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_087506863.1 CBE68_RS14725 ROK family protein
Query= SwissProt::A5U654 (265 letters) >NCBI__GCF_002165625.1:WP_087506863.1 Length = 256 Score = 227 bits (578), Expect = 2e-64 Identities = 110/237 (46%), Positives = 158/237 (66%), Gaps = 2/237 (0%) Query: 22 GIDVGGSGIKGGIVDLDTGQLIGDRIKLLTPQPATPLAVAKTIAEVVNGFGWRGPLGVTY 81 GID+GGSGIKG +VD+ TG+LI +R+++ TPQPATP AVA T+AE+ + W G +G + Sbjct: 5 GIDIGGSGIKGAVVDVTTGELISERLRIPTPQPATPEAVAATVAEICDQLHWHGLVGCGF 64 Query: 82 PGVVTHGVVRTAANVDKSWIGTNARDTIGAELGGQQVTILNDADAAGLAETRYGAGKNNP 141 P + HG+ RTAANVD SW+G N + I + + NDAD AGLAE ++GAGK Sbjct: 65 PAAIQHGIARTAANVDDSWLGANVQ-KIFCDATHLPCYVGNDADVAGLAEMQFGAGKELD 123 Query: 142 GLVVLLTFGTGIGSAVIHNGTLIPNTEFGHL-EVGGKEAEERAASSVKEKNDWTYPKWAK 200 GLV ++T GTG+G+A+ +NG L+ NTE GHL + G+E E RA+ + +++++ + W K Sbjct: 124 GLVFMVTIGTGLGTALFNNGELVANTELGHLFDSKGREWEHRASDAARKRDELDWKYWGK 183 Query: 201 QVIRVLIAIENAIWPDLFIAGGGISRKADKWVPLLENRTPVVPAALQNTAGIVGAAM 257 + + L+ +E WPD FI GGG S+K DK+ ++ V PA N AGI+GAA+ Sbjct: 184 RFNKYLVTLEQLFWPDAFILGGGASKKFDKFADAIDVAATVTPAESLNQAGIIGAAI 240 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: 217 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: 256 Length adjustment: 24 Effective length of query: 241 Effective length of database: 232 Effective search space: 55912 Effective search space used: 55912 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