Align ADP-specific glucokinase (EC 2.7.1.147) (characterized)
to candidate WP_054653999.1 CES79_RS01675 ROK family protein
Query= BRENDA::Q8R8N4 (312 letters) >NCBI__GCF_002217945.1:WP_054653999.1 Length = 320 Score = 196 bits (497), Expect = 8e-55 Identities = 111/311 (35%), Positives = 172/311 (55%), Gaps = 1/311 (0%) Query: 1 MRIGVDLGGTNIAVGLVEEDGKIIATGSRPTKPERGYEAIARDIAELSFELLQRMGISVK 60 M +G+DLGGTNI +GL+ D + PT+ E + + ++ +LL Sbjct: 4 MYLGIDLGGTNIKIGLLNADLTVQMKLKVPTESETNSQTVMANMIAGIKQLLAETQTDTS 63 Query: 61 DVKSMGIGVPGVADNEKGIVIRAVNL-FWTKVPLAKEIRKYIDLPIYMENDANVAALAEA 119 +K++GIGVPG D +KG+ I + N W VP+ + I LP Y++ND V E Sbjct: 64 QIKAVGIGVPGQMDIKKGLSIFSPNFTHWENVPVVQLIEAQFHLPTYIDNDVRVNLYGEW 123 Query: 120 TFGAGRGSKSSVTITLGTGVGSGFILDGKIYSGAHHFAPEIGHMVIGDNGIRCNCGKIGC 179 GAGRG ++ + +TLGTG+G+ I DG++ G + A E+GH+ + +G C CG GC Sbjct: 124 QLGAGRGKQNVLMVTLGTGLGAAIITDGQMMYGKSNSAGELGHLNMYRHGRPCACGSSGC 183 Query: 180 FETYASATALIREGKKAAKRNPNTLILKFANGDIEGITAKNVIDAAKQYDEEALKIFEEY 239 Y SA +++ ++ ++I ++ + D ITAK V +A Q D+ A + +E Sbjct: 184 LGRYVSARGMVKTVQEHLAAGETSVITEWTHNDQAQITAKMVSEAYDQQDQLAQTVMQET 243 Query: 240 VKYLAVGIVNIINLFDPEVIILGGGVANAGDFLLKPLKKEVAENILFKELPYADIRKAEL 299 + L G+ + INL++PE II+GGG+A AGD LL P + +A + L DI A+L Sbjct: 244 GEILGYGLASAINLYNPERIIIGGGMAAAGDRLLTPARAVIAGHALKVAREVCDIVPAQL 303 Query: 300 GNDAGIIGAAI 310 G AG+IGA + Sbjct: 304 GAWAGMIGAGV 314 Lambda K H 0.318 0.140 0.397 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: 279 Number of extensions: 12 Number of successful extensions: 2 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: 312 Length of database: 320 Length adjustment: 27 Effective length of query: 285 Effective length of database: 293 Effective search space: 83505 Effective search space used: 83505 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