Align glucokinase (EC 2.7.1.2) (characterized)
to candidate WP_003464513.1 J416_RS03055 ROK family transcriptional regulator
Query= BRENDA::Q8RDE9 (315 letters) >NCBI__GCF_000359605.1:WP_003464513.1 Length = 392 Score = 155 bits (393), Expect = 1e-42 Identities = 98/312 (31%), Positives = 156/312 (50%), Gaps = 16/312 (5%) Query: 4 FLCGVDLGGTKISTGIVDENGNIIKSIKIPTMAEKGPDVVIERIEESIYQVLKDTGLEMS 63 F +DLG I + D GNI + +I + D + +++ I ++ + Sbjct: 82 FTISIDLGVKHILGVLTDLRGNI-HAEEIIAIDNTAFDFISQQLMNCIDRLKQQAPTSEY 140 Query: 64 NLKGIGIGSPGPLNAKKGIVISPPNLPHWSNVPIVEILSKRLGIEVRLENDANAAAIGEH 123 + GIG+G PG + G ++ PNL W V + + L + + +EN+ANA A GE Sbjct: 141 GIVGIGVGVPGVVTTD-GHILLAPNLG-WKRVSLQQKLYDHYQVPILIENEANAGAYGEK 198 Query: 124 LFGSGRGVDNFVYITVSTGIGGGVIIEGKLYSGENSNAAEIGHHTINFDGPRCNCGNYGC 183 +FG G+ + VYI+ S GIG G++++G+LY G + E+GH TI DG C CGN GC Sbjct: 199 VFGIGQATNQLVYISASIGIGVGLLLDGQLYKGLRGFSGELGHMTIEKDGAACRCGNNGC 258 Query: 184 FEAYASGTAIARFAREGIEKGIKTKIKELAGEGEVKAEHVFEAAKLGDEFAKELVEKEAF 243 +E YAS A+ +EK E A G V + E A G++ A L ++ Sbjct: 259 WELYASEKAL-------LEKA------EQASLGTVTLTDLVEKANQGEDIAIRLFKELGD 305 Query: 244 YLGVGIANIMAFYNPRKIAIGGGVSAQWDMLYEKMMETVRKKALKPNAEVCEVVKAQLGE 303 YLGVG+ N + +NP ++ +G + D + M + + K + N ++ AQLG+ Sbjct: 306 YLGVGVTNTIHIFNPEQVVLGNSLIQAADFILPAMKKRIEKNTIGFNKNDVKLNVAQLGQ 365 Query: 304 NIGVLGAAALLL 315 +LG AA + Sbjct: 366 YSTLLGIAAFTI 377 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: 315 Number of extensions: 16 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: 392 Length adjustment: 29 Effective length of query: 286 Effective length of database: 363 Effective search space: 103818 Effective search space used: 103818 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: 49 (23.5 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