Align ADP-specific glucokinase (EC 2.7.1.147) (characterized)
to candidate WP_012407138.1 NPUN_RS01685 ROK family protein
Query= BRENDA::Q8R8N4 (312 letters) >NCBI__GCF_000020025.1:WP_012407138.1 Length = 319 Score = 143 bits (360), Expect = 6e-39 Identities = 104/323 (32%), Positives = 166/323 (51%), Gaps = 23/323 (7%) Query: 3 IGVDLGGTNIAVGLVEEDGKIIATGSRP-TKPERGYEAIARDIAELSFELLQRMGISV-K 60 + +D GGT +A LV GSR + ER + + A E+++ + S+ + Sbjct: 5 LALDFGGTKLAAALVN-------VGSRKWLRYERRLSPVGAN-ASTDLEIMRSLIYSLLE 56 Query: 61 DVKSMGIGVP--GVADNEKGIVIRAVNLF-WTKVPLAKEIRKYIDLPIYMENDANVAALA 117 D K IGV G D G V + ++ W +PL + + + + ++NDANVAAL Sbjct: 57 DAKPAAIGVSFGGPVDASTGTVRLSHHVAGWENIPLKGLLEEEFGVSVGVDNDANVAALG 116 Query: 118 EATFGAGRGSKSSVTITLGTGVGSGFILDGKIYSGAHHFAPEIGHMVIGDNGIRCNCGKI 177 E FGAG+G S IT+ TGVG G+IL+G+ + GA A EIGH+V+ +G C CGK Sbjct: 117 EHRFGAGQGYDSLFYITVSTGVGGGWILNGQPWRGAGGMAGEIGHIVVDPSGPVCLCGKR 176 Query: 178 GCFETYASATALIREGKKAAKRNP--------NTLILKFANGDIEGITAKNVIDAAKQYD 229 GC E AS + + ++ + P ++ A D+ +T + V +AA D Sbjct: 177 GCVERLASGPYMAQNVREILENEPQRRGGFRDGEILRGLAGDDLTLLTGQLVSEAAAAGD 236 Query: 230 EEALKIFEEYVKYLAVGIVNIINLFDPEVIILGGGVANAGDFLLKPLKKEVAENILFKEL 289 + A ++ + L VGI N+ NL +P+ +LGGGV AG+ + + ++VA E+ Sbjct: 237 DLAKEVLHKAAWALGVGIGNVANLMNPQRFVLGGGVTKAGEDFWR-VVRQVARETALPEV 295 Query: 290 PYADIRKAELGNDAGIIGAAILS 312 + +I A LG+DA + G ++ Sbjct: 296 DF-EIVPAVLGDDAPLWGGVAIA 317 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: 335 Number of extensions: 22 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: 319 Length adjustment: 27 Effective length of query: 285 Effective length of database: 292 Effective search space: 83220 Effective search space used: 83220 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 Apr 09 2024. 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