SBC logo Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred

Fetching Q01631 from www.uniprot.org...

The NucPred score for your sequence is 0.92 (see score help below)

   1  MTRNDGGSRYSSIDSAQSSITAKPFPLTPTSSLGSSMTRPLSPSLQAGSS    50
51 SSNGGHNVSRSASQGARRPAPTRLKTDDGTQFASRSSRDFESSQSQSQPS 100
101 HTQTRSHSLSQATLQSCSQPQLSLNSQQSQSPSQYHSQQTPTQQQPQQQV 150
151 SPTGGSRLTQSPTTPSNASIREHRMSELGGYRREMAAMLDTTGGALSRTS 200
201 SHSQQQPQQPQQQQQQQQQQQGHAAGSVSGTFSNLSQYAPYLGGNNGGGM 250
251 SMGSFLNDSTDNLSVISQLSPGIRPMTARPSQASAGSMEFPDSAYYDDER 300
301 RPSIASITTTASSQGSRTSKTRGGLQKLQQFFGDRDDWPGRDSSEISLPQ 350
351 PSHSGPMSTGKEHRSHSYSLPGSGRSHRDRNYSNATDHHPSTFGSVSTVG 400
401 GRDRDASPVPSRPRTPVPAPEVVPFLYQEADDIARYGEAPVRTSLTGPDR 450
451 DRYIDSSQNPPKTSSSARSGHSIVHLPGHHKHNKSNEDPRALKPSLSRED 500
501 SAASFARDFRNGSSSMMGTRSRAQSPAPSWTGTSRGLKANSISDGTSSPA 550
551 PSHKKGILGRFRRHNKDKEDGSSLRSGSNHTLVHRPSRQDLTRAAESTYP 600
601 ASVYVSDPSEQREVPVRPGYVRQTTAPGFTTKLFTSKKSSSAKQPQDDMD 650
651 EDIGPTDMHMGGGTVYHLDTNLNDMEGILTKPQPMTPLDNSISMRRESEK 700
701 MIVPITTDPEGAWAAPDSWAVRDNKKSLAPQVNEDLCSRQPSEEKEKKSN 750
751 YYIRVFRSDSTWTTLTLPLTATAEDVIMGVAKKTYLPPGAQDSYSLLIKK 800
801 HDLFRVLNSAEQPLRIQKRLFQQIGYQEKDGIDEIGREDNSYICRWVFLK 850
851 EKEADMHLLSPDINFRNQKLNHVDLSGRNLITIPVPLYRKAAEIVSLNLS 900
901 RNLSLDVPRDFIQACTALRDIKYNNNEAQALPKSFATASKLTYLDVSNNR 950
951 LQDLDHSELSKLTGLLKLNLANNCLRSLPPTLGAYKSLRTLNISSNFLDV 1000
1001 FPSFICELETIVDLDLSFNSINNLPDNLMKLRNLEKFVITNNRLSGPISE 1050
1051 SVRDLVSLRELDIRYNQISTIDVLSDLPRLEILSADHNQISKFSGSFERL 1100
1101 RSLKLNSNPIVKFEVKAPVPTLKILNLSNAQLASIDESIDNLMNLERLIL 1150
1151 DSNYFVSLPNQIGNLKKLDHLSMANNHLGELPPEIGCLTELRTLDVHGNN 1200
1201 MRKLPNEIWWANKLEHLNASSNILTEFPKPASRAPQAPGEASPSPGAYPF 1250
1251 PNANKNGLLSRTPSMDDLNGDASRRPSQASSTLLGVAVSPVPSGPDNRKS 1300
1301 SMVSLYGKGGRKTSVVSRSTTQSSTGVITPSNGPRKDSSLSYRFTHTFSG 1350
1351 SLKNLYLADNQLDDDVFEELKHLPELRVLNLSCNDLSDMPQGTIRSWPQL 1400
1401 VELYLSGNELTSLPAEDFLEEHCLLQTLHINGNKFINLPAEISRAKKLQV 1450
1451 LDCSSNNLKYNVTNVPYDWNWNFNRDLRYLNLSGNKRLEIKNNYRQPQSY 1500
1501 RDDDFADTDFSKLTNLRVLGLMEVTHTLPNIPDQTEDRRVRTSEMKAGAY 1550
1551 LPYGMADTLGKNEHLSLFDLVVPRLGSVETDTLVALFDGKELSTGGSKIA 1600
1601 KFLYEEFSRLFILELEKVKGKPNENPADALRRTFLSVNKLLMSLSNSADE 1650
1651 RGLDSHPSRNYAHTVLTKEDLNSGCVATVAYLSELKLYVANVGDVQGMLI 1700
1701 QANGSFKMLTKKHDPADPVERSRIRNAGGWVSRNGRLNDVLNVSRAFGYT 1750
1751 ELLPAVQAAPDITEHTIDDKDETVLIASKELWEHLRPELIVDVARECRSD 1800
1801 LMKASQKLRDLAIAYGSTNKLLIMMIGVANLKQRQAQQFKGQLNATFSMP 1850
1851 QDDPSHVPPSGNKRRKVRAEGPLDSNLMRLNAEVPPPTGQLSIVFTDIKN 1900
1901 STQLWENYPEAMRLAIKLHNEVMRRQLRMIGGFEVKTEGDAFMVSFPTAT 1950
1951 SALLWCFAVQMKLLTVDWPPEVLSNSSCQPIYDRNNNLITRGLSVRMGAH 2000
2001 WGEPLAERDPVTRRMDYYGPMVNKASRISAVADGGQITASSDFITEIHRC 2050
2051 LETYKESVDVDEDSLEDDATAKAIRAELRALSSQGFEVKDMGEKKLKGLE 2100
2101 NPELVYSVYPHALVGRTEQHHAHTESTQNQAALQPYGALATPKPATMDPD 2150
2151 SEIQFEPETIWALWRVALRLEMLCSTLEEPNARGLQAPETELLERMKQRA 2200
2201 GEVTDHFLLNFMEHQISRIETCITSLAVRHIAIGSGPITKLNDLRAPMND 2250
2251 VLSTLKEQMDELARYKAKYGSLDQAETDDATDNNSSGDVDTLDGSDTEQE 2300

Positively and negatively influencing subsequences are coloured according to the following scale:

(non-nuclear) negative ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| positive (nuclear)

with NucPred



If you find NucPred useful, please cite this paper:
NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022
The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold Specificity Sensitivity
see above fraction of proteins predicted to be nuclear that actually are nuclear fraction of true nuclear proteins that are predicted (coverage)
0.10 0.45 0.88
0.20 0.52 0.83
0.30 0.57 0.77
0.40 0.63 0.69
0.50 0.70 0.62
0.60 0.71 0.53
0.70 0.81 0.44
0.80 0.84 0.32
0.90 0.88 0.21
1.00 1.00 0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

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