Align Glucokinase; ATP-dependent glucokinase; ATP-GLK; Glucose kinase; EC 2.7.1.2 (characterized)
to candidate Echvi_3892 Echvi_3892 Transcriptional regulator/sugar kinase
Query= SwissProt::Q9X1I0 (317 letters) >FitnessBrowser__Cola:Echvi_3892 Length = 412 Score = 133 bits (335), Expect = 6e-36 Identities = 85/282 (30%), Positives = 141/282 (50%), Gaps = 7/282 (2%) Query: 38 ENGKEDVIRRIAETILEVSD--GEEAPYVGIGSPGSIDRENGIVRFSPNFPDWHNVPLTD 95 E D I ET ++ S E+ +G+ PG +D NG+ + + + L + Sbjct: 128 EKSTFDKIGDFMETYMQESGIPNEKIIAIGMSMPGLVDSVNGV---NHTYLKFGKKSLVE 184 Query: 96 ELAKRTGKKVFLENDANAFVLGEKWFGAGRGHDHIVALTLGTGIGGGVVTHGYLLTGRDG 155 R +KVF+ENDA A L E F + +++++ + +G GIG G++ G L G G Sbjct: 185 NFEARFDRKVFIENDARAMTLAEFKFSQDQKYNNVLGIFVGWGIGLGIIIDGKLYRGGAG 244 Query: 156 IGAELGHV-VVEPNGPMCNCGTRGCLEAVASATAIRRFLREGYKKYHSSLVYKLAGSP-E 213 E H + E C CG +GCLEAVAS TA+ R E +K S++ ++A E Sbjct: 245 FAGEFSHSPIFESREISCTCGKKGCLEAVASGTAMVRMAEEAIEKDSDSILSRMARERGE 304 Query: 214 KADAKHLFDAARQGDRFALMIRDRVVDALARAVAGYIHIFNPEIVIIGGGISRAGEILFG 273 D + DAA GD+ A+ I V L R ++ I + NP+++I+GG ++ A + L Sbjct: 305 GIDPSLIVDAALAGDQRAITILSDVGLDLGRGISILIQLLNPDLIIVGGSVAEAQQYLIT 364 Query: 274 PLREKVVDYIMPSFVGTYEVVASPLVEDAGILGAASIIKERI 315 P+++ + + M E+ L ++ G+LG +++ E I Sbjct: 365 PIQQALNIFSMAKSREKSELTLYKLGKEVGLLGGVAVVIENI 406 Lambda K H 0.320 0.142 0.418 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: 278 Number of extensions: 17 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: 317 Length of database: 412 Length adjustment: 29 Effective length of query: 288 Effective length of database: 383 Effective search space: 110304 Effective search space used: 110304 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 (21.7 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