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 AO356_28555 AO356_28555 ketodeoxygluconokinase
Query= SwissProt::E0J5J4 (309 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_28555 Length = 333 Score = 291 bits (744), Expect = 2e-83 Identities = 148/306 (48%), Positives = 208/306 (67%), Gaps = 4/306 (1%) Query: 4 KIAVIGECMIEL-SEKGADVKRGFGGDTLNTSVYIARQVDPAALTVHYVTALGTDSFSQQ 62 K+A++GECMIE+ E G + + FGGDTLNT+VY+AR A+ V Y+TA+G+D+FS Sbjct: 18 KVALVGECMIEMRGEPGTAITQTFGGDTLNTAVYLARLNPHGAVAVDYMTAVGSDAFSVA 77 Query: 63 MLDAWHGENVDTSLTQRMENRLPGLYYIETDSTGERTFYYWRNEAAAKFWLESEQSAAIC 122 M +W E + + + +E+ LPGLY+I+TD GER F YWR EAAA+ E ++ + Sbjct: 78 MRRSWLEEGIGDAHVRVIEDALPGLYFIQTDPHGERRFLYWRGEAAARRMFEGPEADVML 137 Query: 123 EELANFDYLYLSGISLAILSPTSREKLLSLLRECRANGGKVIFDNNYRPRLWASKEETQQ 182 + LA++DY+YLSGISLAIL+P R++L+ L R G +++FDNNYRP LW E +Q Sbjct: 138 DALADYDYVYLSGISLAILTPEGRQRLIQALPRARRAGTRIVFDNNYRPHLWLDPESARQ 197 Query: 183 VYQQMLECTDIAFLTLDDEDALWGQQPVEDVIARTHNAGVKEVVVKRGADSCLVSIAGEG 242 VY+ +L+ TD+A LT +D+ AL+G + + + + GV+EV +KRGA SCL+ G Sbjct: 198 VYRDLLQLTDLALLTWEDDVALFGYRDPDALFSAYAQVGVREVALKRGAASCLIQ-CPTG 256 Query: 243 LVDVPAVKLPKEKVIDTTAAGDSFSAGYLAVRLTGGSAENAAKRGHLTASTVIQYRGAII 302 +VPA + V+DTTAAGDSFSA YLA RL GG + AA+ GH A+ V+QYRGA+I Sbjct: 257 RFEVPAQTV--SHVVDTTAAGDSFSAAYLACRLRGGDPQQAARWGHRLAAQVVQYRGALI 314 Query: 303 PREAMP 308 P+ AMP Sbjct: 315 PQAAMP 320 Lambda K H 0.316 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: 294 Number of extensions: 10 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: 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 ( 7.3 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