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 AO353_21745 AO353_21745 ketodeoxygluconokinase
Query= SwissProt::P45416 (310 letters) >FitnessBrowser__pseudo3_N2E3:AO353_21745 Length = 311 Score = 299 bits (766), Expect = 5e-86 Identities = 159/303 (52%), Positives = 203/303 (66%), Gaps = 5/303 (1%) Query: 3 TKNIAIIGECMIELSQKG-ADLNRGFGGDTLNTAVYISRQVKPDALDVHYVTALGTDSFS 61 T IA+IGECMIEL Q+ L + FGGDTLNTAVY+SR++ D V YVTALG DSFS Sbjct: 11 TPRIALIGECMIELQQRADGSLQQSFGGDTLNTAVYLSREMG-DGATVDYVTALGDDSFS 69 Query: 62 SEMMASWQKEGVKTDLIQRLDNKLPGLYFIETDATGERTFYYWRNDAAARYWLESPDADT 121 M SW +EG+ ++QRL +LPGLY I+TDA+GER F YWRN+AA R +P A Sbjct: 70 DAMCQSWSEEGIGLGMVQRLPGRLPGLYCIQTDASGERRFLYWRNEAAVRDCFTTPAAAP 129 Query: 122 ISQQLAQFDYIYLSGISLAILNQASRARLLTVLRACRANGGKVIFDNNYRPRLWQSKEET 181 I LA +D +Y SGI+LA+L +A R +L+ L R +++FDNNYRPRLW S E+ Sbjct: 130 ILAALADYDVLYFSGITLAVLGEAGRKKLIETLIEARQRDARIVFDNNYRPRLWSSVEQA 189 Query: 182 RQAYSDMLACTDIAFLTLDDEDMLWGELPVDEVLKRTHGAGVMEVVIKRGADACLVSIQG 241 R AY ++L D+A LT+DDE L+G V G+ EVV+KRGA+ CL+ G Sbjct: 190 RTAYREVLPYVDLALLTVDDEQALFGFSDEAAVFAAYEQIGIPEVVLKRGAEPCLIRCDG 249 Query: 242 EALLEVPAIKLPKEKVVDTTAAGDSFSAGYLSVRLNGGSAQDAAKRGHLTASTVIQYRGA 301 E+ EVPA+++ E+VVDTTAAGDSFSA YL+ RL G S +AA+ GH AS VIQ GA Sbjct: 250 ES-FEVPALRV--ERVVDTTAAGDSFSAAYLASRLRGASPAEAAEAGHRLASRVIQVPGA 306 Query: 302 IIP 304 +IP Sbjct: 307 LIP 309 Lambda K H 0.318 0.134 0.390 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: 285 Number of extensions: 11 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: 310 Length of database: 311 Length adjustment: 27 Effective length of query: 283 Effective length of database: 284 Effective search space: 80372 Effective search space used: 80372 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 (21.7 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