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_007680610.1 BN137_RS02010 sugar kinase
Query= SwissProt::P50845 (324 letters) >NCBI__GCF_000319285.1:WP_007680610.1 Length = 312 Score = 314 bits (805), Expect = 2e-90 Identities = 162/307 (52%), Positives = 207/307 (67%), Gaps = 3/307 (0%) Query: 3 LDAVTFGESMAMFYANEYGGLHEVSTFSKGLAGAESNVACGLARLGFRMGWMSKVGNDQL 62 LD +T GE+MAMF A E G L +V F K +AGAE NVA GLARLG + W+S+VGND Sbjct: 5 LDVITIGEAMAMFVATEPGDLAQVEHFFKRVAGAELNVATGLARLGLNVSWVSRVGNDSF 64 Query: 63 GTFILQELKKEGVDVSRVIRSQDENPTGLLLKSKVKEG-DPQVTYYRKNSAASTLTTAEY 121 G F+L +L+KEG+ +R + D PTG LKSKV +G DP V Y+RK SAAS L+ ++ Sbjct: 65 GRFVLSQLEKEGIS-TRGVTIDDRFPTGFQLKSKVTDGTDPSVEYFRKGSAASHLSGEDF 123 Query: 122 PRDYFQCAGHLHVTGIPPALSAEMKDFTYHVMNDMRNAGKTISFDPNVRPSLWPDQATMV 181 F A HLH++G+ ALS + H M+ GKTISFDPN+RP LW +A MV Sbjct: 124 NAPLFYSARHLHLSGVAAALSGSSYELLDHAARAMKTQGKTISFDPNLRPVLWKSEAEMV 183 Query: 182 HTINDLAGLADWFFPGIAEGELLTGEKTPEGIADYYLKKGASFVAIKLGKEGAYFKTGTS 241 +N LA LADW PG+ EG +LTG++ PEGIAD+YL +G V IK G +GA+++T + Sbjct: 184 EKLNHLATLADWVLPGLKEGHILTGQQHPEGIADFYLSRGVKAVVIKTGADGAWYQTASG 243 Query: 242 E-GFLEGCRVDRVVDTVGAGDGFAVGVISGILDGLSYKDAVQRGNAIGALQVQAPGDMDG 300 E G +E +VD VVDTVGAGDGFAVGVIS +L+G + A RGN IGAL +Q GD +G Sbjct: 244 EQGTVEAVKVDNVVDTVGAGDGFAVGVISALLEGKTLHQAATRGNKIGALAIQVQGDSEG 303 Query: 301 LPTREKL 307 LPTR +L Sbjct: 304 LPTRAQL 310 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: 338 Number of extensions: 14 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: 324 Length of database: 312 Length adjustment: 27 Effective length of query: 297 Effective length of database: 285 Effective search space: 84645 Effective search space used: 84645 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