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 Pf6N2E2_2046 2-dehydro-3-deoxygluconate kinase (EC 2.7.1.45)
Query= SwissProt::P37647 (309 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2046 Length = 305 Score = 283 bits (725), Expect = 3e-81 Identities = 150/303 (49%), Positives = 201/303 (66%), Gaps = 5/303 (1%) Query: 4 KIAVIGECMIELSEKG-ADVKRGFGGDTLNTSVYIARQVDPAALTVHYVTALGTDSFSQQ 62 +IA+IGECMIEL ++ + + FGGDTLNT+VY+AR + TV YVTALG DSFS Sbjct: 7 RIALIGECMIELQQRADGSLLQSFGGDTLNTAVYLARALGDRG-TVDYVTALGDDSFSDA 65 Query: 63 MLDAWHGENVDTSLTQRMENRLPGLYYIETDSTGERTFYYWRNEAAAKFWLESEQSAAIC 122 M + W EN+ QR+ RLPGLY I+TD+ GER F YWRNEAA + + + I Sbjct: 66 MCENWAAENIGLQRVQRLPGRLPGLYCIQTDAAGERRFLYWRNEAAVRDCFTTPAAGPIL 125 Query: 123 EELANFDYLYLSGISLAILSPTSREKLLSLLRECRANGGKVIFDNNYRPRLWASKEETQQ 182 L +++ LY SG++LA+L R KL+ L E R G V+FDNN+RPRLWAS E + Sbjct: 126 AALPDYEVLYFSGVTLAVLGEQGRGKLIETLVEARRRGALVVFDNNFRPRLWASIEAARV 185 Query: 183 VYQQMLECTDIAFLTLDDEDALWGQQPVEDVIARTHNAGVKEVVVKRGADSCLVSIAGEG 242 Y+ +L ++A LT++DE AL+G E V A G EVV+KRGA++CL+ G+ Sbjct: 186 AYRSVLPYVELALLTVEDEQALFGHADSEAVFAAYAQLGTPEVVLKRGAEACLIRCDGQS 245 Query: 243 LVDVPAVKLPKEKVIDTTAAGDSFSAGYLAVRLTGGSAEDAAKRGHLTASTVIQYRGAII 302 +VPA+++ E+V+DTTAAGDSFSA YLA RL GGS +AA+ GHL AS VIQ GA++ Sbjct: 246 -YEVPALRV--ERVVDTTAAGDSFSAAYLASRLLGGSPVEAAEAGHLLASRVIQVPGALM 302 Query: 303 PRE 305 P++ Sbjct: 303 PKD 305 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: 277 Number of extensions: 9 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: 305 Length adjustment: 27 Effective length of query: 282 Effective length of database: 278 Effective search space: 78396 Effective search space used: 78396 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 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