Align glucokinase subunit (EC 2.7.1.1) (characterized)
to candidate WP_027699343.1 TT13_RS07125 ROK family protein
Query= metacyc::MONOMER-6081 (323 letters) >NCBI__GCF_000691805.2:WP_027699343.1 Length = 405 Score = 68.2 bits (165), Expect = 3e-16 Identities = 55/177 (31%), Positives = 86/177 (48%), Gaps = 11/177 (6%) Query: 5 LLGIDLGGTSIKFGILTLDGQVQEKWAIETNILEDGKHIVPDIVSSIKHR-LELYNL-TK 62 L+ D+G +++ L G++ I+ D + D+ ++ R L L +L T Sbjct: 85 LMTFDIGRNHLRYLAARLTGEILSHDQIDV----DAEMSYEDLKRTMLERVLRLGDLGTI 140 Query: 63 EDFVGIGMGSPGAVDRNLKTVTGAFNLNWAATQEVGTIIEAELGIPFAIDNDANVAALGE 122 VGI +G G V+ N T FN + ++ +E L +P ++N+AN+AA Sbjct: 141 NGLVGISIGIHGVVNDNRVAYT-PFN-RFLLEHDLAHELEVALDVPVFLENEANLAAYYL 198 Query: 123 RWVGAGNNNP---DVVFVTLGTGVGGGIIADGNLIHGVAGAGGEIGHIIVEPDTGFE 176 R N P D V + GVG GII +G L+ G+ GA GEIG +IV D G++ Sbjct: 199 RDFHENNFEPMREDFAVVNVHNGVGAGIIQNGQLVRGIKGAAGEIGRMIVFDDHGWQ 255 Lambda K H 0.316 0.137 0.394 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: 257 Number of extensions: 14 Number of successful extensions: 1 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: 323 Length of database: 405 Length adjustment: 29 Effective length of query: 294 Effective length of database: 376 Effective search space: 110544 Effective search space used: 110544 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