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

NucPred

Fetching Q99590 from www.uniprot.org...

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

   1  MKKKTVCTLNMGDKKYEDMEGEENGDNTISTGLLYSEADRCPICLNCLLE    50
  51  KEVGFPESCNHVFCMTCILKWAETLASCPIDRKPFQAVFKFSALEGYVKV   100
 101  QVKKQLRETKDKKNENSFEKQVSCHENSKSCIRRKAIVREDLLSAKVCDL   150
 151  KWIHRNSLYSETGGKKNAAIKINKPQRSNWSTNQCFRNFFSNMFSSVSHS   200
 201  GESSFTYRAYCTEFIEASEISALIRQKRHELELSWFPDTLPGIGRIGFIP   250
 251  WNVETEVLPLISSVLPRTIFPTSTISFEHFGTSCKGYALAHTQEGEEKKQ   300
 301  TSGTSNTRGSRRKPAMTTPTRRSTRNTRAETASQSQRSPISDNSGCDAPG   350
 351  NSNPSLSVPSSAESEKQTRQAPKRKSVRRGRKPPLLKKKLRSSVAAPEKS   400
 401  SSNDSVDEETAESDTSPVLEKEHQPDVDSSNICTVQTHVENQSANCLKSC   450
 451  NEQIEESEKHTANYDTEERVGSSSSESCAQDLPVLVGEEGEVKKLENTGI   500
 501  EANVLCLESEISENILEKGGDPLEKQDQISGLSQSEVKTDVCTVHLPNDF   550
 551  PTCLTSESKVYQPVSCPLSDLSENVESVVNEEKITESSLVEITEHKDFTL   600
 601  KTEELIESPKLESSEGEIIQTVDRQSVKSPEVQLLGHVETEDVEIIATCD   650
 651  TFGNEDFNNIQDSENNLLKNNLLNTKLEKSLEEKNESLTEHPRSTELPKT   700
 701  HIEQIQKHFSEDNNEMIPMECDSFCSDQNESEVEPSVNADLKQMNENSVT   750
 751  HCSENNMPSSDLADEKVETVSQPSESPKDTIDKTKKPRTRRSRFHSPSTT   800
 801  WSPNKDTPQEKKRPQSPSPRRETGKESRKSQSPSPKNESARGRKKSRSQS   850
 851  PKKDIARERRQSQSRSPKRDTTRESRRSESLSPRRETSRENKRSQPRVKD   900
 901  SSPGEKSRSQSRERESDRDGQRRERERRTRKWSRSRSHSRSPSRCRTKSK   950
 951  SSSFGRIDRDSYSPRWKGRWANDGWRCPRGNDRYRKNDPEKQNENTRKEK  1000
1001  NDIHLDADDPNSADKHRNDCPNWITEKINSGPDPRTRNPEKLKESHWEEN  1050
1051  RNENSGNSWNKNFGSGWVSNRGRGRGNRGRGTYRSSFAYKDQNENRWQNR  1100
1101  KPLSGNSNSSGSESFKFVEQQSYKRKSEQEFSFDTPADRSGWTSASSWAV  1150
1151  RKTLPADVQNYYSRRGRNSSGPQSGWMKQEEETSGQDSSLKDQTNQQVDG  1200
1201  SQLPINMMQPQMNVMQQQMNAQHQPMNIFPYPVGVHAPLMNIQRNPFNIH  1250
1251  PQLPLHLHTGVPLMQVATPTSVSQGLPPPPPPPPPSQQVNYIASQPDGKQ  1300
1301  LQGIPSSSHVSNNMSTPVLPAPTAAPGNTGMVQGPSSGNTSSSSHSKASN  1350
1351  AAVKLAESKVSVAVEASADSSKTDKKLQIQEKAAQEVKLAIKPFYQNKDI  1400
1401  TKEEYKEIVRKAVDKVCHSKSGEVNSTKVANLVKAYVDKYKYSRKGSQKK  1450
1451  TLEEPVSTEKNIG                                       1463

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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