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

NucPred

Fetching Q99PP2 from www.uniprot.org...

The NucPred score for your sequence is 1.00 (see score help below)

   1  MYRSGSRSSVSSHRSKDGSASGPPPGRPVGASSGPTRRPSSPPPPSCSSL    50
  51  RLPARRHRSPSGHRGRWASPSPPRGRRGSPSPPRGRRASPSPTRGRRASP   100
 101  SPPRGRRGSPSPPRARRGSPSPPRSRRHYPPGLGGFRGSIRGESRADFAR   150
 151  DGRGDHPGGGGGSRRRSPGLCSDSSLEESLRITVGNDHFCVSTPERRRLS   200
 201  DRLGSPVDGLQDMDRDDLTDDSVFTRSSQCSRGLERYISREEGPLSPFLG   250
 251  QLDEDYRTRETFLHRPEFSPQSSCHDELLRGTERNRDKLKSSSYSIRSEE   300
 301  RSREAKRPRYDDTEKVHSSGGDHSSFTSGTRNYRQRRSSPSPRFLDPEFR   350
 351  ELDLARRKREEEEEQSRSLSQELVGVGDDQIGCSIPGLAGVLTTSEPGYS   400
 401  LQRPEEVPMMPKKSILKKRIEADMKPSLQLESFSSGASSGEDHPLYSEHS   450
 451  PLPLSGAIAAFTSEIENKGTTVEADLKEPQSNLYQWGPLREIPKDNSEKF   500
 501  DSFLGFKEKLDLKAEGLEQQTDFLLPHERASQDGSGFSRILSMLADPTIT   550
 551  QEKRRRSFPDIEDEEKFLYGDEEEDIKSESPLKSLEDPESAGTRQKANSL   600
 601  PSTPAVKLESLEESNPEYAKIHNLLKTIGLDIGVAEIGKLAARTQERLHG   650
 651  KKPSSRPSADRRLSADRHLSGDRHFSADRCSSVEHSFTADWRSSDPHRPE   700
 701  SRETHHSNTQSPEVSHPHPASPVDPYLRTKNSPPFLKSDHPVCHVSGPEV   750
 751  VGSGFQSSVAVRCMLPSAPSTPIRLPHSAALSQFHIPGASQFAAARIPPN   800
 801  YQGSVIPSASFDAYRHYMAYAASRWPMYPASQPPSHPLSDPHRLLPVTKQ   850
 851  AARSRPNLRVIPTVTPAKPKQEIPVLGSISVKRIPVRVSIPSLIKYNPKK   900
 901  ISDEKNRASQKQKVIEEREKLKTEQEARQKKMFYLTTELERLHKQQGEML   950
 951  RKKRREKDGHKDPLLMEVSRLQDSIMKDIAELHKETEEAEKKQSELDKVA  1000
1001  QILGIDIFDKSLKSSNDSKESTEKPEKEKSKSPEKELSPSNSSSSNKESK  1050
1051  MNEKSCIKSPSSTESLQPTVKQSDQPVAAYEYYDAGSHWCKDCNTTCGTM  1100
1101  FDFFTHMHNKKHTQTLDPYNRPWASKTQSEAKQDTVKRTDKITVPAKGSE  1150
1151  FLIPVTGFYCQLCEEFLGDPISGEQHVKGHQHNENYKKYVEENPLYEERR  1200
1201  NLDRQAGLAVVLETERRRQNELKRKLNEKPKEEKIEKKARIVREVKEDDK  1250
1251  APGELEEQLSEDGSAPEKGEVKGNASLRPQVKEEVKKEPSVASIAASFGK  1300
1301  FSWKKPEKEEEKGSVVTPGAPKEDTVETSKDRDDGKAEVGKAKPIKIKLS  1350
1351  GKTVIAHTSPWTPVVTTSTQTKIRPNLPIPSTVLRKSGSATVSKPAPLNT  1400
1401  FLSIKSSGTSTKPLPVVKESSSDLLLPPDIISKAFGGEEVVLKGSPEEKV  1450
1451  ELAEKNEPSQVPEQMLALLPPPPPPPPPPPPPPPPPPPQAVPQLSAPSPA  1500
1501  QANVVLTPVKSNSVISQTFSLGFQGPNILNPGLPVAFMASEQPTVIPSDE  1550
1551  TAPGVSESDWDQTLISMLVRPPPPLSSVFSEQAKKLEKRNSCLATANAKD  1600
1601  LYDIFYSSGGKGAHETKLSSSTLANGESSSLPRTESSDFSSTCTLNSSMS  1650
1651  SEDLPQCSALVTATEISNLENPISKGMESTGKWSVVDQIDPKSRDSTYSF  1700
1701  LQPLTRLYQNKPYEIVSPKTDTLVMWTSGSSQNDTHKDRPPEGKIRFDLG  1750
1751  EPGPPGTDSTSHLSDTHCQTNGPQKLIEINLIDNQNKNQEVYQSEGCRES  1800
1801  EMKRKTELKGKVATEEEEEEEEEGANSIEDSNSNHGNRNTWEGEIGQPKL  1850
1851  STVDKKGEQSSKLMTGHENTSKVVIELSPSLPSKRTKIDLFPSLLQNPKS  1900
1901  MPELLLLSPAGSGLCLKRQEIWERPEKPGLEDVELQGTRPELTVTIESKV  1950
1951  LENFDTTHLEVEGFASLRNLGDMHANFHNSQTEQTRRSPTALSEKMSEEI  2000
2001  SVSSVMCNPSSSSDIEPVPSFSGFPLESPKTLVLNFETEGAHSSSNSRNG  2050
2051  RITSNSLETGHPVENVGHDLGGERTHQALDLLAGGMLSEDVKETSPLQKD  2100
2101  LLRMESTTVSPSGLGPSPCLPDLVDFVTRTPGVPKQKPCSPLSEPDAFLK  2150
2151  CSSLEMGSPPPEILSVSVSEVAVPQVSEDNDSALNLVKTPPSGSPSRDQV  2200
2201  VGGNVSPREMPEQEAAVDVIPDHTRSNVYNSQDYLNG               2237

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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