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

NucPred

Fetching Q8VHS2 from www.uniprot.org...

The NucPred score for your sequence is 0.24 (see score help below)

   1  MKLKRTAYLLFLYLSSSLLICIKNSFCNKNNTRCLSGPCQNNSTCKHFPQ    50
  51  DNNCCLDTANNLDKDCEDLKDPCFSSPCQGIATCVKIPGEGNFLCQCPPG   100
 101  YSGLNCETATNSCGGNLCQHGGTCRKDPEHPVCICPPGYAGRFCETDHNE   150
 151  CASSPCHNGAMCQDGINGYSCFCVPGYQGRHCDLEVDECVSDPCKNEAVC   200
 201  LNEIGRYTCVCPQEFSGVNCELEIDECRSQPCLHGATCQDAPGGYSCDCA   250
 251  PGFLGEHCELSVNECESQPCLHGGLCVDGRNSYHCDCTGSGFTGMHCESL   300
 301  IPLCWSKPCHNDATCEDTVDSYICHCRPGYTGALCETDINECSSNPCQFW   350
 351  GECVELSSEGLYGNTAGLPSSFSYVGASGYVCICQPGFTGIHCEEDVDEC   400
 401  LLHPCLNGGTCENLPGNYACHCPFDDTSRTFYGGENCSEILLGCTHHQCL   450
 451  NNGKCIPHFQNGQHGFTCQCLSGYAGPLCETVTTLSFGSNGFLWVTSGSH   500
 501  TGIGPECNISLRFHTVQPNALLLIRGNKDVSMKLELLNGCVHLSIEVWNQ   550
 551  LKVLLSISHNTSDGEWHFVEVTIAETLTLALVGGSCKEKCTTKSSVPVEN   600
 601  HQSICALQDSFLGGLPMGTANNSVSVLNIYNVPSTPSFVGCLQDIRFDLN   650
 651  HITLENVSSGLSSNVKAGCLGKDWCESQPCQNRGRCINLWQGYQCECDRP   700
 701  YTGSNCLKEYVAGRFGQDDSTGYAAFSVNDNYGQNFSLSMFVRTRQPLGL   750
 751  LLALENSTYQYVSVWLEHGSLALQTPGSPKFMVNFFLSDGNVHLISLRIK   800
 801  PNEIELYQSSQNLGFISVPTWTIRRGDVIFIGGLPDREKTEVYGGFFKGC   850
 851  VQDVRLNSQTLEFFPNSTNNAYDDPILVNVTQGCPGDNTCKSNPCHNGGV   900
 901  CHSLWDDFSCSCPTNTAGRACEQVQWCQLSPCPPTAECQLLPQGFECIAN   950
 951  AVFSGLSREILFRSNGNITRELTNITFAFRTHDTNVMILHAEKEPEFLNI  1000
1001  SIQDARLFFQLRSGNSFYTLHLMGSQLVNDGTWHQVTFSMIDPVAQTSRW  1050
1051  QMEVNDQTPFVISEVATGSLNFLKDNTDIYVGDQSVDNPKGLQGCLSTIE  1100
1101  IGGIYLSYFENLHGFPGKPQEEQFLKVSTNMVLTGCLPSNACHSSPCLHG  1150
1151  GNCEDSYSSYRCACLSGWSGTHCEINIDECFSSPCIHGNCSDGVAAYHCR  1200
1201  CEPGYTGVNCEVDVDNCKSHQCANGATCVPEAHGYSCLCFGNFTGRFCRH  1250
1251  SRLPSTVCGNEKRNFTCYNGGSCSMFQEDWQCMCWPGFTGEWCEEDINEC  1300
1301  ASDPCINGGLCRDLVNRFLCICDVAFAGERCELDLADDRLLGIFTAVGSG  1350
1351  TLALFFILLLAGVASLIASNKRATQGTYSPSGQEKAGPRVEMWIRMPPPA  1400
1401  LERLI                                               1405

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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