Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate CCNA_03269 CCNA_03269 glucokinase
Query= curated2:Q7P1R6 (348 letters) >FitnessBrowser__Caulo:CCNA_03269 Length = 325 Score = 184 bits (467), Expect = 3e-51 Identities = 118/295 (40%), Positives = 156/295 (52%), Gaps = 9/295 (3%) Query: 12 LLGDVGGSNARFALETAPGVIEDILTLSNERYPTLEDALRDYLAQVGARRVAHAAIGIAN 71 LL DV G + AL + L+ LE+ L D +++ A + AA+ A Sbjct: 7 LLADVNGRDLALALVSPGDAPRGHRDLACASLKALEEHLIDAVSEHSADGLIGAAVCGAG 66 Query: 72 PLNGDLVRMTNCHWSFSIEATRRALGLSTLLLLNDFTALALALPRLPRRELAQVGGGAPR 131 P + +T ++ + R L + LLNDF A AL PRL + + G P Sbjct: 67 PEIDGAIALTAGDFTLTQAWLRAVLKTPRVSLLNDFAACALGAPRLAPSAMRLIHEGKPG 126 Query: 132 PDAPLALIGPGTGLGVSALVPH-AGGWRALAGEGGHTSFAPANEREIGIWRYASARFGHV 190 +A +A+IGP GLGV+AL PH GW + EGGH F P RE+ ++ AR G V Sbjct: 127 RNAQIAVIGPNLGLGVAALTPHRTDGWTPVVSEGGHIDFTPGEPREVPVFEALQARHGRV 186 Query: 191 SHERLLSGSGLSLLHRALCA-LDGAEEAGLAPAEVSARGLSGADARCREALEIFCALLGS 249 S E LS GL+ ++ AL LD ++E LA D REAL IF ALLG+ Sbjct: 187 SAEHFLSQQGLADIYAALGGGLDDSDEVILARVR-------DGDETAREALSIFSALLGA 239 Query: 250 AAGNLALTLGARGGVYIGGGIVPRLSGFFEQSPFRRRFEDKGRMSAYLADIPVYL 304 AG+ AL+ ARGGVYI ++ R+ G +Q+ F RRFEDKGRMSAYL DIPVYL Sbjct: 240 FAGDAALSFAARGGVYINSPLMERIDGLLDQAAFSRRFEDKGRMSAYLKDIPVYL 294 Lambda K H 0.320 0.138 0.420 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: 288 Number of extensions: 14 Number of successful extensions: 3 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: 348 Length of database: 325 Length adjustment: 28 Effective length of query: 320 Effective length of database: 297 Effective search space: 95040 Effective search space used: 95040 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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