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 RR42_RS09470 RR42_RS09470 2-dehydro-3-deoxygluconokinase
Query= SwissProt::P50845 (324 letters) >FitnessBrowser__Cup4G11:RR42_RS09470 Length = 314 Score = 283 bits (724), Expect = 4e-81 Identities = 152/308 (49%), Positives = 195/308 (63%), Gaps = 2/308 (0%) Query: 3 LDAVTFGESMAMFYANEYGGLHEVSTFSKGLAGAESNVACGLARLGFRMGWMSKVGNDQL 62 LD VT GE+M M A E G L V TF K AGAE+NVA GL+RLG ++GW S++G+D + Sbjct: 5 LDVVTLGEAMLMLVAGEAGPLEGVQTFHKRTAGAETNVAIGLSRLGLKVGWASRLGDDSM 64 Query: 63 GTFILQELKKEGVDVSRVIRSQDENPTGLLLKSKVKEG-DPQVTYYRKNSAASTLTTAEY 121 ++L E+++EGVD S+V+ E TG K +V +G DP V Y+R+ SAAS + Sbjct: 65 ARYLLGEMRREGVDCSQVVCEPGER-TGFQFKGRVDDGSDPPVEYHRRGSAASRMNPEHL 123 Query: 122 PRDYFQCAGHLHVTGIPPALSAEMKDFTYHVMNDMRNAGKTISFDPNVRPSLWPDQATMV 181 + + A HLHVTG+ PAL+ + T + MR AG+T+SFDPN+RP+LW M Sbjct: 124 DDRWLRRARHLHVTGVFPALAEGTQAATRQAIATMRAAGRTVSFDPNLRPALWATPELMR 183 Query: 182 HTINDLAGLADWFFPGIAEGELLTGEKTPEGIADYYLKKGASFVAIKLGKEGAYFKTGTS 241 T+N+LA DW PGI EG LTG PE IA +Y +GA V +KLG EGAYF Sbjct: 184 ETLNNLAQQCDWVLPGIEEGRFLTGHAEPERIAAFYRGRGARLVVVKLGAEGAYFDGEAG 243 Query: 242 EGFLEGCRVDRVVDTVGAGDGFAVGVISGILDGLSYKDAVQRGNAIGALQVQAPGDMDGL 301 G + V+RVVDTVGAGDGFAVGVIS +L G + DAV+RG IGA VQ GD +GL Sbjct: 244 TGHVPAFSVERVVDTVGAGDGFAVGVISALLQGRTVADAVRRGAWIGARAVQVRGDTEGL 303 Query: 302 PTREKLAS 309 PT LA+ Sbjct: 304 PTHALLAA 311 Lambda K H 0.317 0.135 0.399 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: 308 Number of extensions: 17 Number of successful extensions: 2 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: 324 Length of database: 314 Length adjustment: 28 Effective length of query: 296 Effective length of database: 286 Effective search space: 84656 Effective search space used: 84656 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