SPPS : Sequence-based Protein Partner Search  
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Example 1

BRMS1, which suppresses metastasis without blocking tumorigenesis in multiple human and murine carcinomas, is a predominantly nuclear protein that has two coiled-coil domains which are suggested to maintain multiple protein-protein interactions.

Step 1. Go to http://www.expasy.org/uniprot/BRMS1_HUMAN, copy BRMS1 sequence in FASTA format from ‘Sequence information Frame’.

>BRSM1_HUMAN
MPVQPPSKDTEEMEAEGDSAAEMNGEEEESEEERSGSQTESEEESSEMDD
EDYERRRSECVSEMLDLEKQFSELKEKLFRERLSQLRLRLEEVGAERAPE
YTEPLGGLQRSLKIRIQVAGIYKGFCLDVIRNKYECELQGAKQHLESEKL
LLYDTLQGELQERIQRLEEDRQSLDLSSEWWDDKLHARGSSRSWDSLPPS
KRKKAPLVSGPYIVYMLQEIDILEDWTAIKKARAAVSPQKRKSDG

Step 2. Go to http://www.dddc.ac.cn/spps/query1.php, register and paste the sequence into ‘Sequence’ Frame.

Step 3. Choose the database as ‘Human Being’

Step 4. Submit the job and you will get e-mail containing job_id. When job is finished, the output is delivered in descending order of probability score (interaction probability), which is sent to registered email address of users as well as achieved as a copy for further possible analysis.

[The following steps are optional]

Step 5. Check the status of job by ‘Job queue status’ in the status bar.

Step 6. Analyze your job in the ‘Result’ Module after the job was finished. Logged in and inputted your job_id followed by clicking ‘Get your result’, an empty table is showed (‘Probability Match’ over 0.9 is default). Input 1 and 0.8 as boundary of ‘Probability Match’ (Click ‘Excute’ button), the BRMS1 partner hits are listed and the most probable Protein partners network from BRMS1 is available (Java virtual machine is needed). Input ‘BRMS1_HUMAN’ into the ‘Known Interaction Match’, partners, which were experimental validated until last our server update, are labeled. In the case, these are HDAC1_HUMAN and HDAC2_HUMAN.

Example2

Step 1. Go to http://www.expasy.org/uniprot/BIN1_HUMAN, copy BIN1 sequence in FASTA format from ‘Sequence information Frame’.

>BIN1_HUMAN
MAEMGSKGVTAGKIASNVQKKLTRAQEKVLQKLGKADETKDEQFEQCVQN
FNKQLTEGTRLQKDLRTYLASVKAMHEASKKLNECLQEVYEPDWPGRDEA
NKIAENNDLLWMDYHQKLVDQALLTMDTYLGQFPDIKSRIAKRGRKLVDY
DSARHHYESLQTAKKKDEAKIAKPVSLLEKAAPQWCQGKLQAHLVAQTNL
LRNQAEEELIKAQKVFEEMNVDLQEELPSLWNSRVGFYVNTFQSIAGLEE
NFHKEMSKLNQNLNDVLVGLEKQHGSNTFTVKAQPSDNAPAKGNKSPSPP
DGSPAATPEIRVNHEPEPAGGATPGATLPKSPSQLRKGPPVPPPPKHTPS
KEVKQEQILSLFEDTFVPEISVTTPSQFEAPGPFSEQASLLDLDFDPLPP
VTSPVKAPTPSGQSIPWDLWEPTESPAGSLPSGEPSAAEGTFAVSWPSQT
AEPGPAQPAEASEVAGGTQPAAGAQEPGETAASEAASSSLPAVVVETFPA
TVNGTVEGGSGAGRLDLPPGFMFKVQAQHDYTATDTDELQLKAGDVVLVI
PFQNPEEQDEGWLMGVKESDWNQHKELEKCRGVFPENFTERVP

Step 2. Go to http://www.dddc.ac.cn/spps/query2.php, register and paste the sequence into ‘Sequence 1’ Frame.

Step 3. Go to http://www.expasy.org/uniprot/DLGP4_HUMAN, copy BIN1 sequence in FASTA format from ‘Sequence information Frame’.

>DLGP4_HUMAN
MKGLGDSRPRHLSDSLDPPHEPLFAGTDRNPYLLSPTEAFAREARFPGQN
TLPGDGLFPLNNQLPPPSSTFPRIHYNSHFEVPEESPFPSHAQATKINRL
PANLLDQFEKQLPIHRDGFSTLQFPRGEAKARGESPGRIRHLVHSVQRLF
FTKAPSLEGTAGKVGGNGSKKGGMEDGKGRRAKSKERAKAGEPKRRSRSN
ISGWWSSDDNLDGEAGAFRSSGPASGLMTLGRQAERSQPRYFMHAYNTIS
GHMLKTTKNNTTELTAPPPPPAPPATCPSLGVGTDTNYVKRGSWSTLTLS
HAHEVCQKTSATLDKSLLKSKSCHQGLAYHYLQVPGGGGEWSTTLLSPRE
TDAAAEGPIPCRRMRSGSYIKAMGDEDSDESGGSPKPSPKTAARRQSYLR
ATQQSLGEQSNPRRSLDRLDSVDMLLPSKCPSWEEDYTPVSDSLNDSSCI
SQIFGQASLIPQLFGHEQQVREAELSDQYEAACESACSEAESTAAETLDL
PLPSYFRSRSHSYLRAIQAGCSQEEDSVSLQSLSPPPSTGSLSNSRTLPS
SSCLVAYKKTPPPVPPRTTSKPFISVTVQSSTESAQDTYLDSQDHKSEVT
SQSGLSNSSDSLDSSTRPPSVTRGGVAPAPEAPEPPPKHAALKSEQGTLT
SSESHPEAAPKRKLSSIGIQERTRRNGSHLSEDNGPKAIDVMAPSSESSV
PSHSMSSRRDTDSDTQDANDSSCKSSERSLPDCTPHPNSISIDAGPRQAP
KIAQIKRNLSYGDNSDPALEASSLPPPDPWLETSSSSPAEPAQPGACRRD
GYWFLKLLQAETERLEGWCCQMDKETKENNLSEEVLGKVLSAVGSAQLLM
SQKFQQFRGLCEQNLNPDANPRPTAQDLAGFWDLLQLSIEDISMKFDELY
HLKANSWQLVETPEKRKEEKKPPPPVPKKPAKSKPAVSRDKASDASDKQR
QEARKRLLAAKRAASVRQNSATESADSIEIYVPEAQTR

Step 4. Go to http://www.dddc.ac.cn/spps/query2.php, paste the sequence into ‘Sequence 2’ Frame

Step 5. Choose the database as ‘Human Being’.

Step 6. Submit the job and you will get e-mail containing job_id. When job is finished, the output is delivered with probability score (interaction probability), which is sent to registered email address of users.

 

Statistics
Human Protein Entries 19,331
  Protein-Protein Interactions 16,443
  Accuracy(%) 83.9
     
C.elegans Protein Entries 2,860
  Protein-Protein Interactions 4,011
  Accuracy(%) 76.0
     
Drosophila Protein Entries 2,388
  Protein-Protein Interactions 21,999
  Accuracy(%) 78.1
     
Yeast Protein Entries 15,213
  Protein-Protein Interactions 15,517
  Accuracy(%) 81.8

News
  • 2006.5 SPPS launched
  • 2006.5 SPPS Database Updated
  • 2006.6 Human Model was added
  • 2006.8 Drosophila Model was added
  • 2006.9 C.elegans Model was added
  • 2006.11 Yeast Model was added
  • 2006.12 Database Updated
  • 2007.1 Indirect Interaction was added
  •  

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