Align N-acetyl-D-glucosamine kinase; EC 2.7.1.59; GlcNAc kinase (uncharacterized)
to candidate WP_089137286.1 CES79_RS11525 ROK family protein
Query= curated2:Q9KRV2 (302 letters) >NCBI__GCF_002217945.1:WP_089137286.1 Length = 300 Score = 94.0 bits (232), Expect = 4e-24 Identities = 72/265 (27%), Positives = 124/265 (46%), Gaps = 23/265 (8%) Query: 6 DVGGTKIEFGAFNEQLERVATERVATPTDDYAKLVETIAGLVHKYDAQFGVEGTVGLGIP 65 D+GGT +++G +N+QLE + + TP +A++ + + L + + G V + +P Sbjct: 14 DIGGTSVKYGYWNQQLENSGSFK--TPKT-WAEMHDKLLSLPSQITQP--IRG-VAISLP 67 Query: 66 GMEDADNGCVL-TVNVPAAKGKPLRADLETKLGRAVKVENDANCFALSEAWDDELKEAAS 124 G D G + T VP G +R +L V ++NDANC L+E W K+ +S Sbjct: 68 GSVDIKKGQISGTTAVPYLNGFAIRKELSDDFQLPVTIQNDANCAGLAETWIGNAKDVSS 127 Query: 125 VMGLILGTGFGGGLVYEGKVFSGRNHVAGEIGHMRLPIDAWFHLGEKAPLLGCGCGNKGC 184 V LI+GTG GG ++ +G++ +G +H GE G+ L G+ L G Sbjct: 128 VALLIIGTGIGGSIIQDGQLLTGHDHFMGEFGYSILN-------GQNKTLSDLG------ 174 Query: 185 MDNYLSGRGFELLYEHYYGEKKKAIDIITAQKEGESKAVEHVERFMELLAICFANIFTAN 244 + + + E A I K+G+ A + + L++ N+ T+ Sbjct: 175 -SPVQMAKKYTRISESL--APVDAPQIFEKAKQGDKLAQNCINDMVHWLSLEVYNLITSF 231 Query: 245 DPHVVVLGGGLSNYDLIYEEMPKRV 269 +P +++GGG+S D E + RV Sbjct: 232 NPDRLLIGGGISIRDDFLEMIRNRV 256 Lambda K H 0.319 0.140 0.422 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: 201 Number of extensions: 8 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 302 Length of database: 300 Length adjustment: 27 Effective length of query: 275 Effective length of database: 273 Effective search space: 75075 Effective search space used: 75075 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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