Align glucokinase (EC 2.7.1.2) (characterized)
to candidate WP_009153825.1 SACMADRAFT_RS10680 ROK family protein
Query= BRENDA::P0A4E1 (317 letters) >NCBI__GCF_000244955.1:WP_009153825.1 Length = 317 Score = 281 bits (718), Expect = 2e-80 Identities = 140/310 (45%), Positives = 195/310 (62%) Query: 3 LTIGVDIGGTKIAAGVVDEEGNILSTHKVPTPTTPEAIVDAIASAVEGARVGHEIVAVGI 62 L IGVD+GGT + AGVVDE+G +L T +V TP+ A+ DA+A ++ R HE+ AVG+ Sbjct: 2 LAIGVDVGGTSVRAGVVDEQGALLDTARVGTPSDELALEDAVAGVIDELRNRHEVGAVGL 61 Query: 63 GAAGYVNRQRSTVYFAPNIDWRQEPLKEKVEARVGLPVVVENDANAAAWGEYKFGGGKGH 122 A +V R +V FAP++ WR P+ ++V RVGLPV +E+DANAAA E++FG +G Sbjct: 62 AVAAFVRSDRRSVMFAPHLPWRGAPVADRVSKRVGLPVTLEHDANAAAVAEHRFGAARGA 121 Query: 123 RNVICITLGTGLGGGIIIGNKLRRGHFGVAAEFGHIRMVPDGLLCGCGSQGCWEQYASGR 182 R + +GTG+G G+++ +L RG GVA E GH+ +VP G C CG GCWE+Y SG Sbjct: 122 RVAALVAIGTGIGAGLLLDGRLFRGAHGVAPELGHLCVVPGGRACPCGKHGCWERYCSGT 181 Query: 183 ALVRYAKQRANATPERAEVLLALGDGTPDGIEGKHISVAARQGCPVAVDSYRELARWAGA 242 AL A + P R+ VL G P I G+ ++ AAR G P+A + ELARW G Sbjct: 182 ALAATAVELLARHPGRSTVLAWETAGDPGSITGRRVAGAARDGDPIAQRAMAELARWLGE 241 Query: 243 GLADLASLFDPSAFIVGGGLSDEGDLVLDPIRKSYKRWLVGGNWRPVADVIAAQLGNKAG 302 GLA +A ++DP ++ GG+S+ L LD R+ Y R + G RP+A + +QLG++ Sbjct: 242 GLALVADVYDPEVVVIAGGVSESAPLFLDEAREHYARAVTGAGHRPLARIRTSQLGDETA 301 Query: 303 LVGAADLARE 312 LVGAA LARE Sbjct: 302 LVGAAALARE 311 Lambda K H 0.318 0.139 0.426 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: 364 Number of extensions: 17 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: 317 Length of database: 317 Length adjustment: 27 Effective length of query: 290 Effective length of database: 290 Effective search space: 84100 Effective search space used: 84100 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