GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kdgK in Dinoroseobacter shibae DFL-12

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 3607860 Dshi_1268 PfkB domain protein (RefSeq)

Query= SwissProt::Q53W83
         (309 letters)



>FitnessBrowser__Dino:3607860
          Length = 333

 Score =  107 bits (268), Expect = 3e-28
 Identities = 85/286 (29%), Positives = 128/286 (44%), Gaps = 17/286 (5%)

Query: 28  LEVYVGGAEVNVAVALARLGVKVGFVGRVGEDELGAMVEERLRAEGVDLTHFRRAPGFTG 87
           L V +GG+  N+A  L + G +   V RV +D +G     +L A GVD TH     G   
Sbjct: 38  LMVAMGGSSANIAAGLVKFGARAALVTRVSDDAVGRYCLNQLAAYGVDATHVTPVAG--- 94

Query: 88  LYLREYLPLGQGRV-----FYYRKGSAGSALAPGAFDPDYLEGVRFLHLSGITPALSPEA 142
              R  L L + R+       YR G+A   ++    +         L  +G   A  P +
Sbjct: 95  -EFRNSLALYESRLADHNSVIYRNGAADFQMSVADVEAVDYSQYGALITAGTVFAAEP-S 152

Query: 143 RAFSLWAMEEAKRRGVRVSLDVNYRQTLW-SPEEARGFLERALPGVDLLFLSEEEAELLF 201
           R+ +  A E A+  G+ +  DV+YR   W SP+ A   L RA    D++  ++EE   + 
Sbjct: 153 RSATFRAFELARAAGLPIIFDVDYRPYSWPSPQVAEEVLSRAGALSDIIVANDEEFGFMA 212

Query: 202 GRVEEALRAL------SAPEVVLKRGAKGAWAFVDGRRVEGSAFAVEAVDPVGAGDAFAA 255
           G +++ L         SA  VV K G +GA  F +G  +    + V A+ P GAGD+F A
Sbjct: 213 GGIDKGLAKARELAQTSAGIVVYKMGPEGAITFANGTELRTGIYPVTALKPTGAGDSFMA 272

Query: 256 GYLAGAVWGLPVEERLRLANLLGASVAASRGDHEGAPYREDLEVLL 301
           G+LA    G  + E +   +   A V A  G     P   +L+  L
Sbjct: 273 GFLASLAEGRELREAVLRGSACAAIVVAKPGCAPAMPDARELDAFL 318


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: 259
Number of extensions: 16
Number of successful extensions: 3
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: 333
Length adjustment: 28
Effective length of query: 281
Effective length of database: 305
Effective search space:    85705
Effective search space used:    85705
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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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