Align ADP-specific glucokinase (EC 2.7.1.147) (characterized)
to candidate WP_085770628.1 B1812_RS05150 ROK family protein
Query= BRENDA::Q8R8N4 (312 letters) >NCBI__GCF_002117405.1:WP_085770628.1 Length = 304 Score = 141 bits (355), Expect = 2e-38 Identities = 103/318 (32%), Positives = 153/318 (48%), Gaps = 30/318 (9%) Query: 1 MRIGVDLGGTNIAVGLVEEDGKIIATGSRPTKPERGYEAIARDIAELSFELLQRMGISVK 60 +R+GVDLGGT ++ G ++ PT P Y AI I L + +G Sbjct: 6 LRVGVDLGGTKTEAIAIDPSGAMLLRRRVPT-PASDYAAILTTIVALVHAIEAELG---- 60 Query: 61 DVKSMGIGVPGVADNEKGIVIRAVNLFWTKVPLAKEIRKYIDLPIYMENDANVAALAEAT 120 V +G+GVPG G + + L + P AK++ + + +ENDAN AL+EAT Sbjct: 61 GVARVGVGVPGWISPRSGFIRNSNTLVLNQRPFAKDLEQALARETRIENDANCFALSEAT 120 Query: 121 FGAGRGSKSSVTITLGTGVGSGFILDGKIYSGAHHFAPEIGHMVIGD------NGIRCNC 174 GA +G + LGTGVG G L G + GA+ A E GH + G RC C Sbjct: 121 DGAAQGRDVVFGVILGTGVGGGLTLRGALLRGANAIAGEWGHNPLPRMSPDEFPGPRCYC 180 Query: 175 GKIGCFETYASATAL-IREGKKAAKRNPNTLILKFANGDIEGITAKNVIDAAKQYDEEAL 233 G++GC ET+ AL +R G+K+ E + A+ V A + AL Sbjct: 181 GRMGCIETFLCGGALALRYGEKSG----------------ESVGAEEVARRADHGEALAL 224 Query: 234 KIFEEYVKYLAVGIVNIINLFDPEVIILGGGVANAGDFLLKPLKKEVAENILFKELPYAD 293 + Y LA + +++N+ DP++I+LGGGV+N D L + L+K V + L Sbjct: 225 DALDSYRDRLARALASVVNIVDPDMIVLGGGVSNI-DRLYEGLEKLVGDYAFTDALATPI 283 Query: 294 IRKAELGNDAGIIGAAIL 311 +R G+ +G+ GAA L Sbjct: 284 VRNRH-GDSSGVRGAAWL 300 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: 251 Number of extensions: 11 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: 304 Length adjustment: 27 Effective length of query: 285 Effective length of database: 277 Effective search space: 78945 Effective search space used: 78945 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