Align glucokinase (EC 2.7.1.2) (characterized)
to candidate WP_009763228.1 MICLODRAFT_RS17985 ROK family transcriptional regulator
Query= BRENDA::Q8RDE9 (315 letters) >NCBI__GCF_000262405.1:WP_009763228.1 Length = 417 Score = 140 bits (353), Expect = 5e-38 Identities = 98/311 (31%), Positives = 145/311 (46%), Gaps = 17/311 (5%) Query: 7 GVDLGGTKISTGIVDENGNIIKSIKIPTMAEKGPDVVIERIEESIYQVLKDTGLEMSNLK 66 G+++ IST +VD G + IP + + P+ V+ I+ I + L Sbjct: 95 GIEIAADHISTLLVDIGGRVRAQRSIP-LPQNDPETVLPVIKAEIEAAQAQLEPPVPQLL 153 Query: 67 GIGIGSPGPLNAKKGIVISPPNLPHWSNVPIVEILSKRLGIEVRLENDANAAAIGEHLFG 126 G+G+ PGP N + + P L W + V + LG V LENDA AAA+GE L G Sbjct: 154 GVGVVMPGPFNVEGMTSVGPTTLSGWFDFDAVARIGDMLGAPVTLENDATAAAVGERLHG 213 Query: 127 SGRGVDNFVYITVSTGIGGGVIIEGKLYSGENSNAAEIGHHTINFDGPRCNCGNYGCFEA 186 R + NF I G+G G++I+G+ Y G N NA EIGH + G C+CG +GC EA Sbjct: 214 VARNLKNFCLIYFGQGLGLGIMIDGRPYRGANGNAGEIGHVRVAKGGRLCSCGQHGCLEA 273 Query: 187 YASGTAIA-RFAREGIEKGIKTKIKELAGEGEVKAEHVFEAAKLGDEFAKELVEKEAFYL 245 YAS ++A + A GI +++ L E +H A +E+ A YL Sbjct: 274 YASFHSLAQKLAAAGIHGIDYAELERLHRE-----KHPVVLA---------WIEEAAGYL 319 Query: 246 GVGIANIMAFYNPRKIAIGGGV-SAQWDMLYEKMMETVRKKALKPNAEVCEVVKAQLGEN 304 +A + ++P I +GG + + L E M A + N ++ + G Sbjct: 320 APQVAMLENLFDPEAIVLGGVLPPGLLEDLVEAMQPLPLSVARRRNRSEARLIHGRTGGL 379 Query: 305 IGVLGAAALLL 315 LGAAAL L Sbjct: 380 TAALGAAALPL 390 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: 311 Number of extensions: 17 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: 417 Length adjustment: 29 Effective length of query: 286 Effective length of database: 388 Effective search space: 110968 Effective search space used: 110968 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