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

NucPred

Fetching Q9P2R6 from www.uniprot.org...

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

   1  MTADKDKDKDKEKDRDRDRDREREKRDKARESENSRPRRSCTLEGGAKNY    50
  51  AESDHSEDEDNDNNSATAEESTKKNKKKPPKKKSRYERTDTGEITSYITE   100
 101  DDVVYRPGDCVYIESRRPNTPYFICSIQDFKLVHNSQACCRSPTPALCDP   150
 151  PACSLPVASQPPQHLSEAGRGPVGSKRDHLLMNVKWYYRQSEVPDSVYQH   200
 201  LVQDRHNENDSGRELVITDPVIKNRELFISDYVDTYHAAALRGKCNISHF   250
 251  SDIFAAREFKARVDSFFYILGYNPETRRLNSTQGEIRVGPSHQAKLPDLQ   300
 301  PFPSPDGDTVTQHEELVWMPGVNDCDLLMYLRAARSMAAFAGMCDGGSTE   350
 351  DGCVAASRDDTTLNALNTLHESGYDAGKALQRLVKKPVPKLIEKCWTEDE   400
 401  VKRFVKGLRQYGKNFFRIRKELLPNKETGELITFYYYWKKTPEAASSRAH   450
 451  RRHRRQAVFRRIKTRTASTPVNTPSRPPSSEFLDLSSASEDDFDSEDSEQ   500
 501  ELKGYACRHCFTTTSKDWHHGGRENILLCTDCRIHFKKYGELPPIEKPVD   550
 551  PPPFMFKPVKEEDDGLSGKHSMRTRRSRGSMSTLRSGRKKQPASPDGRTS   600
 601  PINEDIRSSGRNSPSAASTSSNDSKAETVKKSAKKVKEEASSPLKSNKRQ   650
 651  REKVASDTEEADRTSSKKTKTQEISRPNSPSEGEGESSDSRSVNDEGSSD   700
 701  PKDIDQDNRSTSPSIPSPQDNESDSDSSAQQQMLQAQPPALQAPTGVTPA   750
 751  PSSAPPGTPQLPTPGPTPSATAVPPQGSPTASQAPNQPQAPTAPVPHTHI   800
 801  QQAPALHPQRPPSPHPPPHPSPHPPLQPLTGSAGQPSAPSHAQPPLHGQG   850
 851  PPGPHSLQAGPLLQHPGPPQPFGLPPQASQGQAPLGTSPAAAYPHTSLQL   900
 901  PASQSALQSQQPPREQPLPPAPLAMPHIKPPPTTPIPQLPAPQAHKHPPH   950
 951  LSGPSPFSMNANLPPPPALKPLSSLSTHHPPSAHPPPLQLMPQSQPLPSS  1000
1001  PAQPPGLTQSQNLPPPPASHPPTGLHQVAPQPPFAQHPFVPGGPPPITPP  1050
1051  TCPSTSTPPAGPGTSAQPPCSGAAASGGSIAGGSSCPLPTVQIKEEALDD  1100
1101  AEEPESPPPPPRSPSPEPTVVDTPSHASQSARFYKHLDRGYNSCARTDLY  1150
1151  FMPLAGSKLAKKREEAIEKAKREAEQKAREEREREKEKEKERERERERER  1200
1201  EAERAAKASSSAHEGRLSDPQLSGPGHMRPSFEPPPTTIAAVPPYIGPDT  1250
1251  PALRTLSEYARPHVMSPTNRNHPFYMPLNPTDPLLAYHMPGLYNVDPTIR  1300
1301  ERELREREIREREIRERELRERMKPGFEVKPPELDPLHPAANPMEHFARH  1350
1351  SALTIPPTAGPHPFASFHPGLNPLERERLALAGPQLRPEMSYPDRLAAER  1400
1401  IHAERMASLTSDPLARLQMFNVTPHHHQHSHIHSHLHLHQQDPLHQGSAG  1450
1451  PVHPLVDPLTAGPHLARFPYPPGTLPNPLLGQPPHEHEMLRHPVFGTPYP  1500
1501  RDLPGAIPPPMSAAHQLQAMHAQSAELQRLAMEQQWLHGHPHMHGGHLPS  1550
1551  QEDYYSRLKKEGDKQL                                    1566

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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