Align 2-dehydro-3-deoxygluconokinase (EC 2.7.1.45) (characterized)
to candidate WP_010530530.1 ON01_RS08100 sugar kinase
Query= BRENDA::Q9WXS2 (339 letters) >NCBI__GCF_000224785.1:WP_010530530.1 Length = 333 Score = 209 bits (532), Expect = 8e-59 Identities = 114/325 (35%), Positives = 177/325 (54%), Gaps = 6/325 (1%) Query: 2 KVVTFGEIMLRLSPPDHKRIFQTDSFDVTYGGAEANVAAFLAQMGLDAYFVTKLPNNPLG 61 K++T GE++LRL+P +H+R+ F YGGAEANVA L++ G D F++ P N +G Sbjct: 3 KILTMGELLLRLTPVNHQRLNIGGHFTANYGGAEANVAVSLSRFGHDVSFLSAFPPNDIG 62 Query: 62 DAAAGHLRKFGVKTDYIARGGNRIGIYFLEIGASQRPSKVVYDRAHSAISEAKREDFDWE 121 DAA HL+ GV T + R G R+GIYF E G S R KV+YDR S++ E + DW+ Sbjct: 63 DAALSHLQASGVDTSSVFRLGERLGIYFYEEGFSLRQGKVIYDRKASSVLELPDQYIDWD 122 Query: 122 KILDGARWFHFSGITPPLGKELPLILEDALKVANEKGVTVSCDLNYRARLWTKEEAQKVM 181 ++ D H +GITP L K + ++ A ++ V VS D NYR++LW EEA++ Sbjct: 123 QVYDEVDLLHVTGITPALSKGMKEFTLAGIQEAKKRNVQVSFDFNYRSKLWGVEEAKETF 182 Query: 182 IPFMEYVDVLIANEEDIEKVLGISVEGLDLKTGKLNREAYAKIAEEVTRKYNFKTVGITL 241 + + +VD+ A +D +LG EG D + ++E + E Y K + T Sbjct: 183 LAILPHVDICFAGYKDFVYLLGF--EGPD----EFDKETLERFYREFAELYKIKYLASTR 236 Query: 242 RESISATVNYWSVMVFENGQPHFSNRYEIHIVDRVGAGDSFAGALIYGSLMGFDSQKKAE 301 R S + N + ++ + S+ I+DR+G GD+FA +++ + G ++ E Sbjct: 237 RTVFSTSKNELTGYIYFEDYLYESDHVSFEILDRIGGGDAFASGVLHTIISGLAPEEVIE 296 Query: 302 FAAAASCLKHTIPGDFVVLSIEEIE 326 F + LKH + GD+ S EE+E Sbjct: 297 FGIGSGVLKHMVYGDYNQFSEEEVE 321 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: 309 Number of extensions: 12 Number of successful extensions: 2 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: 333 Length adjustment: 28 Effective length of query: 311 Effective length of database: 305 Effective search space: 94855 Effective search space used: 94855 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