDGDPIAQRAMAELAR 237 Query: 247 ILGEALADAIAFSSPEAIILFGGLAKSGDYIMKPIMKAMENNLLNI-YKGKAKLLVSELK 305 LGE LA PE +++ GG+++S + + + ++ A++ S+L Sbjct: 238 WLGEGLALVADVYDPEVVVIAGGVSESAPLFLDEAREHYARAVTGAGHRPLARIRTSQLG 297 Query: 306 DSDAAVLGASALAWE 320 D + A++GA+ALA E Sbjct: 298 D-ETALVGAAALARE 311 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: 274 Number of extensions: 14 Number of successful extensions: 4 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: 317 Length adjustment: 28 Effective length of query: 298 Effective length of database: 289 Effective search space: 86122 Effective search space used: 86122 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