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

NucPred

Fetching P39880 from www.uniprot.org...

The NucPred score for your sequence is 0.98 (see score help below)

   1  MLCVAGARLKRELDATATVLANRQDESEQSRKRLIEQSREFKKNTPEDLR    50
  51  KQVAPLLKSFQGEIDALSKRSKEAEAAFLNVYKRLIDVPDPVPALDLGQQ   100
 101  LQLKVQRLHDIETENQKLRETLEEYNKEFAEVKNQEVTIKALKEKIREYE   150
 151  QTLKNQAETIALEKEQKLQNDFAEKERKLQETQMSTTSKLEEAEHKVQSL   200
 201  QTALEKTRTELFDLKTKYDEETTAKADEIEMIMTDLERANQRAEVAQREA   250
 251  ETLREQLSSANHSLQLASQIQKAPDVEQAIEVLTRSSLEVELAAKEREIA   300
 301  QLVEDVQRLQASLTKLRENSASQISQLEQQLSAKNSTLKQLEEKLKGQAD   350
 351  YEEVKKELNILKSMEFAPSEGAGTQDAAKPLEVLLLEKNRSLQSENAALR   400
 401  ISNSDLSGSARRKGKDQPESRRPGSLPAPPPSQLPRNPGEQASNTNGTHQ   450
 451  FSPAGLSQDFFSSSLASPSLPLASTGKFALNSLLQRQLMQSFYSKAMQEA   500
 501  GSTSMIFSTGPYSTNSISSQSPLQQSPDVNGMAPSPSQSESAGSVSEGEE   550
 551  MDTAEIARQVKEQLIKHNIGQRIFGHYVLGLSQGSVSEILARPKPWNKLT   600
 601  VRGKEPFHKMKQFLSDEQNILALRSIQGRQRENPGQSLNRLFQEVPKRRN   650
 651  GSEGNITTRIRASETGSDEAIKSILEQAKRELQVQKTAEPAQPSSASGSG   700
 701  NSDDAIRSILQQARREMEAQQAALDPALKQAPLSQSDITILTPKLLSTSP   750
 751  MPTVSSYPPLAISLKKPSAAPEAGASALPNPPALKKEAQDAPGLDPQGAA   800
 801  DCAQGVLRQVKNEVGRSGAWKDHWWSAVQPERRNAASSEEAKAEETGGGK   850
 851  EKGSGGSGGGSQPRAERSQLQGPSSSEYWKEWPSAESPYSQSSELSLTGA   900
 901  SRSETPQNSPLPSSPIVPMSKPTKPSVPPLTPEQYEVYMYQEVDTIELTR   950
 951  QVKEKLAKNGICQRIFGEKVLGLSQGSVSDMLSRPKPWSKLTQKGREPFI  1000
1001  RMQLWLNGELGQGVLPVQGQQQGPVLHSVTSLQDPLQQGCVSSESTPKTS  1050
1051  ASCSPAPESPMSSSESVKSLTELVQQPCPPIEASKDSKPPEPSDPPASDS  1100
1101  QPTTPLPLSGHSALSIQELVAMSPELDTYGITKRVKEVLTDNNLGQRLFG  1150
1151  ETILGLTQGSVSDLLARPKPWHKLSLKGREPFVRMQLWLNDPNNVEKLMD  1200
1201  MKRMEKKAYMKRRHSSVSDSQPCEPPSVGTEYSQGASPQPQHQLKKPRVV  1250
1251  LAPEEKEALKRAYQQKPYPSPKTIEDLATQLNLKTSTVINWFHNYRSRIR  1300
1301  RELFIEEIQAGSQGQAGASDSPSARSGRAAPSSEGDSCDGVEATEGPGSA  1350
1351  DTEEPKSQGEAEREEVPRPAEQTEPPPSGTPGPDDARDDDHEGGPVEGPG  1400
1401  PLPSPASATATAAPAAPEDAATSAAAAPGEGPAAPSSAPPPSNSSSSSAP  1450
1451  RRPSSLQSLFGLPEAAGARDSRDNPLRKKKAANLNSIIHRLEKAASREEP  1500
1501  IEWEF                                               1505

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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