Align ADP-specific glucokinase (EC 2.7.1.147) (characterized)
to candidate WP_007679976.1 BN137_RS02630 fructokinase
Query= BRENDA::Q8R8N4 (312 letters) >NCBI__GCF_000319285.1:WP_007679976.1 Length = 303 Score = 127 bits (318), Expect = 4e-34 Identities = 98/320 (30%), Positives = 153/320 (47%), Gaps = 31/320 (9%) Query: 1 MRIGVDLGGTNIAVGLVEEDGKIIATGSRPTKPERGYEAIARDIAELSFELLQRMGISVK 60 MRIG+DLGGT V + +DG+ PT P Y IA L EL +R Sbjct: 1 MRIGIDLGGTKTEVIALSDDGEQRFRHRVPT-PRNDYPQTVETIAGL-VELAER---ETG 55 Query: 61 DVKSMGIGVPGVADNEKGIVIRAVNLFWTKVPLAKEIRKYIDLPIYMENDANVAALAEAT 120 + ++G+G+PG G+V A + + L K++ + + + NDAN A++EA Sbjct: 56 ERGTVGVGIPGTLSPYTGVVKNANSTWLNGQALDKDLSARLAREVRLANDANCFAVSEAV 115 Query: 121 FGAGRGSKSSVTITLGTGVGSGFILDGKIYSGAHHFAPEIGHMVI---GDNGIR------ 171 GA G+++ + +GTG GSG L G+ + GA+ A E GH + D+ +R Sbjct: 116 DGAAAGAQTVFAVIIGTGCGSGIALGGRSHIGANGNAGEWGHNPLPWMDDDELRYREEVP 175 Query: 172 CNCGKIGCFETYASATALIREGKKAAKRNPNTLILKFANGDIEGITAKNVIDAAKQYDEE 231 C CGK GC ETY S T + + + + + +I + D Sbjct: 176 CYCGKQGCIETYISGTGFATDYHRLSG---------------QPLKGSEIIRLVDEQDAL 220 Query: 232 ALKIFEEYVKYLAVGIVNIINLFDPEVIILGGGVANAGDFLLKPLKKEVAENILFKELPY 291 A Y LA + +I+N+ DP+VI+LGGG++N D L K + + ++ +F Sbjct: 221 AELALSRYELRLAKSLAHIVNVLDPDVIVLGGGMSNV-DRLYKTV-PPLMKHWVFGGECE 278 Query: 292 ADIRKAELGNDAGIIGAAIL 311 +RKA G+ +G+ GAA L Sbjct: 279 TPVRKAVHGDSSGVRGAAWL 298 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: 268 Number of extensions: 16 Number of successful extensions: 5 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: 303 Length adjustment: 27 Effective length of query: 285 Effective length of database: 276 Effective search space: 78660 Effective search space used: 78660 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