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_049904537.1 C447_RS14190 sugar kinase
Query= SwissProt::P50845 (324 letters) >NCBI__GCF_000336675.1:WP_049904537.1 Length = 318 Score = 244 bits (623), Expect = 2e-69 Identities = 136/319 (42%), Positives = 180/319 (56%), Gaps = 1/319 (0%) Query: 1 MKLDAVTFGESMAMFYANEYGGLHEVSTFSKGLAGAESNVACGLARLGFRMGWMSKVGND 60 M VT GE+M + Y + G + F K LAGAE+NVA GLARLG +GW SK+G D Sbjct: 1 MSSRVVTLGETMVLVYPSTTGPMKHAHEFEKSLAGAETNVAIGLARLGHDVGWYSKLGTD 60 Query: 61 QLGTFILQELKKEGVDVSRVIRSQDENPTGLLLKSKVKEGDPQVTYYRKNSAASTLTTAE 120 G ++ ++ EGVD + V DE PTG++ K + + G+P V YYR SAAS ++ + Sbjct: 61 PHGEYLEFFVRGEGVDTTTV-EFTDEAPTGIMFKERREFGEPAVHYYRHGSAASLMSPDD 119 Query: 121 YPRDYFQCAGHLHVTGIPPALSAEMKDFTYHVMNDMRNAGKTISFDPNVRPSLWPDQATM 180 P DY A +LH+TGI PALS +D T AG T+SFDPNVR LW M Sbjct: 120 LPVDYLTNAEYLHLTGITPALSESCRDATLLAAERATEAGMTVSFDPNVRRKLWESDERM 179 Query: 181 VHTINDLAGLADWFFPGIAEGELLTGEKTPEGIADYYLKKGASFVAIKLGKEGAYFKTGT 240 T+ DL L+D PGI EG L G PE IA L GA +KLG GA G+ Sbjct: 180 RETMLDLVSLSDIVLPGIEEGAALFGTDDPEAIAAACLDHGAGTAVVKLGAAGAVVADGS 239 Query: 241 SEGFLEGCRVDRVVDTVGAGDGFAVGVISGILDGLSYKDAVQRGNAIGALQVQAPGDMDG 300 + + G V+RVVD VGAGDGFA G ++ ++G +A + NA+GA GD +G Sbjct: 240 TTERVSGYDVERVVDPVGAGDGFAAGFLASRIEGQGPVEATETANAVGAFATTVAGDTEG 299 Query: 301 LPTREKLASFLSAQRTVHQ 319 LPTR++L F+ + V + Sbjct: 300 LPTRKELDVFVGERDAVRR 318 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: 294 Number of extensions: 16 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: 318 Length adjustment: 28 Effective length of query: 296 Effective length of database: 290 Effective search space: 85840 Effective search space used: 85840 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