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 3609413 Dshi_2797 PfkB domain protein (RefSeq)
Query= SwissProt::Q53W83 (309 letters) >FitnessBrowser__Dino:3609413 Length = 308 Score = 97.8 bits (242), Expect = 3e-25 Identities = 105/312 (33%), Positives = 140/312 (44%), Gaps = 25/312 (8%) Query: 4 VVTAGEPLVALVPQE-PGHLRGKRLLEVYVGGAEVNVAVALARLGVKVGFVGRVGEDELG 62 ++ AGE L+ ++P+ P G GGA N AVAL RLG VG V + D G Sbjct: 2 ILCAGEALIDMLPRALPDGTAG---FAPVAGGAVFNTAVALGRLGADVGLVTGLSRDLFG 58 Query: 63 AMVEERLRAEGVDLTHFRRAPGFTGLYLREYLPLGQGRVFYYRKGSAGSALAPGAFDPDY 122 ++ L A VD + T L L G + +Y + +AG LAP PD Sbjct: 59 EVLMTALAAADVDSDMAVLSDRPTTLAFVT-LTDGHAQYAFYDENTAGRMLAPADM-PDP 116 Query: 123 LEGVRFLHLSGITPALSPEARAFSLWAMEEAKRRGVRVSLDVNYRQTLWSPEEA-RGFLE 181 V L GI+ A+ P A A+ ++ A R V LD N R E R ++ Sbjct: 117 GPEVGTLFFGGISLAVEPCAAAYEALCLKAAAGRVVM--LDPNIRPGFIKDETTFRARID 174 Query: 182 RALPGVDLLFLSEEEAELLFGRVE-----EALRALSAPEVVLKRGAKGAWAFVDGRRVEG 236 R L D++ +S+E+ L G + ALRA V + RG G A Sbjct: 175 RMLAVTDIVKVSDEDLAWLMGPGDLAESAAALRARGPAVVCVTRGGAGVEAHTATGITHV 234 Query: 237 SAFAVEAVDPVGAGDAFAAGYLAG-AVWGLPVEERLRL--------ANLLGASVAASRGD 287 +A AVE VD VGAGD F AG+LAG A G ++RLR A LGA AA Sbjct: 235 AAEAVEVVDTVGAGDTFNAGFLAGLAEAGALDKDRLRALDAPVLTSALRLGAQAAAITVS 294 Query: 288 HEGA--PYREDL 297 GA P+R++L Sbjct: 295 RAGANPPWRDEL 306 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: 238 Number of extensions: 15 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: 309 Length of database: 308 Length adjustment: 27 Effective length of query: 282 Effective length of database: 281 Effective search space: 79242 Effective search space used: 79242 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: 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