SPPS @ DDDC

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.