Align ADP-specific glucokinase (EC 2.7.1.147) (characterized)
to candidate WP_017548855.1 C792_RS0107525 ROK family glucokinase
Query= BRENDA::Q8R8N4 (312 letters) >NCBI__GCF_000330705.1:WP_017548855.1 Length = 319 Score = 172 bits (437), Expect = 7e-48 Identities = 112/312 (35%), Positives = 162/312 (51%), Gaps = 6/312 (1%) Query: 3 IGVDLGGTNIAVGLVEEDGKIIATGSRPTKPERGYEAIARDIAELSFELLQRMGISVKDV 62 + D+GGT+ +G+ +E+ +I PT I D+ + + +G V++ Sbjct: 5 LAADIGGTSCKLGVFDEELNLIEKWEIPTDISEEGSHILADVLDSFRSKEEILGFKVEEC 64 Query: 63 KSMGIGVPGVADNEKGIVIRAVNL-FWTKVPLAKEIRKYIDLPIYMENDANVAALAEATF 121 G+G+PG D EKGI+ +NL K +A + ++NDANVAAL E + Sbjct: 65 LGTGLGMPGPVDFEKGILNGCINLNIKGKRSIATIFSELSGSAAIVDNDANVAALGEQSK 124 Query: 122 GAGRGSKSSVTITLGTGVGSGFILDGKIYSGAHHFAPEIGHMVIGDNG-IRCNCGKIGCF 180 GAG G V ITLGTGVG G I +G++ G EIGH+ + +G +CNCGK GC Sbjct: 125 GAGHGHSEVVMITLGTGVGGGVISEGRLIHGTGGSGGEIGHITVDFDGRFQCNCGKKGCL 184 Query: 181 ETYASATALIR-EGKKAAKRNPNTLILKFANGDIEGITAKNVIDAAKQYDEEALKIFEEY 239 ET ASAT ++ G + + LI G + T+K ++DAA D A + EE Sbjct: 185 ETVASATGMVNLAGYHSDDHENSVLIAAIKEGTL---TSKAIVDAAMTGDPLAEFVVEEA 241 Query: 240 VKYLAVGIVNIINLFDPEVIILGGGVANAGDFLLKPLKKEVAENILFKELPYADIRKAEL 299 +YLAV + +I + +P + GGGV+ AG +L +KK I +I AEL Sbjct: 242 ARYLAVAMSSISVITNPGYFVFGGGVSRAGRYLTDKIKKYYDSLIFPPAADDVEIVMAEL 301 Query: 300 GNDAGIIGAAIL 311 GNDAG+ GAA L Sbjct: 302 GNDAGMYGAARL 313 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: 315 Number of extensions: 20 Number of successful extensions: 4 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 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