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

NucPred

Fetching Q28670 from www.uniprot.org...

The NucPred score for your sequence is 0.33 (see score help below)

   1  MTTLLLVLVALRVIAAAISGDVSDLDNALSVSIPQPSPVRALLGTSLTIP    50
  51  CYFIDPVHPVTTAPSTAPLTPRIKWSRISKDKEVVLLVANEGRVRINSAY   100
 101  QDKVSLPNYPAIPSDATLEIQSLRSNDSGIYRCEVMHGLEDSEATLEVVV   150
 151  KGVVFHYRAISTRYTLDFDRAQRACLQNSAIIATPEQLQAAYEDGFHQCD   200
 201  AGWLADQTVRYPIHTPREGCYGDKDEFPGVRTYGIRDTNETYDVYCFAEE   250
 251  MEGEVFYATSPEKFTFQEAASECRRLGARLATTGQLYLAWQAGMDMCSAG   300
 301  WLADRSVRYPISKARPNCGGNLLGVRTVYVHANQTGYPDPSSRYDAICYT   350
 351  GEDFMDIPENFFGVGGEEDITVQTVTWPDVELPVPRNITEGEARGSVVLT   400
 401  AKPVLDVSPTAPQPEETFAPGVGATAFPGVENGTEEATRPRGFADEATLG   450
 451  PSSATAFTSADLVVQVTAAPGVAEVPGQPRLPGGVVFHYRPGPTRYSLTF   500
 501  EEAQQACLRTGAAMASAEQLQAAYEAGYEQCDAGWLQDQTVRYPIVSPRT   550
 551  PCVGDKDSSPGVRTYGVRPPSETYDVYCYVDRLEGEVFFATRLEQFTFQE   600
 601  ALEFCESHNATLASTGQLYAAWSRGLDRCYAGWLADGSLRYPIVTPRPAC   650
 651  GGDKPGVRTVYLYPNQTGLPDPLSRHHAFCFRGTSEAPSPGPEEGGTATP   700
 701  ASGLEDWIVTQVGPGVAATPRAEERTAVPSFATEPGNQTGWEAASSPVGT   750
 751  SLLPGIPPTWPPTGTAAEGTTEGLSTAAMPSASEGPYTPSSLVARETELP   800
 801  GLGVTSVPPDISGDLTSSGEASGLFGPTGQPLGGSASGLPSGELDSGSLT   850
 851  PTVGSGLPIGSGLASGDEDRIQWSSSTEVGGVTSGAEIPETSASGVGTDL   900
 901  SGLPSGAEIPETFASGVGTDLSGLPSGAEIPETFASGVGTDLSGLPSGAE   950
 951  ILETSASGVGTDLSGLPSGAEILETSASGVGTDLSGLPSGAEILETSASG  1000
1001  VGTDLSGLPSGAEIPETFASGVGTDLSGLPSGAEILETSASGVGTDLSGL  1050
1051  PSGAEIPETSASGVGTDLSGLPSGAEILETSASGVGTDLSGLPSGAEILE  1100
1101  TSASGVGTDLSGLPSGAEILETSASGVGTDLSGLPSGAEILETSASGVGT  1150
1151  DLSGLPSGAEILETSASGVGTDLSGLPSGGEIPETFASGVGDLSGLPPGR  1200
1201  EDLETLTSGVGDLSGLSSGKDGLVGSASGALDFGGTLGSGQIPETSGLPS  1250
1251  GYSGEYSEVDLGSGPSSGLPDFSGLPSGFPTVSLVDTPLVEVVTATTARE  1300
1301  LEGRGTIGISGAGEISGLPSSELDVSGGTSGADISGEADVGGEASGLIVR  1350
1351  GQPSGFPDTSGEAFGVTEVSGLSSGQPDLSGEASGVLFGSGPPFGITDLS  1400
1401  GEPSGQPSGLPEFSGTTHRIPDLVSGATSGSGESSGIAFVDTSVVEVTPT  1450
1451  TLREEEGLGSVEFSGFPSGETGLSGTPETIDVSGQSSGTIDSSGFTSLAP  1500
1501  EVSGSPSGVAEVSGEASGTEITSGLPSGVFDSSGLPSGFPTVSLVDRTLV  1550
1551  ESVTQAPTAQEAEGPSDILELSGVHSGLPDVSGAHSGFLDPSGLQSGLVE  1600
1601  PSGEPPRTPYFSGDFPSTPDVSGEASAATSSSGDISGLPEVTLVTSEFME  1650
1651  GVTRPTVSQELGQGPPMTHVPKLFESSGEALASGDTSGAAPAFPGSGLEA  1700
1701  SSVPESHGETSAYAEPGTKAAAAPDASGEASGSPDSGEITSVFREAAGEG  1750
1751  ASGLEVSSSSLASQQGPREGSASPEVSGESTTSYEIGTETSGLPLATPAA  1800
1801  SEDRAEVSGDLSGRTPVPVDVVTNVPEAEWIQHSQRPAEMWPETKSSSPS  1850
1851  YSGEDTAGTAASPASADTPGEPGPTTAAPRSCAEEPCGPGTCQETEGRVT  1900
1901  CLCPPGHTGEYCDIDIDECLSSPCVNGATCVDASDSFTCLCLPSYGGDLC  1950
1951  ETDQEVCEEGWTKFQGHCYRHFPDRETWVDAEGRCREQQSHLSSIVTPEE  2000
2001  QEFVNNNAQDYQWIGLNDRTIEGDFRWSDGHPLQFENWRPNQPDNFFATG  2050
2051  EDCVVMIWHEKGEWNDVPCNYHLPFTCKKGTVACGDPPVVEHARTFGQKK  2100
2101  DRYEINSLVRYQCAEGFTQRHVPTIRCQPSGHWEEPRITCTHPTTYKRRV  2150
2151  QKRSSRTLQRSQASSAP                                   2167

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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