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 WP_009141415.1 HMPREF9452_RS06915 carbohydrate kinase
Query= SwissProt::Q53W83 (309 letters) >NCBI__GCF_000225705.1:WP_009141415.1 Length = 322 Score = 109 bits (272), Expect = 1e-28 Identities = 92/304 (30%), Positives = 137/304 (45%), Gaps = 29/304 (9%) Query: 24 GKRLLEVYVGGAEVNVAVALARLGVKVGFVGRVGEDELGAMVEERLRAEGVDLTHFRRAP 83 G+++ E GGA NV VA +LG F+G+VG+D G + + L EGVD T P Sbjct: 26 GQKMFERNPGGAPANVLVAARKLGATTAFIGKVGDDMHGTFLRDTLAGEGVDTTGLILDP 85 Query: 84 G-FTGLYLREYLPLGQGRVFYYRKGSAGSALAPGAFDPDYLEGVRFLHLSGITPALSPEA 142 FT L G+ + RK A + L ++ R H+ ++ P A Sbjct: 86 NVFTTLAFVALDERGERAFSFARKPGADTCLNARELALGVIDATRVFHVGSLSLTNEP-A 144 Query: 143 RAFSLWAMEEAKRRGVRVSLDVNYRQTLWSPEEARGFLERALPG-VDLLFLSEEEAELLF 201 R +L A++ A+ G +S D NYR +LW+ + R++ +DL+ +S+EE ELL Sbjct: 145 RGATLAALDRAREAGCVLSYDPNYRSSLWASAQVAQLQMRSIVNRMDLMKISDEECELLT 204 Query: 202 GRVEEALRALSAPEVVLKRGAK-------GAWAFV----DGRRVEGSAFAVEAVDPVGAG 250 G A E +L++G K GA A+V G VEG F + VD GAG Sbjct: 205 G----TRHPEKAAETLLEKGVKVAVVTLGGAGAYVRCAQGGAYVEG--FPTDIVDTTGAG 258 Query: 251 DAFAAGYLAG------AVWGLPVEER---LRLANLLGASVAASRGDHEGAPYREDLEVLL 301 D+F G+L + +E+ R N + + RG P R ++E LL Sbjct: 259 DSFWGGFLTAFCESGVDAADVTLEQACGFARFGNAVASLCVRGRGAIPSMPTRGEVEALL 318 Query: 302 KATQ 305 Q Sbjct: 319 AQQQ 322 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: 271 Number of extensions: 15 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: 322 Length adjustment: 27 Effective length of query: 282 Effective length of database: 295 Effective search space: 83190 Effective search space used: 83190 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 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