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_011779687.1 MVAN_RS12350 ROK family protein
Query= SwissProt::A5U654 (265 letters) >NCBI__GCF_000015305.1:WP_011779687.1 Length = 272 Score = 392 bits (1007), Expect = e-114 Identities = 189/252 (75%), Positives = 214/252 (84%) Query: 13 GATTQRHGFGIDVGGSGIKGGIVDLDTGQLIGDRIKLLTPQPATPLAVAKTIAEVVNGFG 72 G+ + R GFGIDVGGSG+KGGIVDLDTG+L+GDR KLLTPQPATP AV+KTIA+V F Sbjct: 17 GSGSPRRGFGIDVGGSGVKGGIVDLDTGRLVGDRFKLLTPQPATPDAVSKTIADVAAHFD 76 Query: 73 WRGPLGVTYPGVVTHGVVRTAANVDKSWIGTNARDTIGAELGGQQVTILNDADAAGLAET 132 W GPLGVTYPGVV G+V TAANVDK W+G NA++ IG L GQ VT+LNDADAAGLAE Sbjct: 77 WEGPLGVTYPGVVADGIVCTAANVDKGWLGLNAKEVIGGALSGQPVTVLNDADAAGLAEE 136 Query: 133 RYGAGKNNPGLVVLLTFGTGIGSAVIHNGTLIPNTEFGHLEVGGKEAEERAASSVKEKND 192 ++GAG++ G++VLLTFGTGIGSAVIHNG L+PNTEFGHLEVGGKEAE RAASSVKE Sbjct: 137 KFGAGRDKTGVIVLLTFGTGIGSAVIHNGVLLPNTEFGHLEVGGKEAEHRAASSVKEAKG 196 Query: 193 WTYPKWAKQVIRVLIAIENAIWPDLFIAGGGISRKADKWVPLLENRTPVVPAALQNTAGI 252 W+Y +W +V +VL+AIENAIWPDLFI GGGISRKADKWVPLL+NRTPVV A LQNTAGI Sbjct: 197 WSYERWTTEVTKVLVAIENAIWPDLFIVGGGISRKADKWVPLLQNRTPVVAAELQNTAGI 256 Query: 253 VGAAMASVADTT 264 VGAAMAS D T Sbjct: 257 VGAAMASDVDVT 268 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: 337 Number of extensions: 10 Number of successful extensions: 1 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: 272 Length adjustment: 25 Effective length of query: 240 Effective length of database: 247 Effective search space: 59280 Effective search space used: 59280 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