Align ADP-specific glucokinase (EC 2.7.1.147) (characterized)
to candidate CA265_RS23280 CA265_RS23280 sugar kinase
Query= BRENDA::Q8R8N4 (312 letters) >FitnessBrowser__Pedo557:CA265_RS23280 Length = 417 Score = 155 bits (393), Expect = 1e-42 Identities = 82/260 (31%), Positives = 141/260 (54%) Query: 50 ELLQRMGISVKDVKSMGIGVPGVADNEKGIVIRAVNLFWTKVPLAKEIRKYIDLPIYMEN 109 ++L+ GI + +G+PG+ D EKG +PL K +++P+ ++N Sbjct: 138 DILKSAGIQREQFIGCSVGMPGLIDAEKGENYSYFLSDGENIPLTAAFEKMLNMPVVIQN 197 Query: 110 DANVAALAEATFGAGRGSKSSVTITLGTGVGSGFILDGKIYSGAHHFAPEIGHMVIGDNG 169 D N +++AE T G +G K+ + + + GVG G I+DGK+ G F+ E+GHM +NG Sbjct: 198 DVNGSSMAEFTHGMAKGKKNVLVLLMDWGVGLGIIMDGKLRQGTCGFSGELGHMPFVENG 257 Query: 170 IRCNCGKIGCFETYASATALIREGKKAAKRNPNTLILKFANGDIEGITAKNVIDAAKQYD 229 C CGK GC ET AS AL K+ N+++ K +N ++E I +I AA + D Sbjct: 258 ALCYCGKHGCLETIASGNALSEMAKEGILSGKNSMLNKLSNEELERIEPALIIKAANKGD 317 Query: 230 EEALKIFEEYVKYLAVGIVNIINLFDPEVIILGGGVANAGDFLLKPLKKEVAENILFKEL 289 + A+++ ++ GI +I LF+PE+IIL G +A A ++ P+++ + + + Sbjct: 318 QYAIQLLSNVGTHMGKGIAVLIQLFNPELIILSGKIAGAKQYITLPMQQAINTYCMTQIR 377 Query: 290 PYADIRKAELGNDAGIIGAA 309 I +ELG ++ ++G A Sbjct: 378 EKTTIVSSELGENSRLLGYA 397 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: 321 Number of extensions: 19 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: 417 Length adjustment: 29 Effective length of query: 283 Effective length of database: 388 Effective search space: 109804 Effective search space used: 109804 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: 49 (23.5 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