GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Escherichia coli BW25113

Align Fructokinase-1; ZmFRK1; EC 2.7.1.4 (characterized)
to candidate 17812 b3752 ribokinase (NCBI)

Query= SwissProt::Q6XZ79
         (323 letters)



>FitnessBrowser__Keio:17812
          Length = 309

 Score =  111 bits (277), Expect = 3e-29
 Identities = 87/289 (30%), Positives = 137/289 (47%), Gaps = 26/289 (8%)

Query: 38  GGAPANVAIAVSRLGGGAAFVGKLGDDEFGRMLAAILRDNGVDDGGVVFDSGARTALAFV 97
           GG  AN A+A  R G   AF+   GDD  G  +   L  + +D   V    G  T +A +
Sbjct: 41  GGKGANQAVAAGRSGANIAFIACTGDDSIGESVRQQLATDNIDITPVSVIKGESTGVALI 100

Query: 98  TLRADGEREFMFYRNPSADMLLTADELNVELIKRAAVFHYGSISLIAEPCRTAHLRAMEI 157
            +  +GE     +   +A +     E   E I  A+      +  +  P  +  + A +I
Sbjct: 101 FVNGEGENVIGIHAGANAALSPALVEAQRERIANASAL----LMQLESPLESV-MAAAKI 155

Query: 158 AKEAGALLSYDPNLREALWPSREEARTQILSIWDQADIVKVSEVELEFLTGIDSVEDDVV 217
           A +   +++ +P       P+R E   ++L++    DI+  +E E E LTGI    D+  
Sbjct: 156 AHQNKTIVALNPA------PAR-ELPDELLAL---VDIITPNETEAEKLTGIRVENDEDA 205

Query: 218 MK----LWRPTMKLLLVTLGDQGCKYYARDFHGAVPSFKVQQVDTTGAGDAFVGALLQRI 273
            K    L    ++ +L+TLG +G           VP F+VQ VDT  AGD F GAL+   
Sbjct: 206 AKAAQVLHEKGIRTVLITLGSRGVWASVNGEGQRVPGFRVQAVDTIAAGDTFNGALI--- 262

Query: 274 VKDPSSLQDEKKLVESIKFANACGAITTTKKGAIPSLPTEAEVLQLIEK 322
               ++L +EK L E+I+FA+A  AI  T+KGA PS+P   E+   +++
Sbjct: 263 ----TALLEEKPLPEAIRFAHAAAAIAVTRKGAQPSVPWREEIDAFLDR 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: 217
Number of extensions: 13
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: 323
Length of database: 309
Length adjustment: 27
Effective length of query: 296
Effective length of database: 282
Effective search space:    83472
Effective search space used:    83472
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