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_085771876.1 B1812_RS12430 adenosine kinase
Query= SwissProt::Q53W83 (309 letters) >NCBI__GCF_002117405.1:WP_085771876.1 Length = 333 Score = 93.2 bits (230), Expect = 8e-24 Identities = 96/284 (33%), Positives = 127/284 (44%), Gaps = 29/284 (10%) Query: 33 GGAEVNVAVALARLGVKVGFVGRVGEDELGAMVEERLRAEGVDL-THFRRAPGFTGLYLR 91 GG+ N LA LG +VGFVG+V EDE G +R GV T F T L Sbjct: 59 GGSAANTMAGLASLGCRVGFVGKVKEDEAGREFAHDIRKAGVAFETPFATDGAATARCLI 118 Query: 92 EYLPLGQGRVFYYRKGSAGSALAPGAFDPDYLEGVRFLHLSGITPALSPEARAFSLWAME 151 P GQ + + A AL P D + L+L G P A+ L A + Sbjct: 119 FVTPDGQRTMNTFL--GACQALGPADIDEAQAADAKVLYLEGYLWD-PPAAKEAFLKAAK 175 Query: 152 EAKRRGVRVSLDVN-------YRQTLWSPEEARGFLERALPGVDLLFLSEEEAELLFGRV 204 ++ +G +V+L ++ YR +E G + L VD++F +E E L+ Sbjct: 176 LSRAKGRKVALSLSDAFCVDRYR------DEFLGLIRDQL--VDIVFANESELHSLYQTA 227 Query: 205 E-----EALRALSAPEVVLKRGAKGAWAFVDGRRVEGSAFAVEA-VDPVGAGDAFAAGYL 258 + ALRA V+ R A+GA V AFAVE VD GAGD FAAG+L Sbjct: 228 DFDTALVALRAEKGLLGVVTRSAQGALVADAAGVVSVPAFAVEEIVDTTGAGDLFAAGFL 287 Query: 259 AGAVWGLPVEERLRLANLLGASVAASRGDHEGAPYREDLEVLLK 302 AG GLP + R LGA AA H GA ++DL L + Sbjct: 288 AGFTQGLPHDRSAR----LGALAAAEIISHFGARPQKDLAQLAR 327 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: 245 Number of extensions: 9 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: 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 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