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

NucPred

Fetching P32600 from www.uniprot.org...

The NucPred score for your sequence is 0.86 (see score help below)

   1  MNKYINKYTTPPNLLSLRQRAEGKHRTRKKLTHKSHSHDDEMSTTSNTDS    50
  51  NHNGPNDSGRVITGSAGHIGKISFVDSELDTTFSTLNLIFDKLKSDVPQE   100
 101  RASGANELSTTLTSLAREVSAEQFQRFSNSLNNKIFELIHGFTSSEKIGG   150
 151  ILAVDTLISFYLSTEELPNQTSRLANYLRVLIPSSDIEVMRLAANTLGRL   200
 201  TVPGGTLTSDFVEFEVRTCIDWLTLTADNNSSSSKLEYRRHAALLIIKAL   250
 251  ADNSPYLLYPYVNSILDNIWVPLRDAKLIIRLDAAVALGKCLTIIQDRDP   300
 301  ALGKQWFQRLFQGCTHGLSLNTNDSVHATLLVFRELLSLKAPYLRDKYDD   350
 351  IYKSTMKYKEYKFDVIRREVYAILPLLAAFDPAIFTKKYLDRIMVHYLRY   400
 401  LKNIDMNAANNSDKPFILVSIGDIAFEVGSSISPYMTLILDNIREGLRTK   450
 451  FKVRKQFEKDLFYCIGKLACALGPAFAKHLNKDLLNLMLNCPMSDHMQET   500
 501  LMILNEKIPSLESTVNSRILNLLSISLSGEKFIQSNQYDFNNQFSIEKAR   550
 551  KSRNQSFMKKTGESNDDITDAQILIQCFKMLQLIHHQYSLTEFVRLITIS   600
 601  YIEHEDSSVRKLAALTSCDLFIKDDICKQTSVHALHSVSEVLSKLLMIAI   650
 651  TDPVAEIRLEILQHLGSNFDPQLAQPDNLRLLFMALNDEIFGIQLEAIKI   700
 701  IGRLSSVNPAYVVPSLRKTLLELLTQLKFSNMPKKKEESATLLCTLINSS   750
 751  DEVAKPYIDPILDVILPKCQDASSAVASTALKVLGELSVVGGKEMTRYLK   800
 801  ELMPLIINTFQDQSNSFKRDAALTTLGQLAASSGYVVGPLLDYPELLGIL   850
 851  INILKTENNPHIRRGTVRLIGILGALDPYKHREIEVTSNSKSSVEQNAPS   900
 901  IDIALLMQGVSPSNDEYYPTVVIHNLMKILNDPSLSIHHTAAIQAIMHIF   950
 951  QNLGLRCVSFLDQIIPGIILVMRSCPPSQLDFYFQQLGSLISIVKQHIRP  1000
1001  HVEKIYGVIREFFPIIKLQITIISVIESISKALEGEFKRFVPETLTFFLD  1050
1051  ILENDQSNKRIVPIRILKSLVTFGPNLEDYSHLIMPIVVRMTEYSAGSLK  1100
1101  KISIITLGRLAKNINLSEMSSRIVQALVRILNNGDRELTKATMNTLSLLL  1150
1151  LQLGTDFVVFVPVINKALLRNRIQHSVYDQLVNKLLNNECLPTNIIFDKE  1200
1201  NEVPERKNYEDEMQVTKLPVNQNILKNAWYCSQQKTKEDWQEWIRRLSIQ  1250
1251  LLKESPSACLRSCSSLVSVYYPLARELFNASFSSCWVELQTSYQEDLIQA  1300
1301  LCKALSSSENPPEIYQMLLNLVEFMEHDDKPLPIPIHTLGKYAQKCHAFA  1350
1351  KALHYKEVEFLEEPKNSTIEALISINNQLHQTDSAIGILKHAQQHNELQL  1400
1401  KETWYEKLQRWEDALAAYNEKEAAGEDSVEVMMGKLRSLYALGEWEELSK  1450
1451  LASEKWGTAKPEVKKAMAPLAAGAAWGLEQWDEIAQYTSVMKSQSPDKEF  1500
1501  YDAILCLHRNNFKKAEVHIFNARDLLVTELSALVNESYNRAYNVVVRAQI  1550
1551  IAELEEIIKYKKLPQNSDKRLTMRETWNTRLLGCQKNIDVWQRILRVRSL  1600
1601  VIKPKEDAQVRIKFANLCRKSGRMALAKKVLNTLLEETDDPDHPNTAKAS  1650
1651  PPVVYAQLKYLWATGLQDEALKQLINFTSRMAHDLGLDPNNMIAQSVPQQ  1700
1701  SKRVPRHVEDYTKLLARCFLKQGEWRVCLQPKWRLSNPDSILGSYLLATH  1750
1751  FDNTWYKAWHNWALANFEVISMLTSVSKKKQEGSDASSVTDINEFDNGMI  1800
1801  GVNTFDAKEVHYSSNLIHRHVIPAIKGFFHSISLSESSSLQDALRLLTLW  1850
1851  FTFGGIPEATQAMHEGFNLIQIGTWLEVLPQLISRIHQPNQIVSRSLLSL  1900
1901  LSDLGKAHPQALVYPLMVAIKSESLSRQKAALSIIEKMRIHSPVLVDQAE  1950
1951  LVSHELIRMAVLWHEQWYEGLDDASRQFFGEHNTEKMFAALEPLYEMLKR  2000
2001  GPETLREISFQNSFGRDLNDAYEWLMNYKKSKDVSNLNQAWDIYYNVFRK  2050
2051  IGKQLPQLQTLELQHVSPKLLSAHDLELAVPGTRASGGKPIVKISKFEPV  2100
2101  FSVISSKQRPRKFCIKGSDGKDYKYVLKGHEDIRQDSLVMQLFGLVNTLL  2150
2151  QNDAECFRRHLDIQQYPAIPLSPKSGLLGWVPNSDTFHVLIREHREAKKI  2200
2201  PLNIEHWVMLQMAPDYDNLTLLQKVEVFTYALNNTEGQDLYKVLWLKSRS  2250
2251  SETWLERRTTYTRSLAVMSMTGYILGLGDRHPSNLMLDRITGKVIHIDFG  2300
2301  DCFEAAILREKFPEKVPFRLTRMLTYAMEVSGIEGSFRITCENVMKVLRD  2350
2351  NKGSLMAILEAFAFDPLINWGFDLPTKKIEEETGIQLPVMNANELLSNGA  2400
2401  ITEEEVQRVENEHKNAIRNARAMLVLKRITDKLTGNDIRRFNDLDVPEQV  2450
2451  DKLIQQATSVENLCQHYIGWCPFW                            2474

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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