Align Polyphosphate glucokinase; Poly(P) glucokinase; ATP-dependent glucokinase; Polyphosphate--glucose phosphotransferase; EC 2.7.1.63; EC 2.7.1.2 (characterized)
to candidate WP_008992894.1 I215_RS15275 ROK family protein
Query= SwissProt::A5U654 (265 letters) >NCBI__GCF_000300875.1:WP_008992894.1 Length = 254 Score = 202 bits (513), Expect = 7e-57 Identities = 97/239 (40%), Positives = 154/239 (64%), Gaps = 2/239 (0%) Query: 22 GIDVGGSGIKGGIVDLDTGQLIGDRIKLLTPQPATPLAVAKTIAEVVNGFGWRGPLGVTY 81 GID+G +G+KG +VD+D G+L +R ++ TP+PATP A+ + + ++ F W GP+G + Sbjct: 5 GIDIGATGMKGAVVDIDKGELTTERFRIDTPRPATPQAMVEVVKAIIAHFKWTGPVGCGF 64 Query: 82 PGVVTHGVVRTAANVDKSWIGTNARDTIGAELGGQQVTILNDADAAGLAETRYGAGKNNP 141 P + H VV T++N++ W+G N + E G ++NDADAAG+AE +GAGK Sbjct: 65 PSSIHHSVVLTSSNLNPKWVGVNIDELFEKET-GLPFVVVNDADAAGIAEMNFGAGKGKK 123 Query: 142 GLVVLLTFGTGIGSAVIHNGTLIPNTEFGHLEVGG-KEAEERAASSVKEKNDWTYPKWAK 200 GLV+ +T GTG+GS +G LIPN E G L + E+ A+++ ++K++ ++ KW K Sbjct: 124 GLVLTITVGTGLGSCAFFDGKLIPNLELGQLHYKKYNKVEKFASNATRKKHNMSFKKWGK 183 Query: 201 QVIRVLIAIENAIWPDLFIAGGGISRKADKWVPLLENRTPVVPAALQNTAGIVGAAMAS 259 + +VL ++ + PDLFI GGG S+ D++ L+ + PV+PA +N AGI+GAA A+ Sbjct: 184 RFNKVLNYVDLVLCPDLFIIGGGGSKYFDEYKKYLKLKVPVIPAESRNEAGIIGAAYAA 242 Lambda K H 0.314 0.134 0.402 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: 216 Number of extensions: 11 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: 265 Length of database: 254 Length adjustment: 24 Effective length of query: 241 Effective length of database: 230 Effective search space: 55430 Effective search space used: 55430 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: 42 (21.9 bits) S2: 47 (22.7 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