Align ADP-specific glucokinase (EC 2.7.1.147) (characterized)
to candidate WP_054655034.1 CES79_RS06025 ROK family glucokinase
Query= BRENDA::Q8R8N4 (312 letters) >NCBI__GCF_002217945.1:WP_054655034.1 Length = 324 Score = 196 bits (499), Expect = 5e-55 Identities = 118/311 (37%), Positives = 165/311 (53%), Gaps = 1/311 (0%) Query: 3 IGVDLGGTNIAVGLVEEDGKIIATGSRPTKPERGYEAIARDIAELSFELLQRMGISVKDV 62 IG+DLGGT + V +DG I+ S PT + I +I + + G + Sbjct: 6 IGIDLGGTTTKIAFVSQDGDILQKWSIPTDISENGKHIVPNIITSLKKTMTDAGYTKDQF 65 Query: 63 KSMGIGVPGVADNEKGIVIRAVNLFW-TKVPLAKEIRKYIDLPIYMENDANVAALAEATF 121 +G+G PG D E G VI A NL W T + +I+ + L + +ENDANVAAL E Sbjct: 66 MGIGMGTPGAVDIENGTVIGAFNLNWKTTQHVRDQIQAGVGLQLVLENDANVAALGEFWK 125 Query: 122 GAGRGSKSSVTITLGTGVGSGFILDGKIYSGAHHFAPEIGHMVIGDNGIRCNCGKIGCFE 181 GAG + + +TLGTGVG G I G++ G + A EIGH+ + NG C CGK GC E Sbjct: 126 GAGEKDQDVIFVTLGTGVGGGVIAGGQLLHGINGGAGEIGHITVQPNGYLCTCGKRGCLE 185 Query: 182 TYASATALIREGKKAAKRNPNTLILKFANGDIEGITAKNVIDAAKQYDEEALKIFEEYVK 241 Y+SAT ++ K A LK + E +T+K V+ A D A +I ++ Sbjct: 186 QYSSATGIVHVAKDMAAEFTGKSRLKELFDNHEEVTSKMVVYLADNGDILANRIVDKVSS 245 Query: 242 YLAVGIVNIINLFDPEVIILGGGVANAGDFLLKPLKKEVAENILFKELPYADIRKAELGN 301 YL + + N N+ +P II+GGGV+ AG+ LL+P + EN I+ A+LGN Sbjct: 246 YLGLALANCANILNPANIIIGGGVSAAGNTLLQPTTRYFQENTFPAVRDSTRIKLAQLGN 305 Query: 302 DAGIIGAAILS 312 DAG IGAA L+ Sbjct: 306 DAGAIGAASLA 316 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: 341 Number of extensions: 21 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: 324 Length adjustment: 27 Effective length of query: 285 Effective length of database: 297 Effective search space: 84645 Effective search space used: 84645 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