Align ADP-specific glucokinase (EC 2.7.1.147) (characterized)
to candidate CCNA_02549 CCNA_02549 glucokinase
Query= BRENDA::Q8R8N4 (312 letters) >FitnessBrowser__Caulo:CCNA_02549 Length = 296 Score = 130 bits (328), Expect = 3e-35 Identities = 96/318 (30%), Positives = 149/318 (46%), Gaps = 35/318 (11%) Query: 1 MRIGVDLGGTNIAVGLVEEDGKIIATGSRPTKPERG-YEAIARDIAELSFELLQRMGISV 59 +R GVD GGT I V + G +A R KP G Y+ +A L + G S Sbjct: 2 IRFGVDFGGTKIEVAALNAAGDFVA---RVRKPNPGNYDEALEVVAALVADAESMAGGSC 58 Query: 60 KDVKSMGIGVPGVADNEKGIVIRAVNLFWTKVPLAKEIRKYIDLPIYMENDANVAALAEA 119 +G+G+PG G++ A + + P + + + P+ + NDAN AL+EA Sbjct: 59 A---RLGLGIPGSISPRTGLIRNANSTYLNGRPFGENLETRLARPVRIANDANCLALSEA 115 Query: 120 TFGAGRGSKSSVTITLGTGVGSGFILDGKIYSGAHHFAPEIGHMVI------GDNGIRCN 173 GAG G+ +GTG G G ++DGKI +G + E GH + G C Sbjct: 116 ADGAGAGASVVFAAIVGTGCGGGVVVDGKIINGHNGIGGEWGHAPLPWPKPEEYPGPDCW 175 Query: 174 CGKIGCFETYASATALIREGKKAAKRNPNTLILKFANGDIEGITAKNVIDAAKQYDEEAL 233 CG+ GC ET+ + A R+ FANG + + A + D +A Sbjct: 176 CGRKGCLETWIAGPAFARDA-------------GFANG-------QAAMQAIGEGDVKAS 215 Query: 234 KIFEEYVKYLAVGIVNIINLFDPEVIILGGGVANAGDFLLKPLKKEVAENILFKELPYAD 293 + YV LA + + +L DP++I+LGGG++N D L + L +A ++ F ++ Sbjct: 216 AALDRYVDRLARSLAVVCDLIDPDIIVLGGGMSNV-DALYERLPAAIAPHV-FSDIFETP 273 Query: 294 IRKAELGNDAGIIGAAIL 311 +RKA G+ +G+ GA L Sbjct: 274 VRKAVHGDSSGVRGAVWL 291 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: 286 Number of extensions: 18 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: 296 Length adjustment: 27 Effective length of query: 285 Effective length of database: 269 Effective search space: 76665 Effective search space used: 76665 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 17 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