SGD:
(SGD, 2002, <http://genome-www.stanford.edu/Saccharomyces/>)
Protein Sequence:
>YOR011W Chr 15 MSISKYFTPVADGSLTFNGANIQFGADAQGESKKSYDAEDSMPNPANQLNDITFQAEAGE MVLVLGYPTSTLFKTLFHGKTSLSYSPPGSIKFKNNEFKSFSEKCPHQIIYNNEQDVHFP FLTVEQTIDFALSCKFDIPKGERDQIRNELLREFGLSHVLKTIVGNDFFRGVSGGERKRI SIIETFIANGSVYLWDNSTKGLDSATALDFLEILRKMAKATRSVNLVRISQASDKIVDKF DKILMLSDSYQLFYGTVDECLTYFRDTLGIEKDPNDCIIEYLTSILNFQFKNKNLGNLSN SSSASVLKTATGEVTKYTYNSDFDLYDQWKHSSYYRNIKQQIQGSSIDDSIKEVDPSDVS PIFNIPLKKQLLFCTKRAFQRSLGDKAYMTAQFISVVIQSLVIGSLFYEIPLTTIGSYSR GSLTFFSILFFTFLSLADMPIAFQRQPVVKKQSQLHFYTNWVETLSTTVFDYCFKLCLVI VFSIILYFLAHLQYKAARFFIFLLFLSFYNFCMVSLFALTTLVAPTISVANLFAGILLLA IAMYASYVIYLKNMHPWFVWIAYLNPAMYAMEAILSNELYNLKLDCSETIVPRGPTYNDV PFSHKACAWQGATLGNDYVRGRDYLKQGLSYTYHHVWRNFGIIIGFLVFFIACTLFASQY IKPYFNKDEIERNNSRLTRWLPFLNKKRGTRSSARNDSKYVGIPKSHSVSSSSSSLSAVP YQISPSNKEMALNDYNEQPITETVETQKHIISWKNINYTVGTKKLINNASGFISSGLTAL MGESGAGKTTLLNVLSQRVETGVVSGEILIDGHPLTDEDAFKRSIGFVQQQDLHLDLLSV KESLEISCLLRGDGDRAYLDTVSNLLKLPSDILVADLNPTQRKLLSIGVELVTKPSLLLF LDEPTSGLDAEAALTIVKFLKQLSLQGQAIFCTIHQPSKSVISHFDNIFLLKRGGECVFF GPMDDACGYFMSHDNTLVYDKEHDNPADFVIDAVGNSNSSAGKDTAEEALTLNKEAIDWS ALWESSVEKKLVKKETARLEDDARASGVDYTTSLWKQPSYLQQLALITRRQYICTKRDMT YVMAKYCLNGGAGLFIGFSFWHIKHNIIGLQDSIFFCFMALCVSSPLINQIQDKALKTKE VYVAREARSNTYHWTVLLLSQSIIELPLALTSSTLFFVCAFFSCGFNNAGWSAGVFFLNY MLFAAYYSTLGLWLIYTAPNLQTAAVFVAFIYSFTASFCGVMQPYSLFPTFWKFMYRVSP YTYFVETFVSILLHNWEIKCDMSEMVPGQPLTGQSCGQFMEAFIEEYGGYLHNKNTFTVC AYCTYTVGDDFLKNENMSYDHVWRNFGIEWAFVGFNFFAMFAGYYLTYVARIWPKVFKII TKVIPHRGKKPVQN
This database gave
general information regarding the sequence of the AUS1 protein (See below). You
can click on the link to view the protein sequence.
|
|||||||||||||||||||||||||||||
TRIPLES:
(TRIPLES,
2002, <http://ygac.med.yale.edu/triples/triples.htm>)
TRIPLES found no data on
AUS1.
The
Grid: (The Grid, 2002, <http://biodata.mshri.on.ca/grid/index.html>)
This database showed that
YOR011W (AUS1) is an ABC transporter and is located in the membrane.
In addition, the database showed that AUS1 is associated with YIR009W.
This protein is involved in mRNA splicing in the snRNP U2. More information can be found by clicking on the links below.
|
Orf |
Gene/s |
Description |
GO
Annotations |
Links |
||
|
Function |
Process |
Component |
||||
|
YOR011W
|
·
AUS1 |
ABC
ATP-binding cassette protein involved in Uptake of Sterols |
·
membrane
|
|
||
|
Orf |
Gene/s |
Description |
GO
Annotations |
System |
Source/s |
Pubmed |
Links |
||
|
Function |
Process |
Component |
|||||||
|
involved
in splicing |
Two
Hybrid |
MIPS |
|
|
|||||
DIP
(Database of Interacting Proteins): (DIP, 2001, <http://dip.doe-mbi.ucla.edu/dip/Search.cgi?SM=3>)
This database show the interaction of AUS1 with YIR009W.
In this database, YIR009W is referred to
as a “hypthetical protein.” This
is different than in The Grid site, where YIR009W is referred to as MSL1.
|
|
|
|
Protein: ATP-dependent transport protein homolog YOR011w |
|
|
|
|
|
DIP |
Cross
Reference |
Protein
Name/Description |
||||
|
Interaction |
Node |
Links |
PIR |
SWISSPROT |
GENBANK |
|
|
|
--- |
ATP-dependent
transport protein homolog YOR011w |
||||
|
|
hypothetical
protein YIR009w |
|||||
The graph below shows the
interaction of AUS1 (YOR011W) with other proteins. AUS1 is represented by the red dot, in the lower left hand
side of the diagram. YIR009W is
represented by the dot that is directly in the middle.
Figure
courtesy of DIP.
MIPS:
(MIPS, 2002. <http://mips.gsf.de/proj/yeast/CYGD/db/index.html>)
This database revealed that
AUS1 is similar to ABC transport proteins.
This is expected because AUS1 is an ABC transport protein.
YRC
Two-Hybrid Analysis &
Additional
Y2H Results:
Found no results for AUS1.
PDF maps:
Aging,
Membrane,
Degration,
Benno
Figure 1:
No result for AUS1.
Function
Junction: (Function Junction, 2002, < http://genome-www4.stanford.edu/cgi-bin/SGD/functionJunction>)
This database revealed that
AUS1 is associated with proteins that serve as ABC transport proteins as well as
proteins that are associated with RNA synthesis. This is similar to the data
found previously.
In addition, Pathcalling presented the following graph. The graph shows the protein-protein interaction with regards to AUS1. Once again, you can see that AUS1 (YOR011W) is associated with MSL1 (YIR009W).
Figure courtesy of Function Junction
Conclusions:
Although there is not much
information regarding AUS1 in the databases searched, it is apparent that AUS1
indeed codes for a protein that is associated with ABC transport proteins.
In addition, from this search, as well as previous microarray and
literature searches (see website 2 & 3), it seems as though this protein is
associated with replication of DNA in the cell.
SGD:
(SGD, 2002, <http://genome-www.stanford.edu/Saccharomyces/>)
Protein sequence:
>YOR012W Chr 15
MVASSINEESSLAVNLTSDVEKASKTLFKAFEKSYANDYLMKKFFHIPITEKVSRARINA MIHYYTTCYHDLDGEIAEANDFDAVAIWSRPGCHLPATLSDDESFNKIFFSRLDCEEARS HASGNGLLLPLCHRKRS
In addition, this database showed the general characteristics of the protein (See below).
|
Protein
Sequence Calculations |
|
|
N-term |
MVASSIN |
|
C-term |
LCHRKRS |
|
Length(aa) |
137 |
|
MW(Da) |
15,482 |
|
pI |
6.5 |
|
Transcript
Translation Calculations |
|
|
Codon Bias |
0.044 |
|
Codon Adaptation
Index |
0.123 |
|
Frequency of
Optimal Codons |
0.429 |
|
Hydropathicity of
Protein |
-0.310 |
|
Aromaticity Score |
0.102 |
TRIPLES :
(TRIPLES, 2002, <http://ygac.med.yale.edu/triples/triples.htm>)
No data was found for
YOR012W.
The
Grid: (The Grid, 2002, <http://biodata.mshri.on.ca/grid/index.html>)
Returned no data for
YOR012W
DIP:
(Database of Interacting Proteins): (DIP,
2001, <http://dip.doe-mbi.ucla.edu/dip/Search.cgi?SM=3>)
This database did not
provide the names of any proteins that are similar to YOR012W.
In addition, DIP did not provide a protein interaction map for this
protein.
|
|
|||||
|
DIP |
Cross
Reference |
Protein
Name/Description |
|||
|
Node |
Links |
PIR |
SWISSPROT |
GENBANK |
|
|
|
ORF YOR012W |
||||
MIPS:
(MIPS, 2002. <http://mips.gsf.de/proj/yeast/CYGD/db/index.html>)
This database showed that YOR012W is related to YDR391C, which is a hypothetical protein. Since the function of YDR391C is not known, this provides no information regarding the function of YOR012W.
YRC
Two-Hybrid Analysis & Additional
Y2H Results:
Produced no results.
PDF maps: Aging,
Membrane,
Degration,
Benno
Figure 1:
No result for YOR012W.
No information was gained from Function
Junction.
Yale
Gernstein Lab:
(Yale
Gerstein Lab, 2001, < http://bioinfo.mbb.yale.edu/genome/yeast/search.cgi?orf=YOR012W>)
This database stated that
the protein of YOR012W is located in the cytoplasm.
Possible Experiments:
Although this page did not reveal any new information regarding YOR012W, the information that was found on previous pages can be used to hypothesize the function of the protein. Past pages have suggested that YOR012W is associated with DNA replication, specifically either with transcription factors or with DNA repair.
Experiment 1: Proteins involved with transcription factors or with DNA repair are typically located in the nucleus. This contradicts the information found by the Yale Gernstein Lab. This lab found that YOR012W is located in the cytoplasm (see above). Thus, it is important to test to see where the protein is actually located. One way to do this would be to use a fluorescently labeled probe. The probe would contain the complementary sequence of YOR012W, and would move into the cell via a virus or an injection of antibodies. The probe would bind to the YOR012W sequence. After binding, scientists could look at the cell under a microscope and determine where the YOR012W protein is located (in the cytoplasm or the nucleus) by viewing the labeled probe. Thus, the location of YOR012W would be determined.
Although the Gerstein lab believes that YOR012W is found in the cytoplasm, YOR012W typically clusters with genes associated with transcription and DNA repair. Thus, it is likely that this protein is associated with these processes and is found inside the nucleus of the cell. Determining the location of this protein may lead to a better understanding of its function.
Experiment
2:
The microarray website showed that YOR012W is associated with either
transcription or DNA repair. In order to determine which process it is associated with, an
experiment that involves a modified version of the bar code method by Winzeler
(Campbell & Heyer, 166) could be used. In this method, the YOR012W
gene is deleted and then replaced by a specific marker. This marker will
be easily identifiable, and will function as a sort of bar code later in the
experiment. Other bar coded mutants will also be created.
These mutants will lack proteins that are known to be associated with
replication, such as transcription factors and DNA repair proteins. The
mutants would then be spotted out on a microarray chip.
References:
Campbell, AM and Heyer, LJ. Genomics, Proteomics, & Bioinformatics 2003. San Francisco, CA: Pearson Education, Inc.
Database
of Interacting Proteins (DIP), 2001, <http://dip.doe-mbi.ucla.edu/dip/Search.cgi?SM=3>
Accessed 11/11/02
Function
Junction, 2002, < http://genome-www4.stanford.edu/cgi-bin/SGD/functionJunction>
Accessed 11/15/02
MIPS Comprehensive Yeast Genome Database (CYGD),
2002, <http://mips.gsf.de/proj/yeast/CYGD/db/index.html>
Saccharomyces Genome
Database (SGD), 2002, <http://genome-www.stanford.edu/Saccharomyces/>
Accessed 11/13/02
Schwikowski,
Benno; Uetz, Fields. 2000. A
network of protein-protein interactions in yeast. Nature Biotechnology.
18:1257-1261. (PDF files)
The
Grid, 2002, <http://biodata.mshri.on.ca/grid/index.html>.
Accessed 11/14/02
TRIPLES,
2002, <http://ygac.med.yale.edu/triples/triples.htm>.
Accessed 11/11/02
Yale
Gerstein Lab, , 2001, < http://bioinfo.mbb.yale.edu/genome/yeast/search.cgi?orf=YOR012W>
Accessed 11/15/02
YRC
Two-Hybrid Analysis, 2000, <http://depts.washington.edu/%7Eyeastrc/th_11.htm>
Accessed 11/11/02.
YRC
Two-Hybrid Analysis’ Additional YRH Results, 2000, <http://depts.washington.edu/%7Eyeastrc/th_12.htm>
Accessed 11/11/02
Return To Biology Course Materials
Davidson College Biology Department
