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

NucPred

Fetching Q4IB96 from www.uniprot.org...

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

   1  MTEVGAADLSRLLQSKRNECSSIVTSRKRKLRELFVVATQSEGLPHPVLT    50
  51  NPDAPTTTPAEWQFLQANDINQSKTLNEASIPTRPTFSLEVLKKSLAKSI   100
 101  FIANESVPKQTSENSNKSHVTDAQDEQQSNRASLSTKSDAAATSTRPNTP   150
 151  ETSTESATTANPVPPPAKNTQAVLPPADAIEKPIPTTSPDVPASTGANAN   200
 201  SITNEEDRSDPNEVASVPRQPQVTFETGTKGEHVETGTSSVKSGHGVGDS   250
 251  AVTTGVPSTVKPSADVTRSADALSSPGSTAQSATTPAVHDDASTDTSPEH   300
 301  EGPQYVEPAEQKKIEDGTHERDTDKYHQSHQDGDIRAPSTKDLEDRVLEA   350
 351  PPDSAEAQLLQESIRSNVAAENEAALNSESTSQEADTAISAPVSEDVNMS   400
 401  DVDDRVVKAAPTVGEKVEEKRAQQILDTDAKSALATGAPAEISGSKEIPD   450
 451  SQEEAPEQMDVDAPEPKASTESQIGAPISLEKLDAADTGPSSPTPAHIAE   500
 501  VATPPEPVRQNSPPKAERAVTRVSSGAMRPKSVSEIVGVTPRQTPTLEHI   550
 551  STNKSTNHQLTPLTSTPKSPTLRHRHISAHQRQASRSQPSTVVFGKQSKK   600
 601  GEEKSMVTSQHDTILPTEDYYTPLFVQGFAGSSSWMQPIEKILYTANKTV   650
 651  TTPDANLAIQDHQACKVLRRVYHLQQHDKWSLRQPKRCPEPTRPPSHWDV   700
 701  VLQEMKWMRTDFREERKWKRAVAKNLAYACAEWHEATPEERKTLQVQAVV   750
 751  PPKMKPASDVAMVDAEGTNHLTPDLVSSEDVESIDNLDDLIEDFPETIAP   800
 801  SAIFNLQDEDVVFGLRRTAAADQLLEELPMFGAPLQVPKFDLTGPEWDPD   850
 851  AHWRRPALPLSKYVEGHMKLVSDGPPRKRSRYNYQNEDSDDEGEAGFVSS   900
 901  DSTPSLPLPSATDEVALFNPEMKHIRDRLYVGHQFRPPSEYPMPSQSFFE   950
 951  CRSPSQWTIAEDDELRSLVREHSYNWSLISSILAPRSIFNSGAERRTPWE  1000
1001  CFERWINLEGLPADMSKTQYFKAYMGRINTAQNMINIQNQAMAQQQVNQA  1050
1051  NGAVTPGRRRHQSIPFRVERRRNQKHLTMLDAMRKLAKKRETTAQKQQHT  1100
1101  ASQNAANKKTNESASQRPTKTPGEYSRLRYERDQALAEKMAQFASRQEAQ  1150
1151  RRAVLQARAQGQAAQMAAGTPAAVQAGQNSAQAAAAAAAAAAAANGMNGV  1200
1201  GRVNVPNQLAAAAAAATGQARPRMPMQSPAPASMGGVPAHMASGLVPPNQ  1250
1251  MNSVQQAQMQAMQAMQGQHNRMPMPNPPPDVSLMMRAQRISEQQRAAQMH  1300
1301  AQGGPGTPGQGAVGAQQSPPAQMRNAMNGVNGINSNPMNQQSFLNNAQAM  1350
1351  MAQFNQGNLSSPQANGLHMPSGPAGSIAPRPQTQLPAAIQAQLNQLEAQY  1400
1401  RAKNSSLTSEQARQMATEHLTRLMMAQRSAMNAAAGTAGGQGGLAGSIAA  1450
1451  TTSPHQYAALLRQQQQQQASAAAGSPGQQHQQPHQAQHQPQQQQSQQQQA  1500
1501  QAKQQQPQQQVQAHAHAQAQHQAQQQQQQQRQASGSATPSAG          1542

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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