Align 2-dehydro-3-deoxygluconokinase; 2-keto-3-deoxygluconokinase; 3-deoxy-2-oxo-D-gluconate kinase; KDG kinase; EC 2.7.1.45 (characterized)
to candidate 3607860 Dshi_1268 PfkB domain protein (RefSeq)
Query= SwissProt::Q53W83 (309 letters) >FitnessBrowser__Dino:3607860 Length = 333 Score = 107 bits (268), Expect = 3e-28 Identities = 85/286 (29%), Positives = 128/286 (44%), Gaps = 17/286 (5%) Query: 28 LEVYVGGAEVNVAVALARLGVKVGFVGRVGEDELGAMVEERLRAEGVDLTHFRRAPGFTG 87 L V +GG+ N+A L + G + V RV +D +G +L A GVD TH G Sbjct: 38 LMVAMGGSSANIAAGLVKFGARAALVTRVSDDAVGRYCLNQLAAYGVDATHVTPVAG--- 94 Query: 88 LYLREYLPLGQGRV-----FYYRKGSAGSALAPGAFDPDYLEGVRFLHLSGITPALSPEA 142 R L L + R+ YR G+A ++ + L +G A P + Sbjct: 95 -EFRNSLALYESRLADHNSVIYRNGAADFQMSVADVEAVDYSQYGALITAGTVFAAEP-S 152 Query: 143 RAFSLWAMEEAKRRGVRVSLDVNYRQTLW-SPEEARGFLERALPGVDLLFLSEEEAELLF 201 R+ + A E A+ G+ + DV+YR W SP+ A L RA D++ ++EE + Sbjct: 153 RSATFRAFELARAAGLPIIFDVDYRPYSWPSPQVAEEVLSRAGALSDIIVANDEEFGFMA 212 Query: 202 GRVEEALRAL------SAPEVVLKRGAKGAWAFVDGRRVEGSAFAVEAVDPVGAGDAFAA 255 G +++ L SA VV K G +GA F +G + + V A+ P GAGD+F A Sbjct: 213 GGIDKGLAKARELAQTSAGIVVYKMGPEGAITFANGTELRTGIYPVTALKPTGAGDSFMA 272 Query: 256 GYLAGAVWGLPVEERLRLANLLGASVAASRGDHEGAPYREDLEVLL 301 G+LA G + E + + A V A G P +L+ L Sbjct: 273 GFLASLAEGRELREAVLRGSACAAIVVAKPGCAPAMPDARELDAFL 318 Lambda K H 0.320 0.139 0.407 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: 259 Number of extensions: 16 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: 309 Length of database: 333 Length adjustment: 28 Effective length of query: 281 Effective length of database: 305 Effective search space: 85705 Effective search space used: 85705 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: 48 (23.1 bits)
This GapMind analysis is from Sep 17 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