Align N-acetylglucosamine kinase (EC 2.7.1.59) (characterized)
to candidate WP_103231942.1 C1634_RS03565 ROK family protein
Query= metacyc::MONOMER-19002 (326 letters) >NCBI__GCF_002899945.2:WP_103231942.1 Length = 322 Score = 347 bits (889), Expect = e-100 Identities = 170/317 (53%), Positives = 227/317 (71%), Gaps = 2/317 (0%) Query: 5 MEKPYVVGIDIGGTNTVFGIVDARGTIIASGAVKTQVYPTVEEYADEVCKNLLPLIIANG 64 + K +G+DIGGTNT FGIV+ RG ++ G ++T Y VE++ D + +++ P++ G Sbjct: 6 LSKQVALGVDIGGTNTKFGIVNHRGEVLDKGNLRTDAYDKVEDFIDALYESVRPMMEKYG 65 Query: 65 GVDKIKGIGIGAPNGNYYTGTIEFAPNLPWKGVLPLASMFEERLGIPTALTNDANAAAVG 124 GIG+GAPN NYY GTIE APNLPWKGV+P A + + +P +TNDANAAA+G Sbjct: 66 TEAHFDGIGVGAPNANYYKGTIELAPNLPWKGVIPFAELMTAKFNLPCTVTNDANAAALG 125 Query: 125 EMTYGAARGMKDFIMITLGTGVGSGIVINGQVVYGHDGFAGELGHVIVRRDGR-ICGCGR 183 EM +GAARGMKDFIMITLGTGVGSGI+ NG ++YGHDGFAGELGH IV+ GR G Sbjct: 126 EMLFGAARGMKDFIMITLGTGVGSGIIANGSLIYGHDGFAGELGHTIVKPGGRKHWSTGS 185 Query: 184 KGCLETYCSATGVARTAREFLAARTDASLLRNIPAESIVSKDVYDAAVQGDKLAQEIFEF 243 +G LE Y SATG+ TA++ + A S+L P + I SK VY+ A++ D +A E+F + Sbjct: 186 EGSLEAYASATGITITAKK-MRAEFPESMLNQYPEDEINSKTVYECAMKEDPIAIEVFRY 244 Query: 244 TGNILGEALADAIAFSSPEAIILFGGLAKSGDYIMKPIMKAMENNLLNIYKGKAKLLVSE 303 TG LGEA+A+ + FSSP+AI+LFGG+ K+GD+I+KP ME NLL I++ K +L+ SE Sbjct: 245 TGQKLGEAIANFVMFSSPQAILLFGGVIKAGDFILKPAKLHMERNLLPIFRNKVQLVFSE 304 Query: 304 LKDSDAAVLGASALAWE 320 L ++DAA+LGASAL WE Sbjct: 305 LDEADAAILGASALVWE 321 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: 342 Number of extensions: 15 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: 322 Length adjustment: 28 Effective length of query: 298 Effective length of database: 294 Effective search space: 87612 Effective search space used: 87612 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