Align glucokinase (EC 2.7.1.2) (characterized)
to candidate WP_012501493.1 CPAR_RS01220 sugar kinase
Query= BRENDA::Q8RDE9 (315 letters) >NCBI__GCF_000020505.1:WP_012501493.1 Length = 336 Score = 214 bits (546), Expect = 2e-60 Identities = 124/325 (38%), Positives = 184/325 (56%), Gaps = 13/325 (4%) Query: 1 MKKFLCGVDLGGTKISTGIVDENGNIIKSIKIPTMAEKGPDVVIERIE---ESIYQVLKD 57 M + G+DLGGT I T ++DE G I+ PT + GPD VI ++ +YQ + Sbjct: 1 MPSWAIGIDLGGTNIKTAVIDEAGGILFEDAQPTDSAAGPDGVIRQLALLASDLYQQAAE 60 Query: 58 TGLEMSNLKGIGIGSPGPLNAKKGIVISPPNLPHWSNVPIVEILSKRL----GIE--VRL 111 + L+ + GIG+G+PG ++A KG + PPNLP W P+ + L RL GI + + Sbjct: 61 S-LDTGDFAGIGVGAPGAVDAVKGTLSYPPNLPGWGCYPLRDQLQLRLEQAHGISAPILV 119 Query: 112 ENDANAAAIGEHLFGSGRGVDNFVYITVSTGIGGGVIIEGKLYSGENSNAAEIGHHTINF 171 ENDANAAA GE ++G G +F+ +T+ TG+GGG+I++ KLY G A EIG TI+F Sbjct: 120 ENDANAAAYGEAVYGGGSAFRDFMLVTLGTGVGGGIILDRKLYRGPTGTAGEIGFMTIDF 179 Query: 172 DGPRCNCGNYGCFEAYASGTAIARFA-REGIEKGIKTKIKELAGE--GEVKAEHVFEAAK 228 +G + G G E+ I A REG G+ ++ EL + H+ EAAK Sbjct: 180 EGSSVHAGVRGTIESLIGKERIVELACREGASSGLSPRLLELCDRDVAGLSPRHLEEAAK 239 Query: 229 LGDEFAKELVEKEAFYLGVGIANIMAFYNPRKIAIGGGVSAQWDMLYEKMMETVRKKALK 288 GD+FA + ++ LGVG+AN+ A + RK IGGG+SA ++++E + + + L Sbjct: 240 EGDQFALRVWQRIGTILGVGLANVTALMDIRKFVIGGGISAAGELIFEPALMQLHRSTLP 299 Query: 289 PNAEVCEVVKAQLGENIGVLGAAAL 313 + E+V A+LG G+ GAAAL Sbjct: 300 SMHDGLEIVPARLGNKAGMYGAAAL 324 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: 288 Number of extensions: 15 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: 315 Length of database: 336 Length adjustment: 28 Effective length of query: 287 Effective length of database: 308 Effective search space: 88396 Effective search space used: 88396 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