FUNCTIONAL ANALYSIS

Function of 1pujA or the essential GTPase YlqF

Literature supporting conclusion

ProFunc

From a summary of predicted function from our ProFunc results we can see that the most commonly occurring name term is GTPase, followed by GTP binding.

Of the results returned by ProFunc, Interpro, PDB, SSM and DALI and 3D functional template searches all indicated that 1pujA was indeed a GTPase however the most promising results came from UniProt.

UniProt

During the ProFunc analysis UniProt was used to perform a multiple sequence alignment on our protein sequence. The top 2 results were both highly conserved as well as also being YlqF proteins. The rest of the 10 proteins listed were all either GTPase or GTP binding proteins. This sequence search supports the literature in its claim that the YlqF protein is required for the late step of 50s ribosomal subunit assembly.

Aligned sequences:
           %-tage
Seq. id.  identity    Name
--------  --------    ----
Query      -     - Query sequence 
O31743    95.6   - O31743 YlqF protein. 
Q65JP4    84.6   - Q65JP4 YlqF (GTP-binding domain protein). 
Q845L2    70.1   - Q845L2 Hypothetical protein. 
Q9Z9S1    59.9   - Q9Z9S1 YlqF (BH2476 protein). 
Q4MFY1    65.9   - Q4MFY1 Hypothetical protein. 
Q5WFP0    53.5   - Q5WFP0 GTPase. 
Q5HPU7    50.9   - Q5HPU7 GTP-binding protein, putative. 
Q3XZB6    52.4   - Q3XZB6 GTP-binding protein. 
A0Q0X8    49.3   - A0Q0X8 GTP-binding protein, putative. 
Q03KX8    47.6   - Q03KX8 Predicted GTPase.

SymAtlas

SymAtlas is a website useful for researching the expression levels of genes in different tissues. Using this database we have explored the levels of orthologs of 1pujA in both mouse and human genomes.

From the distribution of the human ortholog protein in the human body it is evident that this protein is widely distributed and therefore commonly used. These results are consistent with a protein essential for fundamental biological processes. The results do not provide a greater level of detail than this, however a GTPase would fall into this category

Though the distribution of the mouse ortholog protein is somewhat more scattered than the human ortholog protein it is still relatively common in all major tissues meaning that this is also consistent with our claim that 1pujA is a GTPase.

ProKnow

The ProKnow analysis shows that 1pujA's molecular function is GTP binding and its biological function is small GTPase mediated signal transduction.

GO Code.Bayesian Score.Evidence Rank.Number of Clues.Description 
                        Molecular Function
0005525	    0.9815	     2.8	     6	     GTP binding
0000166	    0.0101	     2.9	     6	     nucleotide binding
0008168	    0.0068	     2.9	     6	     methyltransferase activity
0003924	    0.0016	     2.5	     6	     GTPase activity
                        Biological Process
0007264	    1.0000	     2.8	     6	     small GTPase mediated signal transduction

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