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_007679311.1 BN137_RS03205 sugar kinase
Query= SwissProt::P37647 (309 letters) >NCBI__GCF_000319285.1:WP_007679311.1 Length = 310 Score = 535 bits (1377), Expect = e-157 Identities = 262/306 (85%), Positives = 286/306 (93%) Query: 3 KKIAVIGECMIELSEKGADVKRGFGGDTLNTSVYIARQVDPAALTVHYVTALGTDSFSQQ 62 +KIAVIGECMIELSEKG+ V RGFGGDTLNTSVYIARQV+P AL+VHYVTALG DSFSQQ Sbjct: 4 QKIAVIGECMIELSEKGSQVNRGFGGDTLNTSVYIARQVNPQALSVHYVTALGKDSFSQQ 63 Query: 63 MLDAWHGENVDTSLTQRMENRLPGLYYIETDSTGERTFYYWRNEAAAKFWLESEQSAAIC 122 MLDAW ENV+T+LTQRM+NRLPGLYYIETD GERTF+YWRNEAAA+FWLES+++ AIC Sbjct: 64 MLDAWQAENVNTALTQRMDNRLPGLYYIETDERGERTFWYWRNEAAARFWLESDEADAIC 123 Query: 123 EELANFDYLYLSGISLAILSPTSREKLLSLLRECRANGGKVIFDNNYRPRLWASKEETQQ 182 +LA FDYLYLSGISLAILSP SREKLL LL+ CRANGGKVIFDNNYRPRLWAS+EETQQ Sbjct: 124 AQLAQFDYLYLSGISLAILSPQSREKLLGLLKTCRANGGKVIFDNNYRPRLWASREETQQ 183 Query: 183 VYQQMLECTDIAFLTLDDEDALWGQQPVEDVIARTHNAGVKEVVVKRGADSCLVSIAGEG 242 VYQQML CTDIAFLTLDDEDALWG++PV++VIART AGV+EVV+KRGADSCLV++ GE Sbjct: 184 VYQQMLACTDIAFLTLDDEDALWGEKPVDEVIARTQAAGVREVVIKRGADSCLVAVQGEP 243 Query: 243 LVDVPAVKLPKEKVIDTTAAGDSFSAGYLAVRLTGGSAEDAAKRGHLTASTVIQYRGAII 302 L DVPAVKLPKEKV+DTTAAGDSFSAGYLAVRLTGGSAEDAAKRGHLTASTVIQYRGAII Sbjct: 244 LCDVPAVKLPKEKVVDTTAAGDSFSAGYLAVRLTGGSAEDAAKRGHLTASTVIQYRGAII 303 Query: 303 PREAMP 308 PREAMP Sbjct: 304 PREAMP 309 Lambda K H 0.317 0.132 0.384 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: 420 Number of extensions: 8 Number of successful extensions: 1 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: 310 Length adjustment: 27 Effective length of query: 282 Effective length of database: 283 Effective search space: 79806 Effective search space used: 79806 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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