SDPpred: a tool for prediction of amino acid residues that determine differences in functional specificity of homologous proteins

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Version 1.0

This is the first release of the program. If you observe a bug or suspicious behavior, or get a nonsense result, please send us a note, containing the query alignment and the parameters you've used. Thank you.

FASTA alignment format


This is a common alignment format derived from the FASTA sequence format. The FASTA alignment format is a set of sequences with dashes indicating gaps. The name of each sequence should be placed on a separate line and begin with >. The sequence starts in the next line and may be broken into several lines. Thus the alignment looks like this:

>EC_RbsR
-------------------------MATMKDVARLAGVSTSTVSHVINKD---RFVSEAI
TAKVEAAIKELNYAP---SALARSLKLNQTHTIGMLITASTN-----PFYSELVRGVERS
CFERGYSLVLCNTEGD-EQRMNRNLETLMQK-RVDGLLLLCTETHQPSREIMQRYPTVPT
--VMMDW--APFDGDSDLIQDNSLLGGDLATQYLIDKGHTR-IACITG-PLDKTPARLR-
-----LEGYRAAMKRAGLNIPDGYEVTG---DFEFNGGFDAMRQLLSHP--LRPQAVFTG
NDAMAVGVYQALYQAE-LQVPQDIAVIGYDDIE---LASFMTPPLTTIHQPKDELGELAI
DVLIHRITQPT------LQQQRLQLTPILMERGSA------------------------
>Pp_RbsR
-------------------------MATIKDVAALAGISYTTVSHVLNKT---RPVSEQV
RLKVEAAIIELDYVP---SAVARSLKARSTATIGLLVPNSVN-----PYFAELARGIEDA
CERNGYCVILCNSDDN-PQKQRSYLRVLLEK-RIDGLVVASVGQDD---DLLQSLASVRT
PMVIVDR--ELEGVDADLVRIDHEQGAYLATRHLLELGHRD-VAYIGG-PAETGVTQLR-
-----LSGFRRAMAEAGAPVPGSRVLHC---DFTSPGGHAAAAQVLEG---KRPSAIFAG
NDMIGFGVLRAAAERN-ISVPGELSVIGFDDIE---LSRYVYPSLTTVGQSIRELGESAA
SLLLTRIATPRQG----AAEQRIVAPRIVLRESTGPRPDLFNDY---------------
>BS_RbsR
-------------------------MATIKDVAGAAGVSVATVSRNLNDN---GYVHEET
RTRVIAAMAKLNYYP---NEVARSLYKRESRLIGLLLPDITN-----PFFPQLARGAEDE
LNREGYRLIFGNSDEE-LKKELEYLQTFKQN-HVAGIIAAT------NYPDLEEYSGMNY
PVVFLDR--TLEG-APSVSS-DGYTGVKLAAQAIIHGKSQR-ITLLRG-PAHLPTAQDR-
-----FNGALEILKQA--EVDFQVIETA---SFSIKDAQSMAKELFASY--PATDGVIAS
NDIQAAAVLHEALRRG-KNVPEDIQIIGYDDIP---QSGLLFPPLSTIKQPAYDMGKEAA
KLLLGIIKKQP------LAETAIQMPVTYIGRKTTRKED--------------------
>SACR_LACLA
-------------------------MIKLEDVANKAGVSVTTVSRVINRK---GYLSDAT
ISKVEKAMQDLHYIP---NAAARSLQGKSLKLIGLVFPTIKN-----IFYAELIEKIEQA
LFIRGYKAMLATTEHD-EQKERDYLALLLSN-QVDGIIYGS------HNLKAHDYIAIEA
PIVAFDR--LLTP-ETTVVSSDNFEGGILATKALINSGSKK-IAIFTGNDNTNSPTYLR-
-----RDGYLLELERN--QLKTHIIKIP---SQWTLLRKKVEIKKILEN--NDFDGVFCT
DDLTAILVKDLAS-----NLKKSLNVVGFDGTE---FIENYYPNLTTIKQPINDLAELLV
DLIIRKIDGD-------NIDITYQLPVQLHYGID-------------------------


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