Align glucokinase (EC 2.7.1.2) (characterized)
to candidate WP_012101992.1 CKL_RS07855 ROK family protein
Query= BRENDA::Q8RDE9 (315 letters) >NCBI__GCF_000016505.1:WP_012101992.1 Length = 317 Score = 266 bits (679), Expect = 6e-76 Identities = 135/312 (43%), Positives = 203/312 (65%), Gaps = 4/312 (1%) Query: 2 KKFLCGVDLGGTKISTGIVDENGNIIKSIKIPTMAEKGPDVVIERIEESIYQVLKDTGLE 61 +K++ GVDLGGTKI+ +VD G II +PT AE+G +++ I + I +V+ G+ Sbjct: 3 EKYVIGVDLGGTKIAAALVDFKGTIICKYTLPTKAEEGEKYILDNIIKIIEKVVNFGGVC 62 Query: 62 MSNLKGIGIGSPGPLNAKKGIVISPPNLPHWSNVPIVEILSKRLGIEVRLENDANAAAIG 121 +K IG+G+PGPL+ KG +I PNLP + N IV L + + L+ND NAAAI Sbjct: 63 SKKIKCIGLGAPGPLDIDKGKIICTPNLP-FKNFNIVSPLKNHFKMPIFLDNDGNAAAIA 121 Query: 122 EHLFGSGRGVDNFVYITVSTGIGGGVIIEGKLYSGENSNAAEIGHHTINFDGPRCNCGNY 181 EH+FG+G+G++N V+ITVSTGIGGG I+ G++Y G NA EIGH T++ GP CNCGN+ Sbjct: 122 EHMFGAGKGINNMVFITVSTGIGGGAILNGQIYRGNTKNALEIGHMTLDAQGPLCNCGNF 181 Query: 182 GCFEAYASGTAIARFAREGIEKGIKTKIKELAGEGEVKAEHVFEAAKLGDEFAKELVEKE 241 GC E ASGTAIAR A++ ++ G T LA + ++ VF+ A+LGD ++ +++ Sbjct: 182 GCAEVMASGTAIAREAKKAVKMGYNT---TLALYKNITSKEVFKEAQLGDSISQNILDTT 238 Query: 242 AFYLGVGIANIMAFYNPRKIAIGGGVSAQWDMLYEKMMETVRKKALKPNAEVCEVVKAQL 301 YLG+ +ANI+ +P + IGGGVS ++++K+ E V+++ ++ ++ A L Sbjct: 239 LNYLGICVANIITCLDPEAVIIGGGVSKGGKIIFDKINEVVKRRCFGTVSKNTRILPALL 298 Query: 302 GENIGVLGAAAL 313 G + GV+GAAAL Sbjct: 299 GTDAGVIGAAAL 310 Lambda K H 0.316 0.138 0.398 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: 302 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: 315 Length of database: 317 Length adjustment: 27 Effective length of query: 288 Effective length of database: 290 Effective search space: 83520 Effective search space used: 83520 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 (21.6 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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