Align 2-dehydro-3-deoxygluconokinase (EC 2.7.1.45) (characterized)
to candidate WP_049771195.1 SWIT_RS08585 sugar kinase
Query= BRENDA::Q9WXS2 (339 letters) >NCBI__GCF_000016765.1:WP_049771195.1 Length = 345 Score = 195 bits (496), Expect = 1e-54 Identities = 119/326 (36%), Positives = 167/326 (51%), Gaps = 7/326 (2%) Query: 2 KVVTFGEIMLRLSPPDHKRIFQTDSFDVTYGGAEANVAAFLAQMGLDAYFVTKLPNNPLG 61 + V FGE++LRLS PD + Q D +GGAEANVAA LA +G A VT LP N LG Sbjct: 15 RCVVFGELLLRLSAPDRGLLLQRPGLDSCFGGAEANVAAGLASLGRPAAIVTALPRNRLG 74 Query: 62 DAAAGHLRKFGVKTDYIARGGNRIGIYFLEIGASQRPSKVVYDRAHSAISEAKREDFDWE 121 DAA +R G+ + R R+G+YFL+ GA RP +V+YDR S+ + A + FDW Sbjct: 75 DAALAAVRGMGIDCSGVLRTAGRMGLYFLDSGAGFRPGQVIYDRNDSSFARADADRFDWP 134 Query: 122 KILDGARWFHFSGITPPLGKELPLILEDALKVANEKGVTVSCDLNYRARLW-TKEEAQKV 180 +L GA H SGITP LG A A E G+ VS D+N+R LW + EEA + Sbjct: 135 TLLRGAGRLHLSGITPALGAGPAAAARRAAATAGELGIPVSFDVNFRPSLWRSPEEAPPL 194 Query: 181 MIPFMEYVDVLIANEEDIEKVLGISVEGLDLKTGKLNREAYAKIAEEVTRKYNFKTVGIT 240 + DVL AN DI + + G +L A+A + + + + Sbjct: 195 LRALANEADVLFANAHDIALLTDEAFAGHPEDEQRLVARAFALFPKLKVIASSRRAMSAA 254 Query: 241 LRESISATVNYWSVMVFENGQPHFSNRYEIHIVDRVGAGDSFAGALIYGSLMGFDSQKKA 300 R S+S VN +G + ++VDR+G GD+ A ++ G D + A Sbjct: 255 DRLSVSVKVN------GRDGMATSPEKTLSNVVDRIGTGDALAAGVLAGLGPSHDIARAA 308 Query: 301 EFAAAASCLKHTIPGDFVVLSIEEIE 326 E+ A CLKH+IPGD + + ++E Sbjct: 309 EWGLALFCLKHSIPGDASLADMSDLE 334 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: 262 Number of extensions: 14 Number of successful extensions: 3 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: 345 Length adjustment: 29 Effective length of query: 310 Effective length of database: 316 Effective search space: 97960 Effective search space used: 97960 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 Apr 09 2024. 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