http://compbio.biosci.uq.edu.au/mediawiki/api.php?action=feedcontributions&user=Daniel+Federr&feedformat=atomMDWiki - User contributions [en]2024-03-29T11:18:32ZUser contributionsMediaWiki 1.39.6http://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Hypothetical_protein_Method&diff=14517Hypothetical protein Method2009-06-15T07:52:31Z<p>Daniel Federr: /* Evolution */</p>
<hr />
<div>=='''Evolution'''==<br />
<br />
Sequences for evolutionary analysis were gathered from NCBI using BLASTP (refseq). These were selected from different phyla on the basis of sequence identity (>30%). More distantly related sequences were obtained using the Psi-BLAST algorithm available at Interpro. Selected sequences were gathered in FASTA format and input into a .txt file [http://compbio.chemistry.uq.edu.au/mediawiki/upload/c/c0/Fewerseqforalign.txt]sequentially. ClustalX 1.83 [1] was then used to generate a multiple sequence alignment for the above sequences using the following parameters;<br />
<br />
[[Image:clus.jpg]]<br />
<br />
'''Figure 1:''' Clustalx 1.83 alignment parameters [1]<br />
<br />
<br />
Following alignment; sequences were trimmed in Clustalx [1] from residues 31-184 to remove extending ‘tails’ for more accurate phylogenetic analysis. The alignment file was then saved as an .aln file and exported to MEGA 4.0 [2] using the program’s conversion to MEGA format tool. MEGA [2] was then used to construct a bootstrapped neighbour joining tree using the following parameters;<br />
<br />
[[Image:mega.jpg]]<br />
<br />
'''Figure 2:''' Mega alignment parameters [2], Gamma parameter was established using Quartet puzzling [3]. <br />
<br />
<br />
A bootstrapped tree representing radiation was then copied to Microsoft power point 2007 to emphasise key features and significant bootstrap values.<br />
<br />
=='''Structure'''==<br />
<br />
<br />
=='''Function'''==<br />
<br />
The main methods for the function of our protein involved the us of STRING analysis and Profunc analysis. This involved the submitting of our protein to the respective services, after which they provided their separate anaylsis of the specified protein. Literature was used to confirm any speculations garnished from the results obtained. <br />
<br />
<br />
[[Hypothetical protein Abstract | Abstract ]] | [[Hypothetical protein Introduction | Introduction]] | [[Hypothetical protein Method| Method]] | <br />
[[Hypothetical protein Results | Results]] | [[Hypothetical protein Discussion | Discussion]] | [[Hypothetical protein Conclusion | Conclusion ]] | [[Hypothetical protein References | References ]]<BR><br />
<br />
<br />
<br />
<br />
[[hypothetical protein LOC282969 isoform 1 | Go Back To Main Page]]</div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Hypothetical_protein_Method&diff=14516Hypothetical protein Method2009-06-15T07:50:28Z<p>Daniel Federr: /* Evolution */</p>
<hr />
<div>=='''Evolution'''==<br />
<br />
Sequences for evolutionary analysis were gathered from NCBI using BLASTP (refseq). These were selected from different phyla on the basis of sequence identity (>30%). More distantly related sequences were obtained using the Psi-BLAST algorithm available at Interpro. Selected sequences were gathered in FASTA format and input into a .txt file sequentially. ClustalX 1.83 [1] was then used to generate a multiple sequence alignment for the above sequences using the following parameters;<br />
<br />
[[Image:clus.jpg]]<br />
<br />
'''Figure 1:''' Clustalx 1.83 alignment parameters [1]<br />
<br />
<br />
Following alignment; sequences were trimmed in Clustalx [1] from residues 31-184 to remove extending ‘tails’ for more accurate phylogenetic analysis. The alignment file was then saved as an .aln file and exported to MEGA 4.0 [2] using the program’s conversion to MEGA format tool. MEGA [2] was then used to construct a bootstrapped neighbour joining tree using the following parameters;<br />
<br />
[[Image:mega.jpg]]<br />
<br />
'''Figure 2:''' Mega alignment parameters [2], Gamma parameter was established using Quartet puzzling [3]. <br />
<br />
<br />
A bootstrapped tree representing radiation was then copied to Microsoft power point 2007 to emphasise key features and significant bootstrap values.<br />
<br />
=='''Structure'''==<br />
<br />
<br />
=='''Function'''==<br />
<br />
The main methods for the function of our protein involved the us of STRING analysis and Profunc analysis. This involved the submitting of our protein to the respective services, after which they provided their separate anaylsis of the specified protein. Literature was used to confirm any speculations garnished from the results obtained. <br />
<br />
<br />
[[Hypothetical protein Abstract | Abstract ]] | [[Hypothetical protein Introduction | Introduction]] | [[Hypothetical protein Method| Method]] | <br />
[[Hypothetical protein Results | Results]] | [[Hypothetical protein Discussion | Discussion]] | [[Hypothetical protein Conclusion | Conclusion ]] | [[Hypothetical protein References | References ]]<BR><br />
<br />
<br />
<br />
<br />
[[hypothetical protein LOC282969 isoform 1 | Go Back To Main Page]]</div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=File:Conres.jpg&diff=14508File:Conres.jpg2009-06-15T06:06:34Z<p>Daniel Federr: </p>
<hr />
<div></div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Hypothetical_protein_Discussion&diff=14507Hypothetical protein Discussion2009-06-15T06:06:20Z<p>Daniel Federr: </p>
<hr />
<div><br />
[[Image:conres.jpg]]<br />
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<br />
<br />
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<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
[[Hypothetical protein Abstract | Abstract ]] | [[Hypothetical protein Introduction | Introduction]] | [[Hypothetical protein Method| Method]] | <br />
[[Hypothetical protein Results | Results]] | [[Hypothetical protein Discussion | Discussion]] | [[Hypothetical protein Conclusion | Conclusion ]] | [[Hypothetical protein References | References ]]<BR><br />
<br />
<br />
<br />
[[hypothetical protein LOC282969 isoform 1 | Go Back To Main Page]]</div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Hypothetical_protein_Results&diff=14482Hypothetical protein Results2009-06-15T04:51:22Z<p>Daniel Federr: /* Radiation Tree showing relevant bootstrap values */</p>
<hr />
<div>[[Hypothetical protein Abstract | Abstract ]] | [[Hypothetical protein Introduction | Introduction]] | [[Hypothetical protein Method| Method]] | <br />
[[Hypothetical protein Results | Results]] | [[Hypothetical protein Discussion | Discussion]] | [[Hypothetical protein Conclusion | Conclusion ]] | [[Hypothetical protein References | References ]]<BR><br />
<br />
=='''Evolution'''==<br />
<br />
===Sequences===<br />
Sequences (FASTA format) gathered for MSA (including query), available via the following link: <br />
[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Image:Fewerseqforalign.txt]<br />
-----------<br />
===Multiple Sequence Alignment===<br />
[[Image:hypotheticalmsa1xx.jpg]]<br />
Multiple sequence alignment generated using Clustalx 1.83 [1].<br />
<br />
-------------<br />
<br />
===Original Curved Bootstrapped Tree===<br />
[[Image:hypotreexx21.jpg]]<br />
Curved phylogenetic tree with bootstrap values, obtained using MEGA 4.0 [2]<br />
----------------<br />
<br />
===Radiation Tree showing relevant bootstrap values===<br />
[[Image:radiationtreexx22.jpg]]<br />
<br />
Phylogenetic tree representing radiation, obtained using MEGA 4.0 [2] and manually edited in Microsoft Power Point 2007.<br />
<br />
=='''Structure'''==<br />
<br />
=='''Function'''==<br />
<br />
===Blast Search===<br />
<br />
[[Image:blasthp.jpg]]<br />
<br />
The results from the blast search showed a conserved FucU/RbsD domain.<br />
<br />
===String Analysis===<br />
<br />
[[Image:String.jpg]]<br />
<br />
This string analysis shows possible protein - protein interactions. The red protein in the middle represents the target protein and the three surrounding proteins represent interacting proteins.<br />
The larger yellow and green proteins may be releated due to cooccurrence, where as the smaller blue protien may be related due to repeatedly occurring in close proximity to the target protein, however the posible interactions shown in the analysis are inconclusive and unsubstantiated. experimental evidence is needed to prove such relationships<br><br />
<br />
<br />
===Interpro Scan result===<br />
<br />
[[Image:Interpro1.gif]]<br />
<br />
This image shows the results of a InterProScan. The InterProScan search identifies sequence motifs from several databases.These results show that the target protein belongs to the RbsD/FucU superfamily (Purple and red lines)<br />
The gray line shows an possible binding histadine site. <br />
<br />
<br />
===PDB Sequence Match===<br />
<br />
[[Image:PDB1.jpg]]<br />
<br />
This PDB scan compares structure alignment. The highest structural match with our sequence is shown to be involved in an d-ribose high affinity transport system. This supports the theory that our hypothetical protein is involved in the ABC transport system of ribose in prokaryote cells.<br />
<br />
<br />
[[hypothetical protein LOC282969 isoform 1 | Go Back To Main Page]]</div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Hypothetical_protein_Results&diff=14481Hypothetical protein Results2009-06-15T04:51:00Z<p>Daniel Federr: /* Evolution */</p>
<hr />
<div>[[Hypothetical protein Abstract | Abstract ]] | [[Hypothetical protein Introduction | Introduction]] | [[Hypothetical protein Method| Method]] | <br />
[[Hypothetical protein Results | Results]] | [[Hypothetical protein Discussion | Discussion]] | [[Hypothetical protein Conclusion | Conclusion ]] | [[Hypothetical protein References | References ]]<BR><br />
<br />
=='''Evolution'''==<br />
<br />
===Sequences===<br />
Sequences (FASTA format) gathered for MSA (including query), available via the following link: <br />
[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Image:Fewerseqforalign.txt]<br />
-----------<br />
===Multiple Sequence Alignment===<br />
[[Image:hypotheticalmsa1xx.jpg]]<br />
Multiple sequence alignment generated using Clustalx 1.83 [1].<br />
<br />
-------------<br />
<br />
===Original Curved Bootstrapped Tree===<br />
[[Image:hypotreexx21.jpg]]<br />
Curved phylogenetic tree with bootstrap values, obtained using MEGA 4.0 [2]<br />
----------------<br />
<br />
===Radiation Tree showing relevant bootstrap values===<br />
[[Image:radiationtreexx22.jpg]]<br />
<br />
Phylogenetic tree representing radiation, Obtained using MEGA 4.0 [2] and manually edited in Microsoft Power Point 2007.<br />
<br />
=='''Structure'''==<br />
<br />
=='''Function'''==<br />
<br />
===Blast Search===<br />
<br />
[[Image:blasthp.jpg]]<br />
<br />
The results from the blast search showed a conserved FucU/RbsD domain.<br />
<br />
===String Analysis===<br />
<br />
[[Image:String.jpg]]<br />
<br />
This string analysis shows possible protein - protein interactions. The red protein in the middle represents the target protein and the three surrounding proteins represent interacting proteins.<br />
The larger yellow and green proteins may be releated due to cooccurrence, where as the smaller blue protien may be related due to repeatedly occurring in close proximity to the target protein, however the posible interactions shown in the analysis are inconclusive and unsubstantiated. experimental evidence is needed to prove such relationships<br><br />
<br />
<br />
===Interpro Scan result===<br />
<br />
[[Image:Interpro1.gif]]<br />
<br />
This image shows the results of a InterProScan. The InterProScan search identifies sequence motifs from several databases.These results show that the target protein belongs to the RbsD/FucU superfamily (Purple and red lines)<br />
The gray line shows an possible binding histadine site. <br />
<br />
<br />
===PDB Sequence Match===<br />
<br />
[[Image:PDB1.jpg]]<br />
<br />
This PDB scan compares structure alignment. The highest structural match with our sequence is shown to be involved in an d-ribose high affinity transport system. This supports the theory that our hypothetical protein is involved in the ABC transport system of ribose in prokaryote cells.<br />
<br />
<br />
[[hypothetical protein LOC282969 isoform 1 | Go Back To Main Page]]</div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Hypothetical_protein_Results&diff=14480Hypothetical protein Results2009-06-15T04:48:23Z<p>Daniel Federr: /* Radiation Tree showing relevant bootstrap values */</p>
<hr />
<div>[[Hypothetical protein Abstract | Abstract ]] | [[Hypothetical protein Introduction | Introduction]] | [[Hypothetical protein Method| Method]] | <br />
[[Hypothetical protein Results | Results]] | [[Hypothetical protein Discussion | Discussion]] | [[Hypothetical protein Conclusion | Conclusion ]] | [[Hypothetical protein References | References ]]<BR><br />
<br />
=='''Evolution'''==<br />
<br />
===Sequences===<br />
Sequences (FASTA format) gathered for MSA (including query), available via the following link: <br />
[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Image:Fewerseqforalign.txt]<br />
-----------<br />
===Multiple Sequence Alignment===<br />
[[Image:hypotheticalmsa1xx.jpg]]<br />
'''Figure 3:''' Multiple sequence alignment generated using Clustalx 1.83 [1].<br />
<br />
-------------<br />
<br />
===Original Curved Bootstrapped Tree===<br />
[[Image:hypotreexx21.jpg]]<br />
'''Figure 4:''' Curved phylogenetic tree with bootstrap values, obtained using MEGA 4.0 [2]<br />
----------------<br />
<br />
===Radiation Tree showing relevant bootstrap values===<br />
[[Image:radiationtreexx22.jpg]]<br />
<br />
'''Figure 5:''' Phylogenetic tree representing radiation, Obtained using MEGA 4.0 [2] and manually edited in Microsoft Power Point 2007.<br />
<br />
=='''Structure'''==<br />
<br />
=='''Function'''==<br />
<br />
===Blast Search===<br />
<br />
[[Image:blasthp.jpg]]<br />
<br />
The results from the blast search showed a conserved FucU/RbsD domain.<br />
<br />
===String Analysis===<br />
<br />
[[Image:String.jpg]]<br />
<br />
This string analysis shows possible protein - protein interactions. The red protein in the middle represents the target protein and the three surrounding proteins represent interacting proteins.<br />
The larger yellow and green proteins may be releated due to cooccurrence, where as the smaller blue protien may be related due to repeatedly occurring in close proximity to the target protein, however the posible interactions shown in the analysis are inconclusive and unsubstantiated. experimental evidence is needed to prove such relationships<br><br />
<br />
<br />
===Interpro Scan result===<br />
<br />
[[Image:Interpro1.gif]]<br />
<br />
This image shows the results of a InterProScan. The InterProScan search identifies sequence motifs from several databases.These results show that the target protein belongs to the RbsD/FucU superfamily (Purple and red lines)<br />
The gray line shows an possible binding histadine site. <br />
<br />
<br />
===PDB Sequence Match===<br />
<br />
[[Image:PDB1.jpg]]<br />
<br />
This PDB scan compares structure alignment. The highest structural match with our sequence is shown to be involved in an d-ribose high affinity transport system. This supports the theory that our hypothetical protein is involved in the ABC transport system of ribose in prokaryote cells.<br />
<br />
<br />
[[hypothetical protein LOC282969 isoform 1 | Go Back To Main Page]]</div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Hypothetical_protein_Results&diff=14479Hypothetical protein Results2009-06-15T04:48:09Z<p>Daniel Federr: /* Original Curved Bootstrapped Tree */</p>
<hr />
<div>[[Hypothetical protein Abstract | Abstract ]] | [[Hypothetical protein Introduction | Introduction]] | [[Hypothetical protein Method| Method]] | <br />
[[Hypothetical protein Results | Results]] | [[Hypothetical protein Discussion | Discussion]] | [[Hypothetical protein Conclusion | Conclusion ]] | [[Hypothetical protein References | References ]]<BR><br />
<br />
=='''Evolution'''==<br />
<br />
===Sequences===<br />
Sequences (FASTA format) gathered for MSA (including query), available via the following link: <br />
[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Image:Fewerseqforalign.txt]<br />
-----------<br />
===Multiple Sequence Alignment===<br />
[[Image:hypotheticalmsa1xx.jpg]]<br />
'''Figure 3:''' Multiple sequence alignment generated using Clustalx 1.83 [1].<br />
<br />
-------------<br />
<br />
===Original Curved Bootstrapped Tree===<br />
[[Image:hypotreexx21.jpg]]<br />
'''Figure 4:''' Curved phylogenetic tree with bootstrap values, obtained using MEGA 4.0 [2]<br />
----------------<br />
<br />
==Radiation Tree showing relevant bootstrap values==<br />
[[Image:radiationtreexx22.jpg]]<br />
<br />
'''Figure 5:''' Phylogenetic tree representing radiation, Obtained using MEGA 4.0 [2] and manually edited in Microsoft Power Point 2007.<br />
<br />
=='''Structure'''==<br />
<br />
=='''Function'''==<br />
<br />
===Blast Search===<br />
<br />
[[Image:blasthp.jpg]]<br />
<br />
The results from the blast search showed a conserved FucU/RbsD domain.<br />
<br />
===String Analysis===<br />
<br />
[[Image:String.jpg]]<br />
<br />
This string analysis shows possible protein - protein interactions. The red protein in the middle represents the target protein and the three surrounding proteins represent interacting proteins.<br />
The larger yellow and green proteins may be releated due to cooccurrence, where as the smaller blue protien may be related due to repeatedly occurring in close proximity to the target protein, however the posible interactions shown in the analysis are inconclusive and unsubstantiated. experimental evidence is needed to prove such relationships<br><br />
<br />
<br />
===Interpro Scan result===<br />
<br />
[[Image:Interpro1.gif]]<br />
<br />
This image shows the results of a InterProScan. The InterProScan search identifies sequence motifs from several databases.These results show that the target protein belongs to the RbsD/FucU superfamily (Purple and red lines)<br />
The gray line shows an possible binding histadine site. <br />
<br />
<br />
===PDB Sequence Match===<br />
<br />
[[Image:PDB1.jpg]]<br />
<br />
This PDB scan compares structure alignment. The highest structural match with our sequence is shown to be involved in an d-ribose high affinity transport system. This supports the theory that our hypothetical protein is involved in the ABC transport system of ribose in prokaryote cells.<br />
<br />
<br />
[[hypothetical protein LOC282969 isoform 1 | Go Back To Main Page]]</div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Hypothetical_protein_Results&diff=14478Hypothetical protein Results2009-06-15T04:48:00Z<p>Daniel Federr: /* Sequences */</p>
<hr />
<div>[[Hypothetical protein Abstract | Abstract ]] | [[Hypothetical protein Introduction | Introduction]] | [[Hypothetical protein Method| Method]] | <br />
[[Hypothetical protein Results | Results]] | [[Hypothetical protein Discussion | Discussion]] | [[Hypothetical protein Conclusion | Conclusion ]] | [[Hypothetical protein References | References ]]<BR><br />
<br />
=='''Evolution'''==<br />
<br />
===Sequences===<br />
Sequences (FASTA format) gathered for MSA (including query), available via the following link: <br />
[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Image:Fewerseqforalign.txt]<br />
-----------<br />
===Multiple Sequence Alignment===<br />
[[Image:hypotheticalmsa1xx.jpg]]<br />
'''Figure 3:''' Multiple sequence alignment generated using Clustalx 1.83 [1].<br />
<br />
-------------<br />
<br />
==Original Curved Bootstrapped Tree==<br />
[[Image:hypotreexx21.jpg]]<br />
'''Figure 4:''' Curved phylogenetic tree with bootstrap values, obtained using MEGA 4.0 [2]<br />
----------------<br />
==Radiation Tree showing relevant bootstrap values==<br />
[[Image:radiationtreexx22.jpg]]<br />
<br />
'''Figure 5:''' Phylogenetic tree representing radiation, Obtained using MEGA 4.0 [2] and manually edited in Microsoft Power Point 2007.<br />
<br />
=='''Structure'''==<br />
<br />
=='''Function'''==<br />
<br />
===Blast Search===<br />
<br />
[[Image:blasthp.jpg]]<br />
<br />
The results from the blast search showed a conserved FucU/RbsD domain.<br />
<br />
===String Analysis===<br />
<br />
[[Image:String.jpg]]<br />
<br />
This string analysis shows possible protein - protein interactions. The red protein in the middle represents the target protein and the three surrounding proteins represent interacting proteins.<br />
The larger yellow and green proteins may be releated due to cooccurrence, where as the smaller blue protien may be related due to repeatedly occurring in close proximity to the target protein, however the posible interactions shown in the analysis are inconclusive and unsubstantiated. experimental evidence is needed to prove such relationships<br><br />
<br />
<br />
===Interpro Scan result===<br />
<br />
[[Image:Interpro1.gif]]<br />
<br />
This image shows the results of a InterProScan. The InterProScan search identifies sequence motifs from several databases.These results show that the target protein belongs to the RbsD/FucU superfamily (Purple and red lines)<br />
The gray line shows an possible binding histadine site. <br />
<br />
<br />
===PDB Sequence Match===<br />
<br />
[[Image:PDB1.jpg]]<br />
<br />
This PDB scan compares structure alignment. The highest structural match with our sequence is shown to be involved in an d-ribose high affinity transport system. This supports the theory that our hypothetical protein is involved in the ABC transport system of ribose in prokaryote cells.<br />
<br />
<br />
[[hypothetical protein LOC282969 isoform 1 | Go Back To Main Page]]</div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Hypothetical_protein_Results&diff=14477Hypothetical protein Results2009-06-15T04:47:46Z<p>Daniel Federr: /* Multiple Sequence Alignment */</p>
<hr />
<div>[[Hypothetical protein Abstract | Abstract ]] | [[Hypothetical protein Introduction | Introduction]] | [[Hypothetical protein Method| Method]] | <br />
[[Hypothetical protein Results | Results]] | [[Hypothetical protein Discussion | Discussion]] | [[Hypothetical protein Conclusion | Conclusion ]] | [[Hypothetical protein References | References ]]<BR><br />
<br />
=='''Evolution'''==<br />
<br />
==Sequences==<br />
<br />
Sequences (FASTA format) gathered for MSA (including query), available via the following link: <br />
[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Image:Fewerseqforalign.txt]<br />
-----------<br />
===Multiple Sequence Alignment===<br />
[[Image:hypotheticalmsa1xx.jpg]]<br />
'''Figure 3:''' Multiple sequence alignment generated using Clustalx 1.83 [1].<br />
<br />
-------------<br />
<br />
==Original Curved Bootstrapped Tree==<br />
[[Image:hypotreexx21.jpg]]<br />
'''Figure 4:''' Curved phylogenetic tree with bootstrap values, obtained using MEGA 4.0 [2]<br />
----------------<br />
==Radiation Tree showing relevant bootstrap values==<br />
[[Image:radiationtreexx22.jpg]]<br />
<br />
'''Figure 5:''' Phylogenetic tree representing radiation, Obtained using MEGA 4.0 [2] and manually edited in Microsoft Power Point 2007.<br />
<br />
=='''Structure'''==<br />
<br />
=='''Function'''==<br />
<br />
===Blast Search===<br />
<br />
[[Image:blasthp.jpg]]<br />
<br />
The results from the blast search showed a conserved FucU/RbsD domain.<br />
<br />
===String Analysis===<br />
<br />
[[Image:String.jpg]]<br />
<br />
This string analysis shows possible protein - protein interactions. The red protein in the middle represents the target protein and the three surrounding proteins represent interacting proteins.<br />
The larger yellow and green proteins may be releated due to cooccurrence, where as the smaller blue protien may be related due to repeatedly occurring in close proximity to the target protein, however the posible interactions shown in the analysis are inconclusive and unsubstantiated. experimental evidence is needed to prove such relationships<br><br />
<br />
<br />
===Interpro Scan result===<br />
<br />
[[Image:Interpro1.gif]]<br />
<br />
This image shows the results of a InterProScan. The InterProScan search identifies sequence motifs from several databases.These results show that the target protein belongs to the RbsD/FucU superfamily (Purple and red lines)<br />
The gray line shows an possible binding histadine site. <br />
<br />
<br />
===PDB Sequence Match===<br />
<br />
[[Image:PDB1.jpg]]<br />
<br />
This PDB scan compares structure alignment. The highest structural match with our sequence is shown to be involved in an d-ribose high affinity transport system. This supports the theory that our hypothetical protein is involved in the ABC transport system of ribose in prokaryote cells.<br />
<br />
<br />
[[hypothetical protein LOC282969 isoform 1 | Go Back To Main Page]]</div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Hypothetical_protein_Results&diff=14476Hypothetical protein Results2009-06-15T04:46:54Z<p>Daniel Federr: /* Sequences */</p>
<hr />
<div>[[Hypothetical protein Abstract | Abstract ]] | [[Hypothetical protein Introduction | Introduction]] | [[Hypothetical protein Method| Method]] | <br />
[[Hypothetical protein Results | Results]] | [[Hypothetical protein Discussion | Discussion]] | [[Hypothetical protein Conclusion | Conclusion ]] | [[Hypothetical protein References | References ]]<BR><br />
<br />
=='''Evolution'''==<br />
<br />
==Sequences==<br />
<br />
Sequences (FASTA format) gathered for MSA (including query), available via the following link: <br />
[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Image:Fewerseqforalign.txt]<br />
-----------<br />
==Multiple Sequence Alignment==<br />
[[Image:hypotheticalmsa1xx.jpg]]<br />
'''Figure 3:''' Multiple sequence alignment generated using Clustalx 1.83 [1].<br />
<br />
-------------<br />
==Original Curved Bootstrapped Tree==<br />
[[Image:hypotreexx21.jpg]]<br />
'''Figure 4:''' Curved phylogenetic tree with bootstrap values, obtained using MEGA 4.0 [2]<br />
----------------<br />
==Radiation Tree showing relevant bootstrap values==<br />
[[Image:radiationtreexx22.jpg]]<br />
<br />
'''Figure 5:''' Phylogenetic tree representing radiation, Obtained using MEGA 4.0 [2] and manually edited in Microsoft Power Point 2007.<br />
<br />
=='''Structure'''==<br />
<br />
=='''Function'''==<br />
<br />
===Blast Search===<br />
<br />
[[Image:blasthp.jpg]]<br />
<br />
The results from the blast search showed a conserved FucU/RbsD domain.<br />
<br />
===String Analysis===<br />
<br />
[[Image:String.jpg]]<br />
<br />
This string analysis shows possible protein - protein interactions. The red protein in the middle represents the target protein and the three surrounding proteins represent interacting proteins.<br />
The larger yellow and green proteins may be releated due to cooccurrence, where as the smaller blue protien may be related due to repeatedly occurring in close proximity to the target protein, however the posible interactions shown in the analysis are inconclusive and unsubstantiated. experimental evidence is needed to prove such relationships<br><br />
<br />
<br />
===Interpro Scan result===<br />
<br />
[[Image:Interpro1.gif]]<br />
<br />
This image shows the results of a InterProScan. The InterProScan search identifies sequence motifs from several databases.These results show that the target protein belongs to the RbsD/FucU superfamily (Purple and red lines)<br />
The gray line shows an possible binding histadine site. <br />
<br />
<br />
===PDB Sequence Match===<br />
<br />
[[Image:PDB1.jpg]]<br />
<br />
This PDB scan compares structure alignment. The highest structural match with our sequence is shown to be involved in an d-ribose high affinity transport system. This supports the theory that our hypothetical protein is involved in the ABC transport system of ribose in prokaryote cells.<br />
<br />
<br />
[[hypothetical protein LOC282969 isoform 1 | Go Back To Main Page]]</div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Hypothetical_protein_Results&diff=14474Hypothetical protein Results2009-06-15T04:46:25Z<p>Daniel Federr: /* Evolution */</p>
<hr />
<div>[[Hypothetical protein Abstract | Abstract ]] | [[Hypothetical protein Introduction | Introduction]] | [[Hypothetical protein Method| Method]] | <br />
[[Hypothetical protein Results | Results]] | [[Hypothetical protein Discussion | Discussion]] | [[Hypothetical protein Conclusion | Conclusion ]] | [[Hypothetical protein References | References ]]<BR><br />
<br />
=='''Evolution'''==<br />
<br />
==Sequences==<br />
<br />
Sequences (FASTA format) gathered for MSA (including query), available via the following link: <br />
[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Image:Fewerseqforalign.txt]<br />
-----------<br />
'''Multiple Sequence Alignment:'''<br />
[[Image:hypotheticalmsa1xx.jpg]]<br />
'''Figure 3:''' Multiple sequence alignment generated using Clustalx 1.83 [1].<br />
<br />
-------------<br />
'''Original Curved Bootstrapped Tree:'''<br />
[[Image:hypotreexx21.jpg]]<br />
'''Figure 4:''' Curved phylogenetic tree with bootstrap values, obtained using MEGA 4.0 [2]<br />
----------------<br />
'''Radiation Tree showing relevant bootstrap values:'''<br />
[[Image:radiationtreexx22.jpg]]<br />
<br />
'''Figure 5:''' Phylogenetic tree representing radiation, Obtained using MEGA 4.0 [2] and manually edited in Microsoft Power Point 2007.<br />
<br />
=='''Structure'''==<br />
<br />
=='''Function'''==<br />
<br />
===Blast Search===<br />
<br />
[[Image:blasthp.jpg]]<br />
<br />
The results from the blast search showed a conserved FucU/RbsD domain.<br />
<br />
===String Analysis===<br />
<br />
[[Image:String.jpg]]<br />
<br />
This string analysis shows possible protein - protein interactions. The red protein in the middle represents the target protein and the three surrounding proteins represent interacting proteins.<br />
The larger yellow and green proteins may be releated due to cooccurrence, where as the smaller blue protien may be related due to repeatedly occurring in close proximity to the target protein, however the posible interactions shown in the analysis are inconclusive and unsubstantiated. experimental evidence is needed to prove such relationships<br><br />
<br />
<br />
===Interpro Scan result===<br />
<br />
[[Image:Interpro1.gif]]<br />
<br />
This image shows the results of a InterProScan. The InterProScan search identifies sequence motifs from several databases.These results show that the target protein belongs to the RbsD/FucU superfamily (Purple and red lines)<br />
The gray line shows an possible binding histadine site. <br />
<br />
<br />
===PDB Sequence Match===<br />
<br />
[[Image:PDB1.jpg]]<br />
<br />
This PDB scan compares structure alignment. The highest structural match with our sequence is shown to be involved in an d-ribose high affinity transport system. This supports the theory that our hypothetical protein is involved in the ABC transport system of ribose in prokaryote cells.<br />
<br />
<br />
[[hypothetical protein LOC282969 isoform 1 | Go Back To Main Page]]</div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Hypothetical_protein_Results&diff=14473Hypothetical protein Results2009-06-15T04:45:16Z<p>Daniel Federr: /* Evolution */</p>
<hr />
<div>[[Hypothetical protein Abstract | Abstract ]] | [[Hypothetical protein Introduction | Introduction]] | [[Hypothetical protein Method| Method]] | <br />
[[Hypothetical protein Results | Results]] | [[Hypothetical protein Discussion | Discussion]] | [[Hypothetical protein Conclusion | Conclusion ]] | [[Hypothetical protein References | References ]]<BR><br />
<br />
=='''Evolution'''==<br />
<br />
'''Sequences:'''<br />
<br />
Sequences (FASTA format) gathered for MSA (including query), available via the following link: <br />
[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Image:Fewerseqforalign.txt]<br />
-----------<br />
'''Multiple Sequence Alignment:'''<br />
[[Image:hypotheticalmsa1xx.jpg]]<br />
'''Figure 3:''' Multiple sequence alignment generated using Clustalx 1.83 [1].<br />
<br />
-------------<br />
'''Original Curved Bootstrapped Tree:'''<br />
[[Image:hypotreexx21.jpg]]<br />
'''Figure 4:''' Curved phylogenetic tree with bootstrap values, obtained using MEGA 4.0 [2]<br />
----------------<br />
'''Radiation Tree showing relevant bootstrap values:'''<br />
[[Image:radiationtreexx22.jpg]]<br />
<br />
'''Figure 5:''' Phylogenetic tree representing radiation, Obtained using MEGA 4.0 [2] and manually edited in Microsoft Power Point 2007.<br />
<br />
=='''Structure'''==<br />
<br />
=='''Function'''==<br />
<br />
===Blast Search===<br />
<br />
[[Image:blasthp.jpg]]<br />
<br />
The results from the blast search showed a conserved FucU/RbsD domain.<br />
<br />
===String Analysis===<br />
<br />
[[Image:String.jpg]]<br />
<br />
This string analysis shows possible protein - protein interactions. The red protein in the middle represents the target protein and the three surrounding proteins represent interacting proteins.<br />
The larger yellow and green proteins may be releated due to cooccurrence, where as the smaller blue protien may be related due to repeatedly occurring in close proximity to the target protein, however the posible interactions shown in the analysis are inconclusive and unsubstantiated. experimental evidence is needed to prove such relationships<br><br />
<br />
<br />
===Interpro Scan result===<br />
<br />
[[Image:Interpro1.gif]]<br />
<br />
This image shows the results of a InterProScan. The InterProScan search identifies sequence motifs from several databases.These results show that the target protein belongs to the RbsD/FucU superfamily (Purple and red lines)<br />
The gray line shows an possible binding histadine site. <br />
<br />
<br />
===PDB Sequence Match===<br />
<br />
[[Image:PDB1.jpg]]<br />
<br />
This PDB scan compares structure alignment. The highest structural match with our sequence is shown to be involved in an d-ribose high affinity transport system. This supports the theory that our hypothetical protein is involved in the ABC transport system of ribose in prokaryote cells.<br />
<br />
<br />
[[hypothetical protein LOC282969 isoform 1 | Go Back To Main Page]]</div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Hypothetical_protein_Results&diff=14470Hypothetical protein Results2009-06-15T04:44:13Z<p>Daniel Federr: /* Evolution */</p>
<hr />
<div>[[Hypothetical protein Abstract | Abstract ]] | [[Hypothetical protein Introduction | Introduction]] | [[Hypothetical protein Method| Method]] | <br />
[[Hypothetical protein Results | Results]] | [[Hypothetical protein Discussion | Discussion]] | [[Hypothetical protein Conclusion | Conclusion ]] | [[Hypothetical protein References | References ]]<BR><br />
<br />
=='''Evolution'''==<br />
<br />
'''Sequences:'''<br />
<br />
Sequences (FASTA format) gathered for MSA (including query), available via the following link: <br />
[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Image:Fewerseqforalign.txt]<br />
-----------<br />
'''Multiple Sequence Alignment:'''<br />
[[Image:hypotheticalmsa1xx.jpg]]<br />
'''Figure 3:''' Multiple sequence alignment generated using Clustalx 1.83 [1].<br />
<br />
-------------<br />
'''Original Curved Bootstrapped Tree:'''<br />
[[Image:hypotreexx21.jpg]]<br />
'''Figure 4:''' Curved phylogenetic tree with bootstrap values, obtained using MEGA 4.0 [2]<br />
----------------<br />
'''Radiation Tree showing relevant bootstrap values:'''<br />
[[Image:radiationtreexx22.jpg]]<br />
<br />
'''Figure 5:''' Phylogenetic tree representing radiation of Ribose/Fucose transporter of different organisms, Obtained using MEGA 4.0 [2] and manually edited in Microsoft Power Point 2007.<br />
<br />
=='''Structure'''==<br />
<br />
=='''Function'''==<br />
<br />
===Blast Search===<br />
<br />
[[Image:blasthp.jpg]]<br />
<br />
The results from the blast search showed a conserved FucU/RbsD domain.<br />
<br />
===String Analysis===<br />
<br />
[[Image:String.jpg]]<br />
<br />
This string analysis shows possible protein - protein interactions. The red protein in the middle represents the target protein and the three surrounding proteins represent interacting proteins.<br />
The larger yellow and green proteins may be releated due to cooccurrence, where as the smaller blue protien may be related due to repeatedly occurring in close proximity to the target protein, however the posible interactions shown in the analysis are inconclusive and unsubstantiated. experimental evidence is needed to prove such relationships<br><br />
<br />
<br />
===Interpro Scan result===<br />
<br />
[[Image:Interpro1.gif]]<br />
<br />
This image shows the results of a InterProScan. The InterProScan search identifies sequence motifs from several databases.These results show that the target protein belongs to the RbsD/FucU superfamily (Purple and red lines)<br />
The gray line shows an possible binding histadine site. <br />
<br />
<br />
===PDB Sequence Match===<br />
<br />
[[Image:PDB1.jpg]]<br />
<br />
This PDB scan compares structure alignment. The highest structural match with our sequence is shown to be involved in an d-ribose high affinity transport system. This supports the theory that our hypothetical protein is involved in the ABC transport system of ribose in prokaryote cells.<br />
<br />
<br />
[[hypothetical protein LOC282969 isoform 1 | Go Back To Main Page]]</div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Hypothetical_protein_Results&diff=14469Hypothetical protein Results2009-06-15T04:43:41Z<p>Daniel Federr: /* Evolution */</p>
<hr />
<div>[[Hypothetical protein Abstract | Abstract ]] | [[Hypothetical protein Introduction | Introduction]] | [[Hypothetical protein Method| Method]] | <br />
[[Hypothetical protein Results | Results]] | [[Hypothetical protein Discussion | Discussion]] | [[Hypothetical protein Conclusion | Conclusion ]] | [[Hypothetical protein References | References ]]<BR><br />
<br />
=='''Evolution'''==<br />
<br />
'''Sequences:'''<br />
<br />
Sequences (FASTA format) gathered for MSA (including query), available via the following link: <br />
[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Image:Fewerseqforalign.txt]<br />
-----------<br />
'''Multiple Sequence Alignment:'''<br />
[[Image:hypotheticalmsa1xx.jpg]]<br />
'''Figure 3:''' Multiple sequence alignment generated using Clustalx 1.83 [1].<br />
<br />
-------------<br />
'''Original Curved Bootstrapped Tree:'''<br />
[[Image:hypotreexx21.jpg]]<br />
'''Figure 4:''' Curved phylogenetic tree with bootstrap values, obtained using MEGA 4.0 [2]<br />
----------------<br />
'''Radiation Tree showing relevant bootstrap values:'''<br />
[[Image:radiationtreexx22.jpg]]<br />
<br />
'''Figure 5:''' Phylogenetic tree representing radiation of Ribose/Fucose transporter, Obtained using MEGA 4.0 [2] and manually edited in Microsoft Power Point 2007.<br />
<br />
=='''Structure'''==<br />
<br />
=='''Function'''==<br />
<br />
===Blast Search===<br />
<br />
[[Image:blasthp.jpg]]<br />
<br />
The results from the blast search showed a conserved FucU/RbsD domain.<br />
<br />
===String Analysis===<br />
<br />
[[Image:String.jpg]]<br />
<br />
This string analysis shows possible protein - protein interactions. The red protein in the middle represents the target protein and the three surrounding proteins represent interacting proteins.<br />
The larger yellow and green proteins may be releated due to cooccurrence, where as the smaller blue protien may be related due to repeatedly occurring in close proximity to the target protein, however the posible interactions shown in the analysis are inconclusive and unsubstantiated. experimental evidence is needed to prove such relationships<br><br />
<br />
<br />
===Interpro Scan result===<br />
<br />
[[Image:Interpro1.gif]]<br />
<br />
This image shows the results of a InterProScan. The InterProScan search identifies sequence motifs from several databases.These results show that the target protein belongs to the RbsD/FucU superfamily (Purple and red lines)<br />
The gray line shows an possible binding histadine site. <br />
<br />
<br />
===PDB Sequence Match===<br />
<br />
[[Image:PDB1.jpg]]<br />
<br />
This PDB scan compares structure alignment. The highest structural match with our sequence is shown to be involved in an d-ribose high affinity transport system. This supports the theory that our hypothetical protein is involved in the ABC transport system of ribose in prokaryote cells.<br />
<br />
<br />
[[hypothetical protein LOC282969 isoform 1 | Go Back To Main Page]]</div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Hypothetical_protein_Results&diff=14467Hypothetical protein Results2009-06-15T04:43:01Z<p>Daniel Federr: /* Evolution */</p>
<hr />
<div>[[Hypothetical protein Abstract | Abstract ]] | [[Hypothetical protein Introduction | Introduction]] | [[Hypothetical protein Method| Method]] | <br />
[[Hypothetical protein Results | Results]] | [[Hypothetical protein Discussion | Discussion]] | [[Hypothetical protein Conclusion | Conclusion ]] | [[Hypothetical protein References | References ]]<BR><br />
<br />
=='''Evolution'''==<br />
<br />
'''Sequences:'''<br />
<br />
Sequences (FASTA format) gathered for MSA (including query), available via the following link: <br />
[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Image:Fewerseqforalign.txt]<br />
-----------<br />
'''Multiple Sequence Alignment:'''<br />
[[Image:hypotheticalmsa1xx.jpg]]<br />
'''Figure 3:''' Multiple sequence alignment generated using Clustalx 1.83 [1].<br />
<br />
-------------<br />
'''Original Curved Bootstrapped Tree:'''<br />
[[Image:hypotreexx21.jpg]]<br />
'''Figure 4:''' Curved phylogenetic tree with bootstrap values, obtained using MEGA 4.0 [2]<br />
----------------<br />
'''Radiation tree featuring selected bootstrap values:'''<br />
[[Image:radiationtreexx22.jpg]]<br />
<br />
'''Figure 5:''' Phylogenetic tree representing radiation of Ribose/Fucose transporter, Obtained using MEGA 4.0 [2] and manually edited in Microsoft Power Point 2007.<br />
<br />
=='''Structure'''==<br />
<br />
=='''Function'''==<br />
<br />
[[Image:blasthp.jpg]]<br />
<br />
The results from the blast search showed a conserved FucU/RbsD domain.<br />
<br />
<br />
[[hypothetical protein LOC282969 isoform 1 | Go Back To Main Page]]<br />
<br />
<br />
===Interpro Scan result===<br />
<br />
[[Image:Interpro1.gif]]<br />
<br />
This image shows the results of a InterProScan. The InterProScan search identifies sequence motifs from several databases.These results show that the target protein belongs to the RbsD/FucU superfamily (Purple and red lines)<br />
The gray line shows an possible binding histadine site. <br />
<br />
<br />
===PDB Sequence Match===<br />
<br />
[[Image:PDB1.jpg]]<br />
<br />
This PDB scan compares structure alignment. The highest structural match with our sequence is shown to be involved in an d-ribose high affinity transport system. This supports the theory that our hypothetical protein is involved in the ABC transport system of ribose in prokaryote cells.</div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=File:Radiationtreexx22.jpg&diff=14466File:Radiationtreexx22.jpg2009-06-15T04:42:02Z<p>Daniel Federr: </p>
<hr />
<div></div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Hypothetical_protein_Results&diff=14463Hypothetical protein Results2009-06-15T04:40:50Z<p>Daniel Federr: /* Evolution */</p>
<hr />
<div>[[Hypothetical protein Abstract | Abstract ]] | [[Hypothetical protein Introduction | Introduction]] | [[Hypothetical protein Method| Method]] | <br />
[[Hypothetical protein Results | Results]] | [[Hypothetical protein Discussion | Discussion]] | [[Hypothetical protein Conclusion | Conclusion ]] | [[Hypothetical protein References | References ]]<BR><br />
<br />
=='''Evolution'''==<br />
<br />
'''Sequences:'''<br />
<br />
Sequences (FASTA format) gathered for MSA (including query), available via the following link: <br />
[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Image:Fewerseqforalign.txt]<br />
-----------<br />
'''Multiple Sequence Alignment:'''<br />
[[Image:hypotheticalmsa1xx.jpg]]<br />
'''Figure 3:''' Multiple sequence alignment generated using Clustalx 1.83 [1].<br />
<br />
-------------<br />
'''Original Curved Bootstrapped Tree:'''<br />
[[Image:hypotreexx21.jpg]]<br />
'''Figure 4:''' Curved phylogenetic tree with bootstrap values, obtained using MEGA 4.0 [2]<br />
----------------<br />
'''Radiation tree:'''<br />
[[Image:radiationtreexx22.jpg]]<br />
'''Figure 5:''' Phylogenetic tree representing radiation of Ribose/Fucose transporter, Obtained using MEGA 4.0 [2] and manually edited in Microsoft Power Point 2007.<br />
<br />
=='''Structure'''==<br />
<br />
=='''Function'''==<br />
<br />
[[Image:blasthp.jpg]]<br />
<br />
The results from the blast search showed a conserved FucU/RbsD domain.<br />
<br />
<br />
[[hypothetical protein LOC282969 isoform 1 | Go Back To Main Page]]<br />
<br />
<br />
===Interpro Scan result===<br />
<br />
[[Image:Interpro1.gif]]<br />
<br />
This image shows the results of a InterProScan. The InterProScan search identifies sequence motifs from several databases.These results show that the target protein belongs to the RbsD/FucU superfamily (Purple and red lines)<br />
The gray line shows an possible binding histadine site. <br />
<br />
<br />
===PDB Sequence Match===<br />
<br />
[[Image:PDB1.jpg]]<br />
<br />
This PDB scan compares structure alignment. The highest structural match with our sequence is shown to be involved in an d-ribose high affinity transport system. This supports the theory that our hypothetical protein is involved in the ABC transport system of ribose in prokaryote cells. <br />
<br />
===Residue Conservation Analysis===<br />
<br />
[[Image:pymol.png]]<br />
<br />
In this anaysis the residues are highlighted in different colours representing the levels of conservity. The red residues are the most conserved followed by pink, orange ect. <BR><br />
The yellow residue is highly conserved. acourding to certain literature it is very functionally important in the related ribose_fucu superfamily. <br />
<br />
<br />
===Fold Match===<br />
<br />
[[Image:FoldMatch.jpg]]<br />
<br />
This anaysis compares the similiar folds between structures. This again shows that the same d-ribose high affinity transport from the previous PDB analysis has the highest similarity, thus again reinforces the close relationship of our protein with ribose transport systems in prokaryote bacteria. This suggests similar function.</div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Hypothetical_protein_Results&diff=14458Hypothetical protein Results2009-06-15T04:35:42Z<p>Daniel Federr: /* Evolution */</p>
<hr />
<div>[[Hypothetical protein Abstract | Abstract ]] | [[Hypothetical protein Introduction | Introduction]] | [[Hypothetical protein Method| Method]] | <br />
[[Hypothetical protein Results | Results]] | [[Hypothetical protein Discussion | Discussion]] | [[Hypothetical protein Conclusion | Conclusion ]] | [[Hypothetical protein References | References ]]<BR><br />
<br />
=='''Evolution'''==<br />
<br />
'''Sequences:'''<br />
<br />
Sequences (FASTA format) gathered for MSA (including query), available via the following link: <br />
[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Image:Fewerseqforalign.txt]<br />
-----------<br />
'''Multiple Sequence Alignment:'''<br />
[[Image:hypotheticalmsa1xx.jpg]]<br />
'''Figure 3:''' Multiple sequence alignment generated using Clustalx 1.83 [1].<br />
[[hypothetical protein LOC282969 isoform 1 | Go Back To Main Page]]<br />
-------------<br />
'''Original Curved Bootstrapped Tree:'''<br />
[[Image:hypotreexx21.jpg]]<br />
'''Figure 4:''' Curved phylogenetic tree with bootstrap values, obtained using MEGA 4.0 [2]<br />
<br />
=='''Structure'''==<br />
<br />
=='''Function'''==<br />
<br />
[[Image:blasthp.jpg]]<br />
<br />
The results from the blast search showed a conserved FucU/RbsD domain.</div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=File:Hypotreexx21.jpg&diff=14454File:Hypotreexx21.jpg2009-06-15T04:33:20Z<p>Daniel Federr: </p>
<hr />
<div></div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Hypothetical_protein_Results&diff=14451Hypothetical protein Results2009-06-15T04:32:03Z<p>Daniel Federr: /* Evolution */</p>
<hr />
<div>[[Hypothetical protein Abstract | Abstract ]] | [[Hypothetical protein Introduction | Introduction]] | [[Hypothetical protein Method| Method]] | <br />
[[Hypothetical protein Results | Results]] | [[Hypothetical protein Discussion | Discussion]] | [[Hypothetical protein Conclusion | Conclusion ]] | [[Hypothetical protein References | References ]]<BR><br />
<br />
=='''Evolution'''==<br />
<br />
'''Sequences:'''<br />
<br />
Sequences (FASTA format) gathered for MSA (including query), available via the following link: <br />
[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Image:Fewerseqforalign.txt]<br />
-----------<br />
'''Multiple Sequence Alignment:'''<br />
[[Image:hypotheticalmsa1xx.jpg]]<br />
'''Figure 3:''' Multiple sequence alignment generated using Clustalx 1.83 [1].<br />
[[hypothetical protein LOC282969 isoform 1 | Go Back To Main Page]]<br />
-------------<br />
'''Original Curved Bootstrap Tree:'''<br />
[[Image:hypotreexx21.jpg]]</div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Hypothetical_protein_Results&diff=14443Hypothetical protein Results2009-06-15T04:15:20Z<p>Daniel Federr: /* Evolution */</p>
<hr />
<div>[[Hypothetical protein Abstract | Abstract ]] | [[Hypothetical protein Introduction | Introduction]] | [[Hypothetical protein Method| Method]] | <br />
[[Hypothetical protein Results | Results]] | [[Hypothetical protein Discussion | Discussion]] | [[Hypothetical protein Conclusion | Conclusion ]] | [[Hypothetical protein References | References ]]<BR><br />
<br />
=='''Evolution'''==<br />
<br />
'''Sequences:'''<br />
<br />
Sequences (FASTA format) gathered for MSA (including query), available via the following link: <br />
[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Image:Fewerseqforalign.txt]<br />
-----------<br />
'''Multiple Sequence Alignment:'''<br />
[[Image:hypotheticalmsa1xx.jpg]]<br />
'''Figure 3:''' Multiple sequence alignment generated using Clustalx 1.83 [1].<br />
[[hypothetical protein LOC282969 isoform 1 | Go Back To Main Page]]<br />
-------------</div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Hypothetical_protein_Results&diff=14442Hypothetical protein Results2009-06-15T04:14:57Z<p>Daniel Federr: /* Evolution */</p>
<hr />
<div>[[Hypothetical protein Abstract | Abstract ]] | [[Hypothetical protein Introduction | Introduction]] | [[Hypothetical protein Method| Method]] | <br />
[[Hypothetical protein Results | Results]] | [[Hypothetical protein Discussion | Discussion]] | [[Hypothetical protein Conclusion | Conclusion ]] | [[Hypothetical protein References | References ]]<BR><br />
<br />
=='''Evolution'''==<br />
<br />
'''Sequences:'''<br />
<br />
Sequences (FASTA format) gathered for MSA (including query), available via the following link: <br />
[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Image:Fewerseqforalign.txt]<br />
-----------<br />
'''MSA:'''<br />
[[Image:hypotheticalmsa1xx.jpg]]<br />
'''Figure 3:''' Multiple sequence alignment generated using Clustalx 1.83 [1].<br />
[[hypothetical protein LOC282969 isoform 1 | Go Back To Main Page]]</div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Hypothetical_protein_Results&diff=14441Hypothetical protein Results2009-06-15T04:14:25Z<p>Daniel Federr: /* Evolution */</p>
<hr />
<div>[[Hypothetical protein Abstract | Abstract ]] | [[Hypothetical protein Introduction | Introduction]] | [[Hypothetical protein Method| Method]] | <br />
[[Hypothetical protein Results | Results]] | [[Hypothetical protein Discussion | Discussion]] | [[Hypothetical protein Conclusion | Conclusion ]] | [[Hypothetical protein References | References ]]<BR><br />
<br />
=='''Evolution'''==<br />
<br />
'''Sequences:'''<br />
<br />
Sequences gathered for MSA (including query),FASTA format, available via the following link: <br />
[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Image:Fewerseqforalign.txt]<br />
-----------<br />
'''MSA:'''<br />
[[Image:hypotheticalmsa1xx.jpg]]<br />
'''Figure 3:''' Multiple sequence alignment generated using Clustalx 1.83 [1].<br />
[[hypothetical protein LOC282969 isoform 1 | Go Back To Main Page]]</div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Hypothetical_protein_Results&diff=14440Hypothetical protein Results2009-06-15T04:14:10Z<p>Daniel Federr: /* Evolution */</p>
<hr />
<div>[[Hypothetical protein Abstract | Abstract ]] | [[Hypothetical protein Introduction | Introduction]] | [[Hypothetical protein Method| Method]] | <br />
[[Hypothetical protein Results | Results]] | [[Hypothetical protein Discussion | Discussion]] | [[Hypothetical protein Conclusion | Conclusion ]] | [[Hypothetical protein References | References ]]<BR><br />
<br />
=='''Evolution'''==<br />
<br />
Sequences gathered for MSA (including query),FASTA format, available via the following link: <br />
[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Image:Fewerseqforalign.txt]<br />
-----------<br />
'''MSA:'''<br />
[[Image:hypotheticalmsa1xx.jpg]]<br />
'''Figure 3:''' Multiple sequence alignment generated using Clustalx 1.83 [1].<br />
[[hypothetical protein LOC282969 isoform 1 | Go Back To Main Page]]</div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Hypothetical_protein_Results&diff=14439Hypothetical protein Results2009-06-15T04:14:02Z<p>Daniel Federr: /* Evolution */</p>
<hr />
<div>[[Hypothetical protein Abstract | Abstract ]] | [[Hypothetical protein Introduction | Introduction]] | [[Hypothetical protein Method| Method]] | <br />
[[Hypothetical protein Results | Results]] | [[Hypothetical protein Discussion | Discussion]] | [[Hypothetical protein Conclusion | Conclusion ]] | [[Hypothetical protein References | References ]]<BR><br />
<br />
=='''Evolution'''==<br />
<br />
Sequences gathered for MSA (including query),FASTA format, available via the following link: <br />
[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Image:Fewerseqforalign.txt]<br />
-----------<br />
MSA:<br />
[[Image:hypotheticalmsa1xx.jpg]]<br />
'''Figure 3:''' Multiple sequence alignment generated using Clustalx 1.83 [1].<br />
[[hypothetical protein LOC282969 isoform 1 | Go Back To Main Page]]</div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Hypothetical_protein_Results&diff=14438Hypothetical protein Results2009-06-15T04:13:36Z<p>Daniel Federr: /* Evolution */</p>
<hr />
<div>[[Hypothetical protein Abstract | Abstract ]] | [[Hypothetical protein Introduction | Introduction]] | [[Hypothetical protein Method| Method]] | <br />
[[Hypothetical protein Results | Results]] | [[Hypothetical protein Discussion | Discussion]] | [[Hypothetical protein Conclusion | Conclusion ]] | [[Hypothetical protein References | References ]]<BR><br />
<br />
=='''Evolution'''==<br />
<br />
Sequences gathered for MSA (including query),FASTA format, available via the following link: <br />
[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Image:Fewerseqforalign.txt]<br />
-----------<br />
Figure representing the multiple sequence alignment generated using Clustalx 1.83 [1]:<br />
<br />
[[Image:hypotheticalmsa1xx.jpg]]<br />
'''Figure 3:''' Multiple sequence alignment generated using Clustalx 1.83 [1].<br />
[[hypothetical protein LOC282969 isoform 1 | Go Back To Main Page]]</div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Hypothetical_protein_Results&diff=14437Hypothetical protein Results2009-06-15T04:13:23Z<p>Daniel Federr: /* Evolution */</p>
<hr />
<div>[[Hypothetical protein Abstract | Abstract ]] | [[Hypothetical protein Introduction | Introduction]] | [[Hypothetical protein Method| Method]] | <br />
[[Hypothetical protein Results | Results]] | [[Hypothetical protein Discussion | Discussion]] | [[Hypothetical protein Conclusion | Conclusion ]] | [[Hypothetical protein References | References ]]<BR><br />
<br />
=='''Evolution'''==<br />
<br />
Sequences gathered for MSA (including query),FASTA format, available via the following link: <br />
[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Image:Fewerseqforalign.txt]<br />
<br />
Figure representing the multiple sequence alignment generated using Clustalx 1.83 [1]:<br />
<br />
[[Image:hypotheticalmsa1xx.jpg]]<br />
'''Figure 3:''' Multiple sequence alignment generated using Clustalx 1.83 [1].<br />
[[hypothetical protein LOC282969 isoform 1 | Go Back To Main Page]]</div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Hypothetical_protein_Results&diff=14436Hypothetical protein Results2009-06-15T04:12:30Z<p>Daniel Federr: /* Evolution */</p>
<hr />
<div>[[Hypothetical protein Abstract | Abstract ]] | [[Hypothetical protein Introduction | Introduction]] | [[Hypothetical protein Method| Method]] | <br />
[[Hypothetical protein Results | Results]] | [[Hypothetical protein Discussion | Discussion]] | [[Hypothetical protein Conclusion | Conclusion ]] | [[Hypothetical protein References | References ]]<BR><br />
<br />
=='''Evolution'''==<br />
<br />
Sequences gathered for MSA (including query),FASTA format, available via the following link: <br />
[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Image:Fewerseqforalign.txt]<br />
<br />
Multiple sequence alignment generated using Clustalx 1.83 [1]:<br />
<br />
[[Image:hypotheticalmsa1xx.jpg]]<br />
'''Figure 3:''' Multiple sequence alignment generated using Clustalx 1.83 [1].<br />
[[hypothetical protein LOC282969 isoform 1 | Go Back To Main Page]]</div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Hypothetical_protein_Results&diff=14435Hypothetical protein Results2009-06-15T04:11:22Z<p>Daniel Federr: /* Evolution */</p>
<hr />
<div>[[Hypothetical protein Abstract | Abstract ]] | [[Hypothetical protein Introduction | Introduction]] | [[Hypothetical protein Method| Method]] | <br />
[[Hypothetical protein Results | Results]] | [[Hypothetical protein Discussion | Discussion]] | [[Hypothetical protein Conclusion | Conclusion ]] | [[Hypothetical protein References | References ]]<BR><br />
<br />
=='''Evolution'''==<br />
<br />
Sequences gathered for MSA (including query),FASTA format, available via the following link: <br />
[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Image:Fewerseqforalign.txt]<br />
<br />
[[Image:hypotheticalmsa1xx.jpg]]<br />
'''Figure 3:''' Multiple sequence alignment generated using Clustalx 1.83 [1].<br />
[[hypothetical protein LOC282969 isoform 1 | Go Back To Main Page]]</div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Hypothetical_protein_Results&diff=14434Hypothetical protein Results2009-06-15T04:10:55Z<p>Daniel Federr: /* Evolution */</p>
<hr />
<div>[[Hypothetical protein Abstract | Abstract ]] | [[Hypothetical protein Introduction | Introduction]] | [[Hypothetical protein Method| Method]] | <br />
[[Hypothetical protein Results | Results]] | [[Hypothetical protein Discussion | Discussion]] | [[Hypothetical protein Conclusion | Conclusion ]] | [[Hypothetical protein References | References ]]<BR><br />
<br />
=='''Evolution'''==<br />
<br />
Sequences gathered for MSA (including query),FASTA format, available via the following link: <br />
[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Image:Fewerseqforalign.txt]<br />
<br />
[[Image:hypotheticalmsa1xx.jpg]]'''Figure 3:''' Multiple sequence alignment generated using Clustalx 1.83 [1].<br />
[[hypothetical protein LOC282969 isoform 1 | Go Back To Main Page]]</div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Hypothetical_protein_Results&diff=14432Hypothetical protein Results2009-06-15T04:10:39Z<p>Daniel Federr: /* Evolution */</p>
<hr />
<div>[[Hypothetical protein Abstract | Abstract ]] | [[Hypothetical protein Introduction | Introduction]] | [[Hypothetical protein Method| Method]] | <br />
[[Hypothetical protein Results | Results]] | [[Hypothetical protein Discussion | Discussion]] | [[Hypothetical protein Conclusion | Conclusion ]] | [[Hypothetical protein References | References ]]<BR><br />
<br />
=='''Evolution'''==<br />
<br />
Sequences gathered for MSA (including query),FASTA format, available via the following link: <br />
[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Image:Fewerseqforalign.txt]<br />
<br />
[[Image:hypotheticalmsa1xx.jpg]]<br />
'''Figure 3:''' Multiple sequence alignment generated using Clustalx 1.83 [1].<br />
[[hypothetical protein LOC282969 isoform 1 | Go Back To Main Page]]</div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=File:Hypotheticalmsa1xx.jpg&diff=14431File:Hypotheticalmsa1xx.jpg2009-06-15T04:09:10Z<p>Daniel Federr: </p>
<hr />
<div></div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Hypothetical_protein_Results&diff=14429Hypothetical protein Results2009-06-15T04:05:32Z<p>Daniel Federr: /* Evolution */</p>
<hr />
<div>[[Hypothetical protein Abstract | Abstract ]] | [[Hypothetical protein Introduction | Introduction]] | [[Hypothetical protein Method| Method]] | <br />
[[Hypothetical protein Results | Results]] | [[Hypothetical protein Discussion | Discussion]] | [[Hypothetical protein Conclusion | Conclusion ]] | [[Hypothetical protein References | References ]]<BR><br />
<br />
=='''Evolution'''==<br />
<br />
Sequences gathered for MSA (including query),FASTA format, available via the following link: <br />
[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Image:Fewerseqforalign.txt]<br />
<br />
[[Image:hypotheticalmsa1xx.jpg]]<br />
[[Image:hypotheticalmsa2xx.jpg]]<br />
<br />
[[hypothetical protein LOC282969 isoform 1 | Go Back To Main Page]]</div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Hypothetical_protein_Results&diff=14427Hypothetical protein Results2009-06-15T04:03:48Z<p>Daniel Federr: /* Evolution */</p>
<hr />
<div>[[Hypothetical protein Abstract | Abstract ]] | [[Hypothetical protein Introduction | Introduction]] | [[Hypothetical protein Method| Method]] | <br />
[[Hypothetical protein Results | Results]] | [[Hypothetical protein Discussion | Discussion]] | [[Hypothetical protein Conclusion | Conclusion ]] | [[Hypothetical protein References | References ]]<BR><br />
<br />
=='''Evolution'''==<br />
<br />
Sequences gathered for MSA (including query),FASTA format, available via the following link: <br />
[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Image:Fewerseqforalign.txt]<br />
<br />
<br />
<br />
[[hypothetical protein LOC282969 isoform 1 | Go Back To Main Page]]</div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Hypothetical_protein_Results&diff=14426Hypothetical protein Results2009-06-15T04:03:09Z<p>Daniel Federr: /* Evolution */</p>
<hr />
<div>[[Hypothetical protein Abstract | Abstract ]] | [[Hypothetical protein Introduction | Introduction]] | [[Hypothetical protein Method| Method]] | <br />
[[Hypothetical protein Results | Results]] | [[Hypothetical protein Discussion | Discussion]] | [[Hypothetical protein Conclusion | Conclusion ]] | [[Hypothetical protein References | References ]]<BR><br />
<br />
=='''Evolution'''==<br />
<br />
Sequences gathered for MSA (including query),FASTA format, available via the following link: <br />
[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Image:Fewerseqforalign.txt]<br />
<br />
<br />
<br />
[[hypothetical protein LOC282969 isoform 1 | Go Back To Main Page]]<br />
<br />
[[Image:msa1.jpg]]<br />
[[Image:msa2.jpg]]</div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Hypothetical_protein_Results&diff=14423Hypothetical protein Results2009-06-15T04:01:27Z<p>Daniel Federr: /* Evolution */</p>
<hr />
<div>[[Hypothetical protein Abstract | Abstract ]] | [[Hypothetical protein Introduction | Introduction]] | [[Hypothetical protein Method| Method]] | <br />
[[Hypothetical protein Results | Results]] | [[Hypothetical protein Discussion | Discussion]] | [[Hypothetical protein Conclusion | Conclusion ]] | [[Hypothetical protein References | References ]]<BR><br />
<br />
=='''Evolution'''==<br />
<br />
Sequences gathered for MSA (including query),FASTA format, available via the following link: <br />
[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Image:Fewerseqforalign.txt]<br />
<br />
<br />
<br />
[[hypothetical protein LOC282969 isoform 1 | Go Back To Main Page]]</div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Hypothetical_protein_Results&diff=14422Hypothetical protein Results2009-06-15T04:01:20Z<p>Daniel Federr: /* Evolution */</p>
<hr />
<div>[[Hypothetical protein Abstract | Abstract ]] | [[Hypothetical protein Introduction | Introduction]] | [[Hypothetical protein Method| Method]] | <br />
[[Hypothetical protein Results | Results]] | [[Hypothetical protein Discussion | Discussion]] | [[Hypothetical protein Conclusion | Conclusion ]] | [[Hypothetical protein References | References ]]<BR><br />
<br />
=='''Evolution'''==<br />
<br />
Sequences gathered for MSA (including query),FASTA format, available via the following link: <br />
<br />
[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Image:Fewerseqforalign.txt]<br />
<br />
<br />
<br />
[[hypothetical protein LOC282969 isoform 1 | Go Back To Main Page]]</div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Hypothetical_protein_Results&diff=14421Hypothetical protein Results2009-06-15T04:01:05Z<p>Daniel Federr: /* Evolution */</p>
<hr />
<div>[[Hypothetical protein Abstract | Abstract ]] | [[Hypothetical protein Introduction | Introduction]] | [[Hypothetical protein Method| Method]] | <br />
[[Hypothetical protein Results | Results]] | [[Hypothetical protein Discussion | Discussion]] | [[Hypothetical protein Conclusion | Conclusion ]] | [[Hypothetical protein References | References ]]<BR><br />
<br />
=='''Evolution'''==<br />
<br />
Sequences gathered for MSA (including query),FASTA format, available via the following link:[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Image:Fewerseqforalign.txt]<br />
<br />
<br />
<br />
[[hypothetical protein LOC282969 isoform 1 | Go Back To Main Page]]</div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Hypothetical_protein_Results&diff=14420Hypothetical protein Results2009-06-15T04:00:40Z<p>Daniel Federr: /* Evolution */</p>
<hr />
<div>[[Hypothetical protein Abstract | Abstract ]] | [[Hypothetical protein Introduction | Introduction]] | [[Hypothetical protein Method| Method]] | <br />
[[Hypothetical protein Results | Results]] | [[Hypothetical protein Discussion | Discussion]] | [[Hypothetical protein Conclusion | Conclusion ]] | [[Hypothetical protein References | References ]]<BR><br />
<br />
=='''Evolution'''==<br />
<br />
Sequences gathered for MSA (including query)-FASTA format, available via the following link:[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Image:Fewerseqforalign.txt]<br />
<br />
<br />
<br />
[[hypothetical protein LOC282969 isoform 1 | Go Back To Main Page]]</div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Hypothetical_protein_Results&diff=14419Hypothetical protein Results2009-06-15T04:00:07Z<p>Daniel Federr: /* Evolution */</p>
<hr />
<div>[[Hypothetical protein Abstract | Abstract ]] | [[Hypothetical protein Introduction | Introduction]] | [[Hypothetical protein Method| Method]] | <br />
[[Hypothetical protein Results | Results]] | [[Hypothetical protein Discussion | Discussion]] | [[Hypothetical protein Conclusion | Conclusion ]] | [[Hypothetical protein References | References ]]<BR><br />
<br />
=='''Evolution'''==<br />
<br />
Sequences gathered for MSA (including query)- available via the following link:<br />
[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Image:Fewerseqforalign.txt]<br />
<br />
<br />
<br />
[[hypothetical protein LOC282969 isoform 1 | Go Back To Main Page]]</div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Hypothetical_protein_Results&diff=14418Hypothetical protein Results2009-06-15T03:58:18Z<p>Daniel Federr: /* Evolution */</p>
<hr />
<div>[[Hypothetical protein Abstract | Abstract ]] | [[Hypothetical protein Introduction | Introduction]] | [[Hypothetical protein Method| Method]] | <br />
[[Hypothetical protein Results | Results]] | [[Hypothetical protein Discussion | Discussion]] | [[Hypothetical protein Conclusion | Conclusion ]] | [[Hypothetical protein References | References ]]<BR><br />
<br />
=='''Evolution'''==<br />
<br />
Sequences gathered for MSA (including query):<br />
[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Image:Fewerseqforalign.txt]<br />
<br />
<br />
<br />
[[hypothetical protein LOC282969 isoform 1 | Go Back To Main Page]]</div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Hypothetical_protein_Results&diff=14417Hypothetical protein Results2009-06-15T03:56:35Z<p>Daniel Federr: /* Evolution */</p>
<hr />
<div>[[Hypothetical protein Abstract | Abstract ]] | [[Hypothetical protein Introduction | Introduction]] | [[Hypothetical protein Method| Method]] | <br />
[[Hypothetical protein Results | Results]] | [[Hypothetical protein Discussion | Discussion]] | [[Hypothetical protein Conclusion | Conclusion ]] | [[Hypothetical protein References | References ]]<BR><br />
<br />
=='''Evolution'''==<br />
<br />
Sequences gathered for MSA (including query):<br />
<br />
<br />
<br />
<br />
<br />
[[hypothetical protein LOC282969 isoform 1 | Go Back To Main Page]]</div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=File:Fewerseqforalign.txt&diff=14416File:Fewerseqforalign.txt2009-06-15T03:55:06Z<p>Daniel Federr: uploaded a new version of "Image:Fewerseqforalign.txt"</p>
<hr />
<div></div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Hypothetical_protein_Results&diff=14414Hypothetical protein Results2009-06-15T03:54:20Z<p>Daniel Federr: /* Evolution' */</p>
<hr />
<div>[[Hypothetical protein Abstract | Abstract ]] | [[Hypothetical protein Introduction | Introduction]] | [[Hypothetical protein Method| Method]] | <br />
[[Hypothetical protein Results | Results]] | [[Hypothetical protein Discussion | Discussion]] | [[Hypothetical protein Conclusion | Conclusion ]] | [[Hypothetical protein References | References ]]<BR><br />
<br />
=='''Evolution'''==<br />
<br />
Sequences gathered for MSA (including query):<br />
<br />
'''Agrobacterium tumefaciens | hypothetical protein Atu2016 [Agrobacterium tumefaciens str. C58]<br />
MLKNIDPALNADVLHALRAMGHGDTLVISDTNFPSDSVARQTTVGKVLHIDNVSAARAMKAILSVLPLDT<br />
PLQPSVGRMEVMGAPDQLEPVQVEVQQEIDAAEGKSAPMYGIERFAFYEKAKQAYCVITTGETRFYGCFL<br />
LTKGVIPPK<br />
Sinorhizobium medicae | RbsD or FucU transport [Sinorhizobium medicae WSM419]<br />
MLKNIDPALNADVLHALRSMGHGDTLVISDTNFPSDAIARQTTLGKLLHIDNVSAARAAKAILSVLPLDT<br />
PLQPSAGRMEVMGAPDEVPGVQREVQAEIDRAEGKPAPMYGIERFAFYEEAKKAYCVITTGETRFYGCFL<br />
FTKGVVPPETI<br />
Rhizobium leguminosarum | putative fucose binding protein [Rhizobium leguminosarum bv. viciae 3841]<br />
MLKNIDPALNADVLHALRSMGHGDTVVVSDTNFPSDSIARQTVLGKLLRIDNVSAARAIEAILSVMPLDT<br />
PLQPSAGRMEIMGAPDEIPPVQQEVQAVIDGAEGKPAPMYGIERFAFYEEAKKAYCVITTGENRFYGCFL<br />
FTKGVIPPEAV<br />
Oceanicola granulosus | FucU, fucose operon fucU protein [Oceanicola granulosus HTCC2516]<br />
MLRNIPPILSPDLLHALAAMGHGDDIVIADANFPGTSMGRRLLRLDGISATDTLEAVLGLLPLDSFVPDP<br />
ALVMEVVDDPDAVPEIVADFQTIIDATADHPAKVARLERFAFYERAKEAFAVIQTGETRLYGNIILKKGV<br />
IG<br />
Sagittula stellata E-37| fucose dissimilation pathway protein [Sagittula stellata E-37]<br />
MLRNIPAILSPDILHTLRAMGHGDILAITDANFPAYSMGCKVHRLDGIPATDVLDAVLTLMPLDSFIPDP<br />
AYTMQVVDDPNAVPEIVARFQDIIDRVSDNPTKIITAERFAFYDRAKSSFAVIQTGETRLYGNILLTKGI<br />
IPPG<br />
Tolumonas auensis | RbsD or FucU transport [Tolumonas auensis DSM 9187]<br />
MLKNIPPFMDAELLWILAAMGHGDELAVVDRNFPARSIANETTSGKLVSLGGMDAPTCISGILELMPLDN<br />
FVPTPVGWMDPVDQPGTILSVHHDVLAACKKAENAEVGHYVIERFDYYAAAKKCFAVVQTSENRPYGCFI<br />
LKKGVVFD<br />
Brucella melitensis | fucose operon FUCU protein [Brucella melitensis 16M]<br />
MLKNINPLLTGSLLAILADMGHGDDLVIVDANYPAQAAGVPVLDFPGISATQVAEAVLSLLPLDDFVDRP<br />
AAVMQAPNEMPAIFKEFEAVIEKAEGRKIPVEPIERFAFYDRARGAFAIIRTGEKRLYGNIIFKKGVIRS<br />
Polaromonas sp. | RbsD or FucU transport [Polaromonas sp. JS666]<br />
MLKNIPPLLTPDALHALASMGHGDDVAIVDANFPAARVAQQSGARLVQLAGTSAPQVLNAVLQLLPLDDF<br />
VPDAAWTMQVVGNATAIPAPVAEFASALAQAGERPAVSLERFDFYERAQSAYLILQTGEQRKYGNIVLRK<br />
GVIASDDE<br />
Danio rerio | hypothetical protein LOC447896 [Danio rerio]<br />
MVILKGIPSVLTPELLYVLAQMGHGDELVLADANFPTSSVCKCGPVEIRADGVRIPELLKAILKLFPLDT<br />
YDESAAVMDLVPSDLLKGLKVPIWDQYSELLKQAGSDGNMKPVERFAFYERAKKAFAVVATGETALYGNL<br />
IIKKGVIPPEEQC<br />
Bos taurus | hypothetical protein LOC613571 [Bos taurus]<br />
MVVLKGVPALLSPELLFALARMGHGDEIVLADVNFPSSSICRGGPEEIRADGLGIPQLLEAVLQLLPLDT<br />
YVQSPAMVMELVPSDRKSGLLTPVWTSYQSILSRAGYEFSLGMGRFAFYERAKKAFAVVATGETALYGNL<br />
ILKKGVLAPKDLC<br />
Hydra magnipapillata | PREDICTED: similar to Protein fucU homolog [Hydra magnipapillata]<br />
MVMLKGIPSILSPELLLVLAKMGHGDEIVLADANFPSASVCKTNGAELIRADGLGCTDLLKAVLELLPLD<br />
TYVDAPVFLMERTPSDKNIDLKTPIWDEFKNVVNNAEQRHVCIKFVERFDFYEQAKRACAVVATGEKALY<br />
GNIILKKGVIKTSN<br />
Haemophilus somnus | RbsD or FucU transport [Haemophilus somnus 2336]<br />
MLKGIHPAISPDLLKILAEMGHGDELVLSDAHFPAHQLHHKVVRADGISINSLLTGITPLFEFDTYTEAP<br />
LIMMQAVEGDSLDPAVEQSYLQTIKSAVGNVPKLARMDRFAFYERAKQAYAVVITGETAKYGNIIIKKGV<br />
TPVK<br />
Leptothrix cholodnii | RbsD or FucU transport [Leptothrix cholodnii SP-6]<br />
MLKGIDPLLTPDLLKVLAEMGHGDEIVIADANFTAASLAIGANGVRKPVLHVSGAGIGRTVEAVIKLLPL<br />
DAAVEQPVAYMQVSDTPAGYRSRLQRDVIAMLADGGHARPEQCQAIERFAFYDRVSGAFAIVLTGDLQPY<br />
GNFILKKGVIGEALDP<br />
Branchiostoma floridae | hypothetical protein BRAFLDRAFT_114245 [Branchiostoma floridae]<br />
MVVLKGIPRILSPELLFVLARMGHGDEIVFADANFPTSSICSSGPIEVRADGHCIPALLKAVLELLPLDT<br />
YVESPAAVMDLVPGDKEKGLKTPVWDTYRGLLKEAGSTAPLEQVERFDFYERAKKAFAVVATGETALYGN<br />
IILKKGVIAPD<br />
Homo sapiens | hypothetical protein LOC282969 isoform 1 [Homo sapiens]<br />
MVALKGVPALLSPELLYALARMGHGDEIVLADLNFPASSICQCGPMEIRADGLGIPQLLEAVLKLLPLDT<br />
YVESPAAVMELVPSDKERGLQTPVWTEYESILRRAGCVRALAKIERFEFYERAKKAFAVVATGETALYGN<br />
LILRKGVLALNPLL<br />
E.coli fucose|B7UHM0|B7UHM0_ECO27 L-fucose mutarotase;<br />
MLKTISPLISPELLKVLAEMGHGDEIIFSDAHFPAHSMGPQVIRADGLLVSDLLQAIIPL<br />
FELDSYAPPLVMMAAVEGDTLDPEVERRYRNALSLQAPCPDIIRINRFAFYERAQKAFAI<br />
VITGERAKYGNILLKKGVTP<br />
Streptococcus pneumoniae|A5LR08|A5LR08_STRPN RbsD/FucU transport protein family protein;<br />
MLKHIPKNISPDLLKTLMEMGHGDEIVLADANYPSASCANKLIRCDGVNIPELLDSILYL<br />
MPLDSYVDSSIQFMNVVSGDDIPKIWGTYRQMIEGHGTDLKTITYLRREDFYERSKKAYA<br />
IVATGETSLYANIILKKGVVVERENV<br />
Roseburia inulinivorans|Q1A686|Q1A686_9FIRM Fucose transport protein;<br />
MLKGIPKILSPELLKVLAEMGHSDRLVISDGNFPAESMGKDAIVIRCDGHGVPEILDAIL<br />
QVFPLDTYVEKPVNLMEVMPGDNVETPIWDTYKEIIAKYDDRGADAVGNIERFAFYDEAK<br />
KVYAIIATGETALYANIMLQKGVVVD<br />
Mus musculus|Q8R2K1|CJ125_MOUSE Protein fucU homolog;<br />
MVALKGIPKVLSPELLFALARMGHGDEIVLADANFPTSSICQCGPVEIRADGLDIPQLLE<br />
AVLRLLPLDTYVESPAAVMDLVPSDKEKGLQTPIWKRYESLLLEADCKKTLMKLERFEFY<br />
ERAKKAFAVVATGEMALYGNIILKKGTLDLGPS<br />
Rattus norvegicus | hypothetical protein LOC293587 [Rattus norvegicus]<br />
MVVLKGIPTVLSPELLFALARMGHGDEIVLADANFPTSSICQCGPIEIRADGLDIPQLLEAVLKLLPLDT<br />
YVESPAAVMDLVPSDKEKGLQTPIWDHYEYLLLKADCKKALRKIERFEFYERAKKAFAVVATGEMALYGN<br />
IILKKGTLDLGPS<br />
Sus scrofa | PREDICTED: similar to Protein fucU homolog [Sus scrofa]<br />
MVALKGIPALLSPELLYALARMGHGDEIVLADVNFPTSSVCRCGPEEIRADGLGIPQLLEAVLTLLPLDT<br />
YVESPAAVMELVPSDRERGLQTPVWTSYQSILLQAGCTSSLTAIERFEFYERAKKAFAVVATGETALYGN<br />
LILKKGVLAPGALSQAC<br />
>Mesorhizobium loti|ref|NP_108576.1| hypothetical protein mlr8491 [Mesorhizobium loti MAFF303099]<br />
MLKGINPLLNADVLQALRAMGHGDDLIIADTNFPSDSVARQTALGRLLRIDASAAEVVKAVLSLYPLDTF<br />
VDDAAARMEIVGKPDEIPSVQKEVQKEIDAAEGKSWPMLPVERYAFYERAKQAYCVIQTGERRFYGCFAF<br />
RKGVIPPDAE<br />
>Bifidobacterium longum|ref|YP_002323773.1| RbsD or FucU transport [Bifidobacterium longum subsp. infantis ATCC 15697]<br />
MLKGIPPIIQPDLLKILSEMGHGDAIVLADAHFPAESVGVRSHVIRYDGQPIEPLLDAVLQLIPLDQYTE<br />
HPVLLMDKVPGDTVDTPIWDRYRQVIDRHEPGKQAGIGMLERFAFYEEAGRSYCIVATGEQSQYANIIIR<br />
KGVIR<br />
>Salmonella typhimurium|ref|NP_462780.1| D-ribose pyranase [Salmonella typhimurium LT2]<br />
MKKGTVLNSEISSVISRLGHTDTLVVCDAGLPIPNSTARIDMALTQGVPSFMQVVDVVTREMQVEAAILA<br />
TEIKQQNPQLHETLLTHLEQLQQHQGNTIKISYTTHEQFKKLTADSQAVIRSGECSPYANVILCAGVTF<br />
VTF<br />
>Bacillus subtilis| D-ribose pyranase [Bacillus subtilis subsp. subtilis str. 168]<br />
MKKHGILNSHLAKILADLGHTDKIVIADAGLPVPDGVLKIDLSLKPGLPAFQDTAAVLAEEMAVEKVIAA<br />
AEIKASNQENAKFLENLFSEQEIEYLSHEEFKLLTKDAKAVIRTGEFTPYANCILQAGVLF<br />
>Vibrio harveyi|YP_001448266.1| D-ribose pyranase [Vibrio harveyi ATCC BAA-1116]<br />
MKKSTLINSEVSRLIATLGHTDEITICDAGLPIPDHVQRIDLALAHGIPGFLDTVRVILSESQIEGVIIA<br />
EEFATVSPVHHDALITELAQESGLTGKPIAINYVSHEDFKVRTSQSRAVVRTGECTPYANVILQAGVVF<br />
>Lactobacillus johnsonii|ref|NP_965069.1| D-ribose pyranase [Lactobacillus johnsonii NCC 533]<br />
MKKTGVMNSNISRVIADMGHMDWLGVGDAGTPVPAETEKIDLSVRPGLPSFIDVLEEVLKELEVQKMYIA<br />
EEIKTENPKQLEAIKRTVPNVEIEFIPHSELKKDLKSSKAFIRTGEETPYSNVILESGVVF<br />
>Photobacterium sp| ribose ABC transporter protein [Photobacterium sp. SKA34]<br />
MKKSTLINSELSYLVATLGHTDEITICDAGLPIPDHVQRIDLALTHGVPSFLDTVRAMLSETCIEGVIMA<br />
EEFAQVSPEHHQALLVELELEQAKIDKKIHIQYVTHEQFKQRTEQSRAIVRTGECTPYANVIFQSGVVF<br />
>Ee.coli Ribose|AE016769_223 High affinity ribose transport protein rbsD [Escherichia coli CFT073]<br />
MEKKMKKGTVLNSDISSVISRLGHTDTLVVCDAGLPIPKSTTRIDMALTQGVPSFMQVLGVVTNEMQVEA<br />
VIIAEEIKQHNPQLHETLLTHLEQLQKHQGNTIEIRYTTHEQFKQQTAESQAVIRSGECSPYANIILCAG<br />
VTF'''<br />
<br />
<br />
<br />
<br />
[[hypothetical protein LOC282969 isoform 1 | Go Back To Main Page]]</div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Hypothetical_protein_Results&diff=14413Hypothetical protein Results2009-06-15T03:52:31Z<p>Daniel Federr: /* Evolution' */</p>
<hr />
<div>[[Hypothetical protein Abstract | Abstract ]] | [[Hypothetical protein Introduction | Introduction]] | [[Hypothetical protein Method| Method]] | <br />
[[Hypothetical protein Results | Results]] | [[Hypothetical protein Discussion | Discussion]] | [[Hypothetical protein Conclusion | Conclusion ]] | [[Hypothetical protein References | References ]]<BR><br />
<br />
==''Evolution'''==<br />
<br />
<br />
<br />
[[hypothetical protein LOC282969 isoform 1 | Go Back To Main Page]]</div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=File:Fewerseqforalign.txt&diff=14412File:Fewerseqforalign.txt2009-06-15T03:50:37Z<p>Daniel Federr: </p>
<hr />
<div></div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Hypothetical_protein_Results&diff=14411Hypothetical protein Results2009-06-15T03:50:11Z<p>Daniel Federr: </p>
<hr />
<div>[[Hypothetical protein Abstract | Abstract ]] | [[Hypothetical protein Introduction | Introduction]] | [[Hypothetical protein Method| Method]] | <br />
[[Hypothetical protein Results | Results]] | [[Hypothetical protein Discussion | Discussion]] | [[Hypothetical protein Conclusion | Conclusion ]] | [[Hypothetical protein References | References ]]<BR><br />
<br />
==''Evolution'''==<br />
<br />
[[Image:Example.jpg]]<br />
<br />
[[hypothetical protein LOC282969 isoform 1 | Go Back To Main Page]]</div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Hypothetical_protein_Method&diff=14409Hypothetical protein Method2009-06-15T03:47:00Z<p>Daniel Federr: </p>
<hr />
<div>=='''Evolution'''==<br />
<br />
Sequences for evolutionary analysis were gathered from NCBI using BLAST (refseq). These were selected from different phyla on the basis of sequence identity (>30%). More distantly related sequences were obtained using the Psi-BLAST algorithm available at Interpro. Selected sequences were gathered in FASTA format and input into a .txt file sequentially. ClustalX 1.83 [1] was then used to generate a multiple sequence alignment for the above sequences using the following parameters;<br />
<br />
[[Image:clus.jpg]]<br />
<br />
'''Figure 1:''' Clustalx 1.83 alignment parameters [1]<br />
<br />
<br />
Following alignment; sequences were trimmed in Clustalx [1] from residues 31-184 to remove extending ‘tails’ for more accurate phylogenetic analysis. The alignment file was then saved as an .aln file and exported to MEGA 4.0 [2] using the program’s conversion to MEGA format tool. MEGA [2] was then used to construct a bootstrapped neighbour joining tree using the following parameters;<br />
<br />
[[Image:mega.jpg]]<br />
<br />
'''Figure 2:''' Mega alignment parameters [2], Gamma parameter was established using Quartet puzzling [3]. <br />
<br />
<br />
A bootstrapped tree representing radiation was then copied to Microsoft power point 2007 to emphasise key features and significant bootstrap values.<br />
<br />
<br />
=='''Structure'''==<br />
<br />
<br />
=='''Function'''==<br />
<br />
[[Hypothetical protein Abstract | Abstract ]] | [[Hypothetical protein Introduction | Introduction]] | [[Hypothetical protein Method| Method]] | <br />
[[Hypothetical protein Results | Results]] | [[Hypothetical protein Discussion | Discussion]] | [[Hypothetical protein Conclusion | Conclusion ]] | [[Hypothetical protein References | References ]]<BR><br />
<br />
<br />
<br />
<br />
[[hypothetical protein LOC282969 isoform 1 | Go Back To Main Page]]</div>Daniel Federrhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Hypothetical_protein_Method&diff=14408Hypothetical protein Method2009-06-15T03:46:09Z<p>Daniel Federr: </p>
<hr />
<div>=='''Evolution'''==<br />
<br />
Sequences for evolutionary analysis were gathered from NCBI using BLAST (refseq). These were selected from different phyla on the basis of sequence identity (>30%). More distantly related sequences were obtained using the Psi-BLAST algorithm available at Interpro. Selected sequences were gathered in FASTA format and input into a .txt file sequentially. ClustalX 1.83 [1] was then used to generate a multiple sequence alignment for the above sequences using the following parameters;<br />
<br />
[[Image:clus.jpg]]<br />
<br />
'''Figure 1:''' Clustalx 1.83 alignment parameters [1]<br />
<br />
<br />
Following alignment; sequences were trimmed in Clustalx [1] from residues 31-184 to remove extending ‘tails’ for more accurate phylogenetic analysis. The alignment file was then saved as an .aln file and exported to MEGA 4.0 [2] using the program’s conversion to MEGA format tool. MEGA [2] was then used to construct a bootstrapped neighbour joining tree using the following parameters;<br />
<br />
[[Image:mega.jpg]]<br />
<br />
'''Figure 2:''' Mega alignment parameters [2], Gamma parameter was established using Quartet puzzling [3]. <br />
<br />
<br />
A bootstrapped tree representing radiation was then copied to Microsoft power point 2007 to emphasise key features and significant bootstrap values.<br />
<br />
<br />
<br />
<br />
<br />
[[Hypothetical protein Abstract | Abstract ]] | [[Hypothetical protein Introduction | Introduction]] | [[Hypothetical protein Method| Method]] | <br />
[[Hypothetical protein Results | Results]] | [[Hypothetical protein Discussion | Discussion]] | [[Hypothetical protein Conclusion | Conclusion ]] | [[Hypothetical protein References | References ]]<BR><br />
<br />
<br />
<br />
<br />
[[hypothetical protein LOC282969 isoform 1 | Go Back To Main Page]]</div>Daniel Federr