Align 2-dehydro-3-deoxygluconokinase (EC 2.7.1.45) (characterized)
to candidate WP_019388253.1 P735_RS0111840 sugar kinase
Query= BRENDA::Q9WXS2 (339 letters) >NCBI__GCF_000283015.1:WP_019388253.1 Length = 348 Score = 305 bits (781), Expect = 1e-87 Identities = 168/346 (48%), Positives = 222/346 (64%), Gaps = 8/346 (2%) Query: 2 KVVTFGEIMLRLSPPDHKRIFQTDSFDVTYGGAEANVAAFLAQMGLDAYFVTKLPNNPLG 61 KVVTFGEIMLRL+P R Q +SFD YGG E+NVA LA G+D FVT+LP N +G Sbjct: 3 KVVTFGEIMLRLAPQGFLRFSQANSFDAIYGGGESNVAVSLANYGVDVDFVTRLPKNDIG 62 Query: 62 DAAAGHLRKFGVKTDYIARGGNRIGIYFLEIGASQRPSKVVYDRAHSAISEAKREDFDWE 121 + A +RK GV D I GG+R+GIYFLE GA R SKVVYDRAHSAI+E K DW+ Sbjct: 63 ECAMMEMRKRGVGVDKIVWGGDRLGIYFLETGAVSRGSKVVYDRAHSAIAEIKSGMIDWD 122 Query: 122 KILDGARWFHFSGITPPLGKELPLILEDALKVANEKGVTVSCDLNYRARLWTKEEA---Q 178 + +G WFH++GITP + + + +A+K A+ KG+T+S DLNYRA+LW +A + Sbjct: 123 AVFEGCEWFHWTGITPAISQGSADVCLEAVKAASAKGITISTDLNYRAKLWKYCDAAHRE 182 Query: 179 KVMIPFMEYVDVLIANEEDIEKVLGISVEGLDLKT--GKLNREAYAKIAEEVTRKY-NFK 235 KVM Y D+++ NEED E GI EG+ ++T + EA+ + E++ K+ K Sbjct: 183 KVMTELTSYCDIVLGNEEDAEMHFGIKPEGITVQTQGHDVKAEAFLSVCEQMMEKFPRAK 242 Query: 236 TVGITLRESISATVNYWSVMVFENGQPHFSNRYEI-HIVDRVGAGDSFAGALIYGSL-MG 293 V TLR SISA+ N W+ ++++ + +Y+I IVDRVG GDSF G LIYG L Sbjct: 243 KVITTLRGSISASHNTWAGVLYDGKTLFQTRQYQITDIVDRVGGGDSFMGGLIYGLLKYP 302 Query: 294 FDSQKKAEFAAAASCLKHTIPGDFVVLSIEEIEKLASGATSGRVER 339 D Q +FA AASCLKHTI GD ++++ E+EKL G SGRV R Sbjct: 303 KDDQNALDFAVAASCLKHTIKGDANLVTVAEVEKLMGGDASGRVAR 348 Lambda K H 0.319 0.136 0.397 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: 352 Number of extensions: 11 Number of successful extensions: 5 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: 339 Length of database: 348 Length adjustment: 29 Effective length of query: 310 Effective length of database: 319 Effective search space: 98890 Effective search space used: 98890 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 (21.8 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