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

NucPred

Fetching Q6P5E4 from www.uniprot.org...

The NucPred score for your sequence is 0.61 (see score help below)

   1  MCSRGDANTADAAAARRVTGLRYNMRLLIALALPCLFSLAEANSKAITTS    50
  51  LTTKWFSAPLLLEASEFLAEDSQEKFWSFVEATQNIGSSDHHDTDHSYYD   100
 101  AVLEAAFRFLSPLQQNLLKFCLSLRSYSASIQAFQQIAVDEPPPEGCKSF   150
 151  LSVHGKQTCDLDTLESLLLTAADRPKPLLFKGDHRYPSSNPESPVVILYS   200
 201  EIGHEEFSNIHHQLISKSNEGKINYVFRHYISNPSKEPVYLSGYGVELAI   250
 251  KSTEYKAKDDTQVKGTEVNATVIGESDPIDEVQGFLFGKLRELYPALEGQ   300
 301  LKEFRKHLVESTNEMAPLKVWQLQDLSFQTAARILAASGALSLVVMKDIS   350
 351  QNFPTKARAITKTAVSAQLRAEVEENQKYFKGTIGLQPGDSALFINGLHI   400
 401  DLDTQDIFSLFDTLRNEARVMEGLHRLGIEGLSLHNILKLNIQPSETDYA   450
 451  VDIRSPAISWVNNLEVDSRYNSWPSSLQELLRPTFPGVIRQIRKNLHNMV   500
 501  FIIDPVHETTAELISIAEMFLSNHIPLRIGFIFVVNDSEDVDGMQDAGVA   550
 551  VLRAYNYVAQEVDGYHAFQTLTQIYNKVRTGETVKVEHVVSVLEKKYPYV   600
 601  EVNSILGIDSAYDQNRKEARGYYEQTGVGPLPVVLFNGMPFEKEQLDPDE   650
 651  LETITMHKILETTTFFQRAVYLGELSHDQDVVEYIMNQPNVVPRINSRIL   700
 701  TAKREYLDLTASNNFYVDDFARFSALDSRGKTAAIANSMNYLTKKGMSSK   750
 751  EIYDDSFIRPVTFWIVGDFDSPSGRQLLYDAIKHQKTSNNVRISMINNPS   800
 801  QEISDSSTPIFRAIWAALQTQASSSAKNFITKMAKEETAEALAAGVDIAE   850
 851  FSVGGMDVSLFKEVFESSRMDFILSHALYCRDVLKLKKGQRVVISNGRII   900
 901  GPLEDNELFNQDDFHLLENIILKTSGQKIKSHIQQLRVEEDVASDLVMKV   950
 951  DALLSAQPKGEARIEYQFFEDKHSAIKLKPKEGETYYDVVAVVDPVTREA  1000
1001  QRLAPLLLVLTQLINMNLRVFMNCQSKLSDMPLKSFYRYVLEPEISFTAD  1050
1051  SSFAKGPIAKFLDMPQSPLFTLNLNTPESWMVESVRTPYDLDNIYLEEVD  1100
1101  SIVAAEYELEYLLLEGHCYDITTGQPPRGLQFTLGTSANPTIVDTIVMAN  1150
1151  LGYFQLKANPGAWILRLRKGRSDDIYRIYSHDGTDSPPDANDVVVILNNF  1200
1201  KSKIIKVKVQKKADMANEDLLSDGTNENESGFWDSFKWGFSGQKAEEVKQ  1250
1251  DKDDIINIFSVASGHLYERFLRIMMLSVLKNTKTPVKFWFLKNYLSPTFK  1300
1301  EFIPYMAKKYNFQYELVQYKWPRWLHQQTEKQRIIWGYKILFLDVLFPLV  1350
1351  VDKFLFVDADQIVRTDLKELRDFNLDGAPYGYTPFCDSRREMDGYRFWKS  1400
1401  GYWASHLAGRKYHISALYVVDLKKFRKIAAGDRLRGQYQGLSQDPNSLSN  1450
1451  LDQDLPNNMIHQVPIKSLPQEWLWCETWCDDASKKRAKTIDLCNNPMTKE  1500
1501  PKLEAAVRIVPEWQDYDQEIKQLQTLFQEEKELGTLHTEETQEGSQKHEE  1550
1551  L                                                   1551

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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