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

NucPred

Fetching Q61282 from www.uniprot.org...

The NucPred score for your sequence is 0.36 (see score help below)

   1  MTTLLLVFVTLRVIAAVISEEVPDHDNSLSVSIPQPSPLKVLLGSSLTIP    50
  51  CYFIDPMHPVTTAPSTAPLTPRIKWSRVSKEKEVVLLVATEGQVRVNSIY   100
 101  QDKVSLPNYPAIPSDATLEIQNLRSNDSGIYRCEVMHGIEDSEATLEVIV   150
 151  KGIVFHYRAISTRYTLDFDRAQRACLQNSAIIATPEQLQAAYEDGFHQCD   200
 201  AGWLADQTVRYPIHTPREGCYGDKDEFPGVRTYGIRDTNETYDVYCFAEE   250
 251  MEGEVFYATSPEKFTFQEAANECRRLGARLATTGQLYLAWQGGMDMCSAG   300
 301  WLADRSVRYPISKARPNCGGNLLGVRTVYLHANQTGYPDPSSRYDAICYT   350
 351  GEDFVDIPENFFGVGGEDDITIQTVTWPDLELPLPRNVTEGEALGSVILT   400
 401  AKPIFDLSPTISEPGEALTLAPEVGSTAFPEAEERTGEATRPWGFPAEVT   450
 451  RGPDSATAFASEDLVVRVTISPGAAEVPGQPRLPGGVVFHYRPGSTRYSL   500
 501  TFEEAQQACMHTGAVIASPEQLQAAYEAGYEQCDAGWLQDQTVRYPIVSP   550
 551  RTPCVGDKDSSPGVRTYGVRPSSETYDVYCYVDKLEGEVFFATRLEQFTF   600
 601  QEARAFCAAQNATLASTGQLYAAWSQGLDKCYAGWLADGTLRYPIITPRP   650
 651  ACGGDKPGVRTVYLYPNQTGLPDPLSKHHAFCFRGVSVAPSPGEEGGSTP   700
 701  TSPSDIEDWIVTQVGPGVDAVPLEPKTTEVPYFTTEPRKQTEWEPAYTPV   750
 751  GTSPQPGIPPTWLPTLPAAEEHTESPSASEEPSASAVPSTSEEPYTSSFA   800
 801  VPSMTELPGSGEASGAPDLSGDFTGSGDASGRLDSSGQPSGGIESGLPSG   850
 851  DLDSSGLSPTVSSGLPVESGSASGDGEVPWSHTPTVGRLPSGGESPEGSA   900
 901  SASGTGDLSGLPSGGEITETSTSGAEETSGLPSGGDGLETSTSGVDDVSG   950
 951  IPTGREGLETSASGVEDLSGLPSGEEGSETSTSGIEDISVLPTGGESLET  1000
1001  SASGVGDLSGLPSGGESLETSASGAEDVTQLPTERGGLETSASGVEDITV  1050
1051  LPTGRESLETSASGVEDVSGLPSGREGLETSASGIEDISVFPTEAEGLDT  1100
1101  SASGGYVSGIPSGGDGTETSASGVEDVSGLPSGGEGLETSASGVEDLGPS  1150
1151  TRDSLETSASGVDVTGFPSGRGDPETSVSGVGDDFSGLPSGKEGLETSAS  1200
1201  GAEDLSGLPSGKEDLVGSASGALDFGKLPPGTLGSGQTPEVNGFPSGFSG  1250
1251  EYSGADIGSGPSSGLPDFSGLPSGFPTVSLVDSTLVEVITATTSSELEGR  1300
1301  GTIGISGSGEVSGLPLGELDSSADISGLPSGTELSGQASGSPDSSGETSG  1350
1351  FFDVSGQPFGSSGVSEETSGIPEISGQPSGTPDTTATSGVTELNELSSGQ  1400
1401  PDVSGDGSGILFGSGQSSGITSVSGETSGISDLSGQPSGFPVFSGTATRT  1450
1451  PDLASGTISGSGESSGITFVDTSFVEVTPTTFREEEGLGSVELSGFPSGE  1500
1501  TELSGTSGTVDVSEQSSGAIDSSGLTSPTPEFSGLPSGVAEVSGEFSGVE  1550
1551  TGSSLPSGAFDGSGLVSGFPTVSLVDRTLVESITQAPTAQEAGEGPSGIL  1600
1601  EFSGAHSGTPDISGELSGSLDLSTLQSGQMETSTETPSSPYFSGDFSSTT  1650
1651  DVSGESIAATTGSGESSGLPEVTLNTSELVEGVTEPTVSQELGHGPSMTY  1700
1701  TPRLFEASGDASASGDLGGAVTNFPGSGIEASVPEASSDLSAYPEAGVGV  1750
1751  SAAPEASSKLSEFPDLHGITSAFHETDLEMTTPSTEVNSNPWTFQEGTRE  1800
1801  GSAAPEVSGESSTTSDIDTGTSGVPSATPMASGDRTEISGEWSDHTSEVN  1850
1851  VAISSTITESEWAQPTRYPTETLQEIESPNPSYSGEETQTAETTMSLTDA  1900
1901  PTLSSSEGSGETESTVADQEQCEEGWTKFQGHCYRHFHDRETWVDAERRC  1950
1951  REQQSHLSSIVTPEEQEFVNKNAQDYQWIGLNDRTIEGDFRWSDGHSLQF  2000
2001  EKWRPNQPDNFFATGEDCVVMIWHERGEWNDVPCNYQLPFTCKKGTVACG  2050
2051  DPPVVEHARTLGQKKDRYEISSLVRYQCTEGFVQRHVPTIRCQPSGHWEE  2100
2101  PRITCTDPNTYKHRLQKRSMRPTRRSRPSMAH                    2132

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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