Align 2-ketogluconokinase (EC 2.7.1.13) (characterized)
to candidate WP_022529424.1 L248_RS06890 sugar kinase
Query= metacyc::MONOMER-12748 (320 letters) >NCBI__GCF_000469325.1:WP_022529424.1 Length = 339 Score = 56.2 bits (134), Expect = 1e-12 Identities = 51/178 (28%), Positives = 80/178 (44%), Gaps = 8/178 (4%) Query: 6 ILSFGETMAMFVAEHGGDLAQVQHFHKRIAGADSNVAIGLARLGFKVAWLSRVGNDSLGR 65 +L+ GE M + Q F G+++NVA+ LA LG A+L+++ +++LG Sbjct: 4 VLTMGEMMLRLKPPEYQRILQADSFAANYGGSEANVAVSLALLGDNAAYLTKLPDNALGD 63 Query: 66 FVLDTLRAEGLDCRFVRCDPIHPTGFQLKSREDGGDDPRVEYFRRGSAASHLAISDLD-P 124 L T+R G+D R +R G + V Y R GS+ + + D P Sbjct: 64 TALATVRKYGVDTRLIRRGGPR-LGIYFFEKGTSVRGTNVVYDRAGSSFALARADEFDWP 122 Query: 125 ALLR-ARHLHATGIPPALSDSARELSGHLMHTQRSAGHSVSF--DPNLRPALW-PSEA 178 LL + + +GI ALS R + L Q H ++ D N R +W P+EA Sbjct: 123 TLLAGVTYFYFSGITAALSAELR--TALLAACQYCQAHDITVVCDVNYRGKMWSPAEA 178 Lambda K H 0.321 0.138 0.414 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: 230 Number of extensions: 9 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 320 Length of database: 339 Length adjustment: 28 Effective length of query: 292 Effective length of database: 311 Effective search space: 90812 Effective search space used: 90812 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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