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

NucPred

Fetching Q01815 from www.uniprot.org...

The NucPred score for your sequence is 0.79 (see score help below)

   1  MVNENTRMYVPEENHQGSNYGSPRPAHANMNANAAAGLAPEHIPTPGAAL    50
  51  SWQAAIDAARQAKLMGSAGNATISTVSSTQRKRQQYGKPKKQGGTTATRP   100
 101  PRALLCLTLKNPIRRACISIVEWKPFEIIILLTIFANCVALAIYIPFPED   150
 151  DSNATNSNLERVEYLFLIIFTVEAFLKVIAYGLLFHPNAYLRNGWNLLDF   200
 201  IIVVVGLFSAILEQATKADGANALGGKGAGFDVKALRAFRVLRPLRLVSG   250
 251  VPSLQVVLNSIIKAMVPLLHIALLVLFVIIIYAIIGLELFMGKMHKTCYN   300
 301  QEGIIDVPAEEDPSPCALETGHGRQCQNGTVCKPGWDGPKHGITNFDNFA   350
 351  FAMLTVFQCITMEGWTDVLYWMQDAMGYELPWVYFVSLVIFGSFFVLNLV   400
 401  LGVLSGEFSKEREKAKARGDFQKLREKQQLEEDLKGYLDWITQAEDIDPE   450
 451  NEDEGMDEDKPRNMSMPTSETESVNTENVAGGDIEGENCGARLAHRISKS   500
 501  KFSRYWRRWNRFCRRKCRAAVKSNVFYWLVIFLVFLNTLTIASEHYNQPH   550
 551  WLTEVQDTANKALLALFTAEMLLKMYSLGLQAYFVSLFNRFDCFIVCGGI   600
 601  LETILVETKIMSPLGISVLRCVRLLRIFKITRYWNSLSNLVASLLNSVRS   650
 651  IASLLLLLFLFIIIFSLLGMQLFGGKFNFDEMQTRRSTFDNFPQSLLTVF   700
 701  QILTGEDWNSVMYDGIMAYGGPSFPGMLVCIYFIILFICGNYILLNVFLA   750
 751  IAVDNLADAESLTSAQKEEEEEKERKKLARTASPEKKQEVMEKPAVEESK   800
 801  EEKIELKSITADGESPPTTKINMDDLQPSENEDKSPHSNPDTAGEEDEEE   850
 851  PEMPVGPRPRPLSELHLKEKAVPMPEASAFFIFSPNNRFRLQCHRIVNDT   900
 901  IFTNLILFFILLSSISLAAEDPVQHTSFRNHILGNADYVFTSIFTLEIIL   950
 951  KMTAYGAFLHKGSFCRNYFNILDLLVVSVSLISFGIQSSAINVVKILRVL  1000
1001  RVLRPLRAINRAKGLKHVVQCVFVAIRTIGNIVIVTTLLQFMFACIGVQL  1050
1051  FKGKLYTCSDSSKQTEAECKGNYITYKDGEVDHPIIQPRSWENSKFDFDN  1100
1101  VLAAMMALFTVSTFEGWPELLYRSIDSHTEDKGPIYNYRVEISIFFIIYI  1150
1151  IIIAFFMMNIFVGFVIVTFQEQGEQEYKNCELDKNQRQCVEYALKARPLR  1200
1201  RYIPKNQHQYKVWYVVNSTYFEYLMFVLILLNTICLAMQHYGQSCLFKIA  1250
1251  MNILNMLFTGLFTVEMILKLIAFKPKGYFSDPWNVFDFLIVIGSIIDVIL  1300
1301  SETNPAEHTQCSPSMSAEENSRISITFFRLFRVMRLVKLLSRGEGIRTLL  1350
1351  WTFIKSFQALPYVALLIVMLFFIYAVIGMQVFGKIALNDTTEINRNNNFQ  1400
1401  TFPQAVLLLFRCATGEAWQDIMLACMPGKKCAPESEPSNSTEGETPCGSS  1450
1451  FAVFYFISFYMLCAFLIINLFVAVIMDNFDYLTRDWSILGPHHLDEFKRI  1500
1501  WAEYDPEAKGRIKHLDVVTLLRRIQPPLGFGKLCPHRVACKRLVSMNMPL  1550
1551  NSDGTVMFNATLFALVRTALRIKTEGNLEQANEELRAIIKKIWKRTSMKL  1600
1601  LDQVVPPAGDDEVTVGKFYATFLIQEYFRKFKKRKEQGLVGKPSQRNALS  1650
1651  LQAGLRTLHDIGPEIRRAISGDLTAEEELDKAMKEAVSAASEDDIFRRAG  1700
1701  GLFGNHVTYYQSDSRGNFPQTFATQRPLHINKTGNNQADTESPSHEKLVD  1750
1751  STFTPSSYSSTGSNANINNANNTALGRFPHPAGYSSTVSTVEGHGPPLSP  1800
1801  AVRVQEAAWKLSSKRCHSRESQGATVNQEIFPDETRSVRMSEEAEYCSEP  1850
1851  SLLSTDMFSYQEDEHRQLTCPEEDKREIQPSPKRSFLRSASLGRRASFHL  1900
1901  ECLKRQKDQGGDISQKTALPLHLVHHQALAVAGLSPLLQRSHSPTTFPRP  1950
1951  CPTPPVTPGSRGRPLRPIPTLRLEGAESSEKLNSSFPSIHCSSWSEETTA  2000
2001  CSGSSSMARRARPVSLTVPSQAGAPGRQFHGSASSLVEAVLISEGLGQFA  2050
2051  QDPKFIEVTTQELADACDMTIEEMENAADNILSGGAQQSPNGTLLPFVNC  2100
2101  RDPGQDRAVAPEDESCAYALGRGRSEEALADSRSYVSNL             2139

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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