GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Cupriavidus basilensis 4G11

Align Fructokinase-1; ZmFRK1; EC 2.7.1.4 (characterized)
to candidate RR42_RS09470 RR42_RS09470 2-dehydro-3-deoxygluconokinase

Query= SwissProt::Q6XZ79
         (323 letters)



>FitnessBrowser__Cup4G11:RR42_RS09470
          Length = 314

 Score =  126 bits (316), Expect = 8e-34
 Identities = 100/311 (32%), Positives = 148/311 (47%), Gaps = 14/311 (4%)

Query: 8   VVSFGEMLIDFVPTVAGVSLAEAPAFLKAPGGAPANVAIAVSRLGGGAAFVGKLGDDEFG 67
           VV+ GE ++  V   AG  L     F K   GA  NVAI +SRLG    +  +LGDD   
Sbjct: 7   VVTLGEAMLMLVAGEAG-PLEGVQTFHKRTAGAETNVAIGLSRLGLKVGWASRLGDDSMA 65

Query: 68  RMLAAILRDNGVDDGGVVFDSGARTALAFVTLRADG-EREFMFYRNPSADMLLTADELNV 126
           R L   +R  GVD   VV + G RT   F     DG +    ++R  SA   +  + L+ 
Sbjct: 66  RYLLGEMRREGVDCSQVVCEPGERTGFQFKGRVDDGSDPPVEYHRRGSAASRMNPEHLDD 125

Query: 127 ELIKRAAVFHY-GSISLIAEPCRTAHLRAMEIAKEAGALLSYDPNLREALWPSREEARTQ 185
             ++RA   H  G    +AE  + A  +A+   + AG  +S+DPNLR ALW + E  R  
Sbjct: 126 RWLRRARHLHVTGVFPALAEGTQAATRQAIATMRAAGRTVSFDPNLRPALWATPELMRET 185

Query: 186 ILSIWDQADIVKVSEVELEFLTGIDSVEDDVVMKLWRPT-MKLLLVTLGDQGCKYYARDF 244
           + ++  Q D V     E  FLTG    E + +   +R    +L++V LG +G  +     
Sbjct: 186 LNNLAQQCDWVLPGIEEGRFLTG--HAEPERIAAFYRGRGARLVVVKLGAEGAYFDGEAG 243

Query: 245 HGAVPSFKVQQ-VDTTGAGDAFVGALLQRIVKDPSSLQDEKKLVESIKFANACGAITTTK 303
            G VP+F V++ VDT GAGD F   ++       S+L   + + ++++     GA     
Sbjct: 244 TGHVPAFSVERVVDTVGAGDGFAVGVI-------SALLQGRTVADAVRRGAWIGARAVQV 296

Query: 304 KGAIPSLPTEA 314
           +G    LPT A
Sbjct: 297 RGDTEGLPTHA 307


Lambda     K      H
   0.319    0.136    0.388 

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: 214
Number of extensions: 7
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: 323
Length of database: 314
Length adjustment: 27
Effective length of query: 296
Effective length of database: 287
Effective search space:    84952
Effective search space used:    84952
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