Function: Siowwei: Difference between revisions

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'''Results on Function Analysis'''
'''Results on Function Analysis'''


 
'''[[2.1 Protein-interaction annotation]]'''
'''''Table 2.1''''' Complete annotation of NUBP2 retrieved from UnitProtKB/Swiss-Prot
'''''Table 2.1''''' Complete annotation of NUBP2 retrieved from UnitProtKB/Swiss-Prot


Line 10: Line 11:
{| class="prettytable"
{| class="prettytable"
| Protein names
| Protein names
| '''Nucleotide-binding protein 2'''''Also known as:''     NBP 2
| '''Nucleotide-binding protein 2''''' Also known as:''     NBP 2


|-
|-
Line 32: Line 33:
{| class="prettytable"
{| class="prettytable"
| Function
| Function
| May contribute to formation of bipolar spindles (By similarity).
| May contribute to formation of bipolar spindles (By similarity to ''E.coli'' MinD homolog).


|-
|-
Line 79: Line 80:


|}
|}
'''Sequence annotation (Features)'''




{| class="prettytable"
|
| Feature key
| Position(s)
| Length
| Description
| Graphical view


|-
| colspan="6" | '''Molecule processing'''


|-
'''[[2.2 Sequence Analysis]]'''
|
| Chain
| <div align="right">[http://beta.uniprot.org/blast/?about=Q9Y5Y2%5B1-271%5D 1 – 271]</div>
| <div align="right">271</div>
| Nucleotide-binding protein 2
|
{| class="prettytable"
|
 
|}




|-
| colspan="6" | '''Regions'''


|-
|
| Nucleotide binding
| <div align="right">[http://beta.uniprot.org/blast/?about=Q9Y5Y2%5B22-29%5D 22 – 29]</div>
| <div align="right">8</div>
| ATP Potential
|
{| class="prettytable"
|
|
|
|}
|}
'''''Table 2.2 '''''Aligned sequence of 2ph1 protein
'''''Table 2.2 '''''Aligned sequence of 2ph1 protein


'''Aligned Sequences:'''
[[Image:Ali.jpg]]
 
%-tage
 
Seq. id. identity Name
 
<nowiki>-------- </nowiki><nowiki>--------</nowiki> <nowiki>----</nowiki>
 
Query - - '''Query sequence '''
 
O30288 100.0 - '''O30288 Nucleotide-binding protein. '''
 
O28015 79.8 - '''O28015 Nucleotide-binding protein. '''
 
B1I1P7 54.1 - '''B1I1P7 Putative uncharacterized protein precursor. '''
 
A5N3E5 50.7 - '''A5N3E5 Predicted nucleotide-binding protein. '''
 
B0ACV7 55.7 - '''B0ACV7 Putative uncharacterized protein. '''
 
A8SJJ8 43.5 - '''A8SJJ8 Putative uncharacterized protein. '''
 
O27244 49.6 - '''O27244 Nucleotide-binding protein (Putative ATPase). '''
 
Q3AQ21 48.3 - '''Q3AQ21 ATP-binding protein, Mrp/Nbp35 family. '''
 
Q48LT6 45.3 - '''Q48LT6 ATP-binding protein, Mrp/Nbp35 family. '''
 
A1RYM9 46.4 - '''A1RYM9 MRP protein-like protein. '''
 
 




'''[[2.3 Sequence motif (domain) analysis]]'''


'''''Table 2.3''''' The diagram and table below show the '''3''' sequence motifs found in the sequence
'''''Table 2.3''''' The diagram and table below show the '''3''' sequence motifs found in the sequence




[[Image:3seq.jpg]]
[[Image:3seq1.jpg]]


{| class="prettytable"
| [[Image:]]


|-
'''''Table 2.4 '''''The diagram and table below show the '''1''' sequence of superfamily found in the sequence
|


|-
| [[Image:|thumb|{| class="prettytable" | colspan="6" | <center></center> | |- | <center>'''Hit'''</center> | <center>'''Scan'''</center> | <center>'''Reference&nbsp;&nbsp;code'''</center> | <center>'''Residue&nbsp;range'''</center> | <center>'''View in&nbsp;&nbsp;RasMol'''</center> | <center>'''Motif name'''</center> | colspan="0" | | |- | colspan="6" | <center></center> | |- | <center>'''&nbsp;1.'''</center> | <center>'''Gene3D'''</center> | <center>[http://gene3d.biochem.ucl.ac.uk/Gene3D/Results/quick_search?results=go&results=features&results=kegg&results=cog&results=interactions&search_term=G3DSA:3.40.50.300 G3DSA:3.40.50.300]</center> | <center>'''17-240'''</center> | <center></center> | <center>'''no description'''</center> | colspan="0" | | |- | <center>'''&nbsp;2.'''</center> | <center>'''HMMPanther'''</center> | <center>[http://panther.appliedbiosystems.com/panther/family.do?clsAccession=PTHR23264:SF4 PTHR23264:SF4]</center> | <center>'''59-246'''</center> | <center></center> | <center>'''MRP-RELATED NUCLEOTIDE-BINDING PROTEIN'''</center> | colspan="0" | | |- | <center>'''&nbsp;3.'''</center> | <center>'''HMMPanther'''</center> | <center>[http://panther.appliedbiosystems.com/panther/family.do?clsAccession=PTHR23264 PTHR23264]</center> | <center>'''59-246'''</center> | <center></center> | <center>'''NUCLEOTIDE-BINDING PROTEIN NBP35(YEAST)-RELATED'''</center> | colspan="0" | | |- | colspan="6" | <center></center> | |}]]


|}
'''''Table 2.4 '''''The diagram and table below show the '''1''' sequence of superfamily found in the sequence


[[Image:seq1.jpg]]


[[Image:seq2.jpg]]


{| class="prettytable"
| [[Image:]]
|-
|


|-
'''[[2.4. Protein-protein interaction]]'''
| [[Image:|thumb|{| class="prettytable" | colspan="7" | |- | <div align="right">'''&nbsp;Hit&nbsp; '''</div> | <center>'''&nbsp;Reference&nbsp;&nbsp;code&nbsp; '''</center> | <center>'''&nbsp;Residue&nbsp;&nbsp;range&nbsp; '''</center> | <center>'''&nbsp;E-value&nbsp; '''</center> | <center>'''&nbsp;View in&nbsp;&nbsp;RasMol&nbsp; '''</center> | <center>'''&nbsp;PDB&nbsp;entry&nbsp; '''</center> | '''Name ''' |- | colspan="7" | |- | <div align="right">'''&nbsp;1&nbsp; '''</div> | <center>[http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?sunid=52540 52540] '''</center> | <center>'''20-7178-103106-124126-197208-240'''</center> | <center>'''4.02e-51 '''</center> | <center>'''&nbsp;&nbsp; '''</center> | <center>[http://www.ebi.ac.uk/pdbsum/1gm5 1gm5]A (d4) '''</center> | '''P-loop containing nucleoside triphosphate hydrolases ''' |- | colspan="7" | |}]]


|}
'''''Figure 1.'' '''Protein-protein interactions search using 2ph1 sequence
'''''Figure 1.'' '''Protein-protein interactions search using 2ph1 sequence




<center>[[Image:]]</center>
<center>[[Image:inter1.jpg]]</center>






{| class="prettytable"
| colspan="3" |
{| class="prettytable"
| colspan="3" | '''Your Input:'''


|-
<center>[[Image:input1.jpg]]</center>
| <center>[[Image:]]</center>
| [http://string.embl.de/newstring_cgi/display_single_node.pl?taskId=xYR99TnzadP2&node=900921&targetmode=proteins AF2382]
| Nucleotide-binding protein (254&nbsp;aa)


|-
|
|
| ''(Archaeoglobus fulgidus)''
|-
| colspan="3" | '''Predicted Functional Partners:'''
|}
| <center>[[Image:]]</center>
| <center>[[Image:]]</center>
| <center>[[Image:]]</center>
| <center>[[Image:]]</center>
| <center>[[Image:]]</center>
| <center>[[Image:]]</center>
| <center>[[Image:]]</center>
| <center>[[Image:]]</center>
| <center>[[Image:]]</center>
|-
| <center>[[Image:]]</center>
| [http://string.embl.de/newstring_cgi/display_single_node.pl?taskId=xYR99TnzadP2&node=900920&targetmode=proteins AF2381]
|
{| class="prettytable"
| Iron-sulfur cluster binding protein (283&nbsp;aa)
|}
| [http://string.embl.de/newstring_cgi/show_neighborhood.pl?taskId=xYR99TnzadP2&node2=900920 •]
| &nbsp;
| [http://string.embl.de/newstring_cgi/show_ajax_phylo_evidence.pl?taskId=xYR99TnzadP2&node2=900920 •]
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| 0.927
|-
| <center>[[Image:]]</center>
| [http://string.embl.de/newstring_cgi/display_single_node.pl?taskId=xYR99TnzadP2&node=900919&targetmode=proteins AF2380]
|
{| class="prettytable"
| Iron-sulfur cluster binding protein (262&nbsp;aa)
|}
| [http://string.embl.de/newstring_cgi/show_neighborhood.pl?taskId=xYR99TnzadP2&node2=900919 •]
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| 0.894
|-
| <center>[[Image:]]</center>
| [http://string.embl.de/newstring_cgi/display_single_node.pl?taskId=xYR99TnzadP2&node=900002&targetmode=proteins metG]
|
{| class="prettytable"
| Methionyl-tRNA synthetase (EC 6.1.1.10) (Methionine--tRNA ligase) (MetRS) (658&nbsp;aa)
|}
| [http://string.embl.de/newstring_cgi/show_neighborhood.pl?taskId=xYR99TnzadP2&node2=900002 •]
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| [http://string.embl.de/newstring_cgi/show_textmining_evidence.pl?taskId=xYR99TnzadP2&node2=900002 •]
| &nbsp;
| 0.827
|-
| <center>[[Image:]]</center>
| [http://string.embl.de/newstring_cgi/display_single_node.pl?taskId=xYR99TnzadP2&node=900917&targetmode=proteins AF2378]
|
{| class="prettytable"
| Hypothetical protein {UniProtKB/TrEMBL-O30292} (144&nbsp;aa)
|}
| [http://string.embl.de/newstring_cgi/show_neighborhood.pl?taskId=xYR99TnzadP2&node2=900917 •]
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| 0.808
|-
| <center>[[Image:]]</center>
| [http://string.embl.de/newstring_cgi/display_single_node.pl?taskId=xYR99TnzadP2&node=900918&targetmode=proteins AF_2379]
|
{| class="prettytable"
| Hypothetical protein AF_2379 (85&nbsp;aa)
|}
| [http://string.embl.de/newstring_cgi/show_neighborhood.pl?taskId=xYR99TnzadP2&node2=900918 •]
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| 0.808
|-
| <center>[[Image:]]</center>
| [http://string.embl.de/newstring_cgi/display_single_node.pl?taskId=xYR99TnzadP2&node=900922&targetmode=proteins AF2383]
|
{| class="prettytable"
| Hypothetical protein {UniProtKB/TrEMBL-O30287} (217&nbsp;aa)
|}
| [http://string.embl.de/newstring_cgi/show_neighborhood.pl?taskId=xYR99TnzadP2&node2=900922 •]
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| 0.729
|-
| <center>[[Image:]]</center>
| [http://string.embl.de/newstring_cgi/display_single_node.pl?taskId=xYR99TnzadP2&node=900916&targetmode=proteins AF2377]
|
{| class="prettytable"
| Hypothetical protein {UniProtKB/TrEMBL-O30293} (107&nbsp;aa)
|}
| [http://string.embl.de/newstring_cgi/show_neighborhood.pl?taskId=xYR99TnzadP2&node2=900916 •]
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| 0.704
|-
| <center>[[Image:]]</center>
| [http://string.embl.de/newstring_cgi/display_single_node.pl?taskId=xYR99TnzadP2&node=899737&targetmode=proteins AF1185]
|
{| class="prettytable"
| Iron-sulfur cluster binding protein (131&nbsp;aa)
|}
| &nbsp;
| &nbsp;
| [http://string.embl.de/newstring_cgi/show_ajax_phylo_evidence.pl?taskId=xYR99TnzadP2&node2=899737 •]
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| 0.485
|-
| <center>[[Image:]]</center>
| [http://string.embl.de/newstring_cgi/display_single_node.pl?taskId=xYR99TnzadP2&node=900911&targetmode=proteins suhB]
|
{| class="prettytable"
| Inositol-1-monophosphatase (EC 3.1.3.25) (IMPase) (Inositol-1- phosphatase) (I-1-Pase) (252&nbsp;aa)
|}
| [http://string.embl.de/newstring_cgi/show_neighborhood.pl?taskId=xYR99TnzadP2&node2=900911 •]
| &nbsp;
| [http://string.embl.de/newstring_cgi/show_ajax_phylo_evidence.pl?taskId=xYR99TnzadP2&node2=900911 •]
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| 0.472
|-
| <center>[[Image:]]</center>
| [http://string.embl.de/newstring_cgi/display_single_node.pl?taskId=xYR99TnzadP2&node=900924&targetmode=proteins AF2385]
|
{| class="prettytable"
| Molybdopterin oxidoreductase
|}
|
|
|
|
|
|
|
|
|
|}
'''''Figure 2. '''''Protein-protein interactions search using ''NUBP2 ''sequence
'''''Figure 2. '''''Protein-protein interactions search using ''NUBP2 ''sequence




<center>[[Image:]]</center>
<center>[[Image:inter2.jpg]]</center>
 
 
 
{| class="prettytable"
| colspan="3" |
{| class="prettytable"
| colspan="3" | '''Your Input:'''
 
|-
| <center>[[Image:]]</center>
| [http://string.embl.de/newstring_cgi/display_single_node.pl?taskId=hKMxlIdcOMTb&node=310453&targetmode=proteins NUBP2]
| Nucleotide binding protein 2 (NBP 2) (271&nbsp;aa)
 
|-
|
|
| ''(Homo sapiens)''
 
|-
| colspan="3" | '''Predicted Functional Partners:'''
 
|}
 
| <center>[[Image:]]</center>
| <center>[[Image:]]</center>
| <center>[[Image:]]</center>
| <center>[[Image:]]</center>
| <center>[[Image:]]</center>
| <center>[[Image:]]</center>
| <center>[[Image:]]</center>
| <center>[[Image:]]</center>
| <center>[[Image:]]</center>
 
|-
| <center>[[Image:]]</center>
| [http://string.embl.de/newstring_cgi/display_single_node.pl?taskId=hKMxlIdcOMTb&node=306506&targetmode=proteins IGFALS]
|
{| class="prettytable"
| Insulin-like growth factor-binding protein complex acid labile chain precursor (ALS) (605&nbsp;aa)
 
|}
 
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| [http://string.embl.de/newstring_cgi/show_textmining_evidence.pl?taskId=hKMxlIdcOMTb&node2=306506 •]
| &nbsp;
| 0.675
 
|-
| <center>[[Image:]]</center>
| [http://string.embl.de/newstring_cgi/display_single_node.pl?taskId=hKMxlIdcOMTb&node=308840&targetmode=proteins MAPK8IP3]
|
{| class="prettytable"
| C-jun-amino-terminal kinase interacting protein 3 (JNK-interacting protein 3) (JIP-3) (JNK MAP kinase scaffold protein 3) (Mitogen- activated protein kinase 8-interacting protein 3) (1342&nbsp;aa)
 
|}
 
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| [http://string.embl.de/newstring_cgi/show_textmining_evidence.pl?taskId=hKMxlIdcOMTb&node2=308840 •]
| &nbsp;
| 0.673
 
|-
| <center>[[Image:]]</center>
| [http://string.embl.de/newstring_cgi/display_single_node.pl?taskId=hKMxlIdcOMTb&node=312214&targetmode=proteins REG3G]
|
{| class="prettytable"
| Regenerating islet-derived protein 3 gamma precursor (Reg III-gamma) (Pancreatitis-associated protein 1B) (PAP IB) (175&nbsp;aa)
 
|}
 
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| [http://string.embl.de/newstring_cgi/show_textmining_evidence.pl?taskId=hKMxlIdcOMTb&node2=312214 •]
| &nbsp;
| 0.619
 
|-
| <center>[[Image:]]</center>
| [http://string.embl.de/newstring_cgi/display_single_node.pl?taskId=hKMxlIdcOMTb&node=310372&targetmode=proteins ENSP00000262027]
|
{| class="prettytable"
| Methionyl-tRNA synthetase (EC 6.1.1.10) (Methionine--tRNA ligase) (MetRS) (900&nbsp;aa)
 
|}
 
| [http://string.embl.de/newstring_cgi/show_neighborhood.pl?taskId=hKMxlIdcOMTb&node2=310372 •]
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| [http://string.embl.de/newstring_cgi/show_textmining_evidence.pl?taskId=hKMxlIdcOMTb&node2=310372 •]
| &nbsp;
| 0.594
 
|-
| <center>[[Image:]]</center>
| [http://string.embl.de/newstring_cgi/display_single_node.pl?taskId=hKMxlIdcOMTb&node=320243&targetmode=proteins RANBP1]
|
{| class="prettytable"
| Ran-specific GTPase-activating protein (Ran binding protein 1) (RanBP1) (201&nbsp;aa)
 
|}
 
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| [http://string.embl.de/newstring_cgi/show_textmining_evidence.pl?taskId=hKMxlIdcOMTb&node2=320243 •]
| &nbsp;
| 0.525
 
|-
| <center>[[Image:]]</center>
| [http://string.embl.de/newstring_cgi/display_single_node.pl?taskId=hKMxlIdcOMTb&node=310063&targetmode=proteins KIF11]
|
{| class="prettytable"
| Kinesin-like protein KIF11 (Kinesin-related motor protein Eg5) (Kinesin-like spindle protein HKSP) (Thyroid receptor interacting protein 5) (TRIP5) (Kinesin-like protein 1) (1056&nbsp;aa)
 
|}
 
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| [http://string.embl.de/newstring_cgi/show_textmining_evidence.pl?taskId=hKMxlIdcOMTb&node2=310063 •]
| &nbsp;
| 0.514
 
|-
| <center>[[Image:]]</center>
| [http://string.embl.de/newstring_cgi/display_single_node.pl?taskId=hKMxlIdcOMTb&node=327885&targetmode=proteins SEPP1]
|
{| class="prettytable"
| Selenoprotein P precursor (SeP) (381&nbsp;aa)
 
|}
 
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| [http://string.embl.de/newstring_cgi/show_textmining_evidence.pl?taskId=hKMxlIdcOMTb&node2=327885 •]
| &nbsp;
| 0.491
 
|-
| <center>[[Image:]]</center>
| [http://string.embl.de/newstring_cgi/display_single_node.pl?taskId=hKMxlIdcOMTb&node=325216&targetmode=proteins NR3C2]
|
{| class="prettytable"
| Mineralocorticoid receptor (MR) (988&nbsp;aa)


|}


| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| [http://string.embl.de/newstring_cgi/show_textmining_evidence.pl?taskId=hKMxlIdcOMTb&node2=325216 •]
| &nbsp;
| 0.477
|-
| <center>[[Image:]]</center>
| [http://string.embl.de/newstring_cgi/display_single_node.pl?taskId=hKMxlIdcOMTb&node=325519&targetmode=proteins CYPA]
|
{| class="prettytable"
| Peptidyl-prolyl cis-trans isomerase A (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin A) (Cyclosporin A-binding protein) (165&nbsp;aa)


|}


| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| [http://string.embl.de/newstring_cgi/show_textmining_evidence.pl?taskId=hKMxlIdcOMTb&node2=325519 •]
| &nbsp;
| 0.443


|-
<center>[[Image:input2.jpg]]</center>
| <center>[[Image:]]</center>
| [http://string.embl.de/newstring_cgi/display_single_node.pl?taskId=hKMxlIdcOMTb&node=312224&targetmode=proteins WDR39]
|
{| class="prettytable"
| WD-repeat protein 39 (Ciao 1 protein) (339&nbsp;aa)


|}
'''[[2.5 Subcellular location]]'''


| &nbsp;
| [http://string.embl.de/newstring_cgi/show_fusion_evidence.pl?taskId=hKMxlIdcOMTb&node2=312224 •]
| &nbsp;
| &nbsp;
| &nbsp;
| &nbsp;
| [http://string.embl.de/newstring_cgi/show_textmining_evidence.pl?taskId=hKMxlIdcOMTb&node2=312224 •]
| &nbsp;
| 0.414


|}
'''Figure 3.''' NUBP2 expressions in human and mouse tissues
'''Figure 3.''' NUBP2 expressions in human and mouse tissues




[[Image:]]
[[Image:exp.jpg]]

Latest revision as of 05:37, 10 June 2008

Results on Function Analysis

2.1 Protein-interaction annotation

Table 2.1 Complete annotation of NUBP2 retrieved from UnitProtKB/Swiss-Prot


Names and origin


Protein names Nucleotide-binding protein 2 Also known as:     NBP 2
Gene names
Name:  NUBP2


Organism Homo sapiens (Human)

General annotation (Comments)


Function May contribute to formation of bipolar spindles (By similarity to E.coli MinD homolog).
Subunit structure Binds NUBP1 and KIFC1 (By similarity).
Subcellular location Nucleus (By similarity). Note=Associated with nucleus during interphase and nucleocytoplasm surrounding mitotic spindles during early mitosis. Enriched around centrosomes during late mitosis (By similarity).
Tissue specificity Widely expressed with highest expression in skeletal muscle.
Developmental stage Expressed in fetal brain, lung, liver and kidney.
Sequence similarities Belongs to the Mrp/NBP35 ATP-binding proteins family.

Ontologies


Keywords
   Cellular component Nucleus
   Ligand ATP-bindingNucleotide-binding
Gene Ontology (GO)
   Molecular function Nucleotide binding

Traceable author statement. Source: ProtInc



2.2 Sequence Analysis


Table 2.2 Aligned sequence of 2ph1 protein

Ali.jpg


2.3 Sequence motif (domain) analysis

Table 2.3 The diagram and table below show the 3 sequence motifs found in the sequence


3seq.jpg 3seq1.jpg


Table 2.4 The diagram and table below show the 1 sequence of superfamily found in the sequence


Seq1.jpg

Seq2.jpg


2.4. Protein-protein interaction

Figure 1. Protein-protein interactions search using 2ph1 sequence


Inter1.jpg



Input1.jpg

Figure 2. Protein-protein interactions search using NUBP2 sequence


Inter2.jpg



Input2.jpg

2.5 Subcellular location


Figure 3. NUBP2 expressions in human and mouse tissues


Exp.jpg

Retrieved from "http://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Function:_Siowwei&oldid=10887"