Align glucokinase; EC 2.7.1.2 (characterized)
to candidate CA265_RS15640 CA265_RS15640 sugar kinase
Query= CharProtDB::CH_014478 (324 letters) >FitnessBrowser__Pedo557:CA265_RS15640 Length = 395 Score = 148 bits (374), Expect = 2e-40 Identities = 88/262 (33%), Positives = 142/262 (54%), Gaps = 5/262 (1%) Query: 65 KSRLVGIGIGAPGPVNFANGSIEVAVNLGWEKFPIKDILEVETSLPVVVDNDANIAAIGE 124 K L+GIGIG PG VN G + + ++D L + LPV +DND+++ A+ E Sbjct: 137 KENLLGIGIGMPGFVNAEKGMNYSFMQVE-NDISLQDYLAKKLRLPVYIDNDSSLIALAE 195 Query: 125 MWKGAGDGAKDLLCVTLGTGVGGGVIANGEIVQGVNGAAGEIGHITSIPEGGAPCNCGKT 184 + G KD+L V +G G G G+I NG++ +G +G AGE HI + C+CGK Sbjct: 196 LNFGEARNLKDVLVVNIGWGTGLGMIINGKLYRGSSGYAGEFSHIP-LSNSNTLCSCGKR 254 Query: 185 GCLETIASATGIVRLTMEELTETDKPSELRTVLEQNGQVTSKDVFDAARSKDGLAMHVVD 244 GCLE S +V+ EE + + + L+T+ + +A +D +A+ ++ Sbjct: 255 GCLEVETSLLVMVQKA-EEAVKNGEETSLKTLFNDKSKSHVDHFLNAVVKQDPVAISILA 313 Query: 245 KVAFHLGLALANSANALNPEKIVLGGGVSRAGEVLLAPVRDYFKRFAFPRVAQGAELAIA 304 AF +G LA + +NPE+IVL G ++AG++LL P++ F PRVA+ E+ + Sbjct: 314 DAAFQIGKGLATLIHIMNPERIVLSGRGAKAGKMLLPPIQQAINEFCIPRVAEQTEIKCS 373 Query: 305 TLGNDAGIIGGAWLV--KSYFE 324 +L ++A ++ A L+ S FE Sbjct: 374 SLSDEAELLAAASLMVENSLFE 395 Lambda K H 0.316 0.137 0.404 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: 255 Number of extensions: 14 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: 324 Length of database: 395 Length adjustment: 29 Effective length of query: 295 Effective length of database: 366 Effective search space: 107970 Effective search space used: 107970 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 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