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_004121794.1 RHSP_RS20075 5-dehydro-2-deoxygluconokinase
Query= SwissProt::Q53W83 (309 letters) >NCBI__GCF_000359745.1:WP_004121794.1 Length = 644 Score = 116 bits (291), Expect = 1e-30 Identities = 94/305 (30%), Positives = 140/305 (45%), Gaps = 29/305 (9%) Query: 2 LEVVTAGEPLVALVPQEPGH-LRGKRLLEVYVGGAEVNVAVALARLGVKVGFVGRVGEDE 60 L+V+T G V L Q+ G L VGG N+A+ ARLG+K G + RVG+++ Sbjct: 14 LDVITIGRSSVDLYGQQIGSKLEDIASFAKSVGGCPANIAIGTARLGLKSGLITRVGDEQ 73 Query: 61 LGAMVEERLRAEGVDLTHFRR-APGFTGLYLREYLPLGQGRVFYYRKGSAGSALAPGAFD 119 +G + E+ EGV + T L L G + +YR A AL D Sbjct: 74 MGRFIREQAAREGVAVDGIATDKERLTALVLLAVEAEGVSPMIFYRSDCADMALNEDDID 133 Query: 120 PDYLEGVRFLHLSGITPALSPEARAFSLWAMEEAKRRGVRVSLDVNYRQTLWS-PEEARG 178 +++ + +SG T P A A+ AK G +V D++YR LW A G Sbjct: 134 ESFIKSSNAVLVSG-THFSKPNTEAAQRKAIRIAKANGRKVIFDIDYRPNLWGLAGHAEG 192 Query: 179 F------------LERALPGVDLLFLSEEE------AELLFGRVEEALRALSAPEVVLKR 220 F ++ LP DL+ +EEE A+ + G ++E +R LS+ +VLKR Sbjct: 193 FERYVKSDRVSSKMKETLPDCDLIVGTEEEIMIASGADDVLGALKE-IRRLSSAVIVLKR 251 Query: 221 GAKGAWAFVD------GRRVEGSAFAVEAVDPVGAGDAFAAGYLAGAVWGLPVEERLRLA 274 GA G + + G F +E + +GAGDAF +G+L G + G P++ A Sbjct: 252 GAMGCIVYEGPISDDLEAGIVGEGFPIEVFNVLGAGDAFMSGFLRGYLRGEPLKTSATWA 311 Query: 275 NLLGA 279 N GA Sbjct: 312 NACGA 316 Lambda K H 0.320 0.139 0.407 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: 455 Number of extensions: 26 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: 309 Length of database: 644 Length adjustment: 32 Effective length of query: 277 Effective length of database: 612 Effective search space: 169524 Effective search space used: 169524 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 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