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_017549879.1 C792_RS0112925 sugar kinase
Query= SwissProt::Q53W83 (309 letters) >NCBI__GCF_000330705.1:WP_017549879.1 Length = 315 Score = 176 bits (447), Expect = 5e-49 Identities = 117/310 (37%), Positives = 168/310 (54%), Gaps = 11/310 (3%) Query: 2 LEVVTAGEPLVALVPQEPGHLRGKRLLEVYVGGAEVNVAVALARLGVKVGFVGRVGEDEL 61 +EV+ GE +VALV + G++R + YV GAE+N + L+RLG +V +GEDEL Sbjct: 1 MEVIGIGESMVALVNEPKGYIRHADSFKPYVAGAEMNTLIGLSRLGHGTSWVSALGEDEL 60 Query: 62 GAMVEERLRAEGVDLTHFRRAPGFTGLYLREYLPLGQGRVFYYRKGSAGSALAPGAFDPD 121 G ++ ++RAE VD +H TG++ ++ LP G V YYR+ SA S + D D Sbjct: 61 GELILHKVRAENVDASHVTHKDKRTGVFFKQILPDGSVDVTYYREDSAASNMDIRDIDMD 120 Query: 122 YLEGVRFLHLSGITPALSPEARAFSLWAMEEAKRRGVRVSLDVNYRQTLWSPEEARGFLE 181 + + L+L+GIT +LS A+ A+ A V V D N R +WS +EAR + Sbjct: 121 AIRRAKVLYLTGITLSLSSSAKEMLFEAVRIA-GDDVTVVFDPNIRLKMWSAKEARETIL 179 Query: 182 RALPGVDLLFLSEEEAELLFG--RVEEAL---RALSAPEVVLKRGAKGAWAFVDGRRVEG 236 LP VD L +E ++L G R EEAL R L +VVLK G +GA DG + G Sbjct: 180 EFLPHVDCLIAGRDEVDILMGAMRPEEALKSFRELGCSKVVLKLGKEGAVYDFDG--IGG 237 Query: 237 SA---FAVEAVDPVGAGDAFAAGYLAGAVWGLPVEERLRLANLLGASVAASRGDHEGAPY 293 S E +DPVGAGDAFAAG ++G + G E + A LG + GD++G P Sbjct: 238 SVKNPKQFEEIDPVGAGDAFAAGIISGLLNGEDPEASVEKACFLGGYITQFVGDYQGFPS 297 Query: 294 REDLEVLLKA 303 + L +++ Sbjct: 298 GDGLRAAMES 307 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: 250 Number of extensions: 14 Number of successful extensions: 4 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: 315 Length adjustment: 27 Effective length of query: 282 Effective length of database: 288 Effective search space: 81216 Effective search space used: 81216 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