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

NucPred

Fetching O35604 from www.uniprot.org...

The NucPred score for your sequence is 0.15 (see score help below)

   1  MGAHHPALGLLLLLLCPAQVFSQSCVWYGECGIATGDKRYNCKYSGPPKP    50
  51  LPKDGYDLVQELCPGLFFDNVSLCCDIQQLQTLKSNLQLPLQFLSRCPSC   100
 101  FYNLMTLFCELTCSPHQSQFLNVTATEDYFDPKTQENKTNVKELEYFVGQ   150
 151  SFANAMYNACRDVEAPSSNEKALGLLCGRDARACNATNWIEYMFNKDNGQ   200
 201  APFTIIPVFSDLSILGMEPMRNATKGCNESVDEVTGPCSCQDCSIVCGPK   250
 251  PQPPPPPMPWRIWGLDAMYVIMWVTYVAFLFVFFGALLAVWCHRRRYFVS   300
 301  EYTPIDSNIAFSVNSSDKGEASCCDPLGAAFDDCLRRMFTKWGAFCVRNP   350
 351  TCIIFFSLAFITVCSSGLVFVQVTTNPVELWSAPHSQARLEKEYFDKHFG   400
 401  PFFRTEQLIIQAPNTSVHIYEPYPAGADVPFGPPLNKEILHQVLDLQIAI   450
 451  ESITASYNNETVTLQDICVAPLSPYNKNCTIMSVLNYFQNSHAVLDSQVG   500
 501  DDFYIYADYHTHFLYCVRAPASLNDTSLLHGPCLGTFGGPVFPWLVLGGY   550
 551  DDQNYNNATALVITFPVNNYYNDTERLQRAWAWEKEFISFVKNYKNPNLT   600
 601  ISFTAERSIEDELNRESNSDVFTVIISYVVMFLYISLALGHIQSCSRLLV   650
 651  DSKISLGIAGILIVLSSVACSLGIFSYMGMPLTLIVIEVIPFLVLAVGVD   700
 701  NIFILVQTYQRDERLQEETLDQQLGRILGEVAPTMFLSSFSETSAFFFGA   750
 751  LSSMPAVHTFSLFAGMAVLIDFLLQITCFVSLLGLDIKRQEKNHLDILCC   800
 801  VRGADDGQGSHASESYLFRFFKNYFAPLLLKDWLRPIVVAVFVGVLSFSV   850
 851  AVVNKVDIGLDQSLSMPNDSYVIDYFKSLAQYLHSGPPVYFVLEEGYNYS   900
 901  SRKGQNMVCGGMGCDNDSLVQQIFNAAELDTYTRVGFAPSSWIDDYFDWV   950
 951  SPQSSCCRLYNVTHQFCNASVMDPTCVRCRPLTPEGKQRPQGKEFMKFLP  1000
1001  MFLSDNPNPKCGKGGHAAYGSAVNIVGDDTYIGATYFMTYHTILKTSADY  1050
1051  TDAMKKARLIASNITETMRSKGSDYRVFPYSVFYVFYEQYLTIIDDTIFN  1100
1101  LSVSLGSIFLVTLVVLGCELWSAVIMCITIAMILVNMFGVMWLWGISLNA  1150
1151  VSLVNLVMSCGISVEFCSHITRAFTMSTKGSRVSRAEEALAHMGSSVFSG  1200
1201  ITLTKFGGIVVLAFAKSQIFEIFYFRMYLAMVLLGATHGLIFLPVLLSYI  1250
1251  GPSVNKAKRHTTYERYRGTERERLLNF                         1277

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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