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

NucPred

Fetching Q8R4K8 from www.uniprot.org...

The NucPred score for your sequence is 0.78 (see score help below)

   1  MRLWSWVLRLGLLSAALGCGLAERPRRVRRDPRAVRPPRPAAGPATCATR    50
  51  AARGRRASPPPPPGGAWEAVRVPRRRQQRAARGAEEPSPPSRALYFSGRG   100
 101  EQLRLRADLELPRDAFTLQVWLRAEGGQKSPAVITGLYDKCSYTSRDRGW   150
 151  VMGIHTTSDQGNRDPRYFFSLKTDRARKVTTIDAHRSYLPGQWVHLAATY   200
 201  DGRLMKLYMNGAQVATSAEQVGGIFSPLTQKCKVLMLGGSALNHNFRGHI   250
 251  EHFSLWKVARTQREIVSDMETRGLHTPLPQLLLQENWDNVKRTWSPMKDG   300
 301  NSPQVEFSNAHGFLLDTNLEPPLCGQTLCDNTEVISSYNQLPSFRQPKVV   350
 351  RYRVVNIYDDHHENPTVSWQQIDFQHQQLAEAFQHYNISWELEVLNINSS   400
 401  SLRHRLILANCDISKIGDEKCDPECNHTLTGHDGGDCRQLRYPAFMKKQQ   450
 451  NGVCDMDCNYERFNFDGGECCDPDITDVTKTCFDPDSPHRAYLDVNELKN   500
 501  ILRLDGSTHLNIFFANSSEEELAGVATWPWDKEALMHLGGIVLNPSFYGI   550
 551  PGHTHTMIHEIGHSLGLYHIFRGISEIQSCSDPCMETEPSFETGDLCNDT   600
 601  NPAPKHKFCGDPGPGNDTCGFHGFFNTPYNNFMSYADDDCTDSFTPNQVS   650
 651  RMHCYLDLVYQSWQPSRKPAPVALAPQVVGHTMDSVMLEWFPPIDGHFFE   700
 701  RELGSACDLCLEGRILVQYAFNASSPMPCGPSGHWSPREAEGHPDVEQPC   750
 751  KSSVRTWSPNSAVNPHTVPPACPEPQGCYLELEFRYPLVPESLTIWVTFV   800
 801  SSDWDSSGAVNDIKLLTISGKNISLGPQNVFCDIPLTIRLRDVGEEVYGI   850
 851  QIYTLDEHLEIDAAMLTSTVDSPLCLQCKPLQYKVLRDPPLLEDVASLLH   900
 901  LNRRFMDTDLKLGSVYQYRIITISGNEESEPSPAAIYTHGSGYCGDGVIQ   950
 951  KDQGEECDDMNKVNGDGCSLFCKQEVSFNCIDEPSRCYFHDGDGMCEEFE  1000
1001  QKTSIKDCGVYTPQGFLDQWASNASVSHQDQQCPGWVVIGQPAASQVCRT  1050
1051  KVIDLSEGISQHAWYPCTITYPYYHLPQTTFWLQTYFSQPMVAAAVIIHL  1100
1101  VTDGTYYGDQKQETISVQLLDTKDQSHDLGLHVLSCRNNPLIIPVVHDLS  1150
1151  QPFYHSQAVHVSFSSPLVAISGVALRSFDNFDPVTLSSCQRGETYSPAEQ  1200
1201  SCVHFACQAADCPELAVGNASLNCSSNHHYHGAQCTVSCQTGYVLQIQRD  1250
1251  DELIKSQVGPSITVTCTEGKWNKQVACEPVDCGIPDHHHVYAASFSCPEG  1300
1301  TTFGRRCSFQCRHPAQLKGNNSFLTCMEDGLWSFPEALCELMCLAPPPVP  1350
1351  NADLQTARCRENKHKVGSFCKYKCKPGYHVPGSSRKSKKRAFKTQCTQDG  1400
1401  SWQEGTCVPVTCDPPPPKFHGLYQCTNGFQFNSECRIKCEDSDASQGRGS  1450
1451  NIIHCRKDGTWSGSFHVCREMQGQCSAPNQLNSNLKLQCPDGYAIGSECA  1500
1501  ISCLDHNSESIILPVNLTVRDIPHWMNPTRVQRIVCTAGLQWYPHPALIH  1550
1551  CVKGCEPFMGDNYCDAINNRAFCNYDGGDCCTSTVKTKKVTPFPMSCDLQ  1600
1601  NDCACRDPEAQEHNRKDLRGYSHG                            1624

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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