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

NucPred

Fetching P23201 from www.uniprot.org...

The NucPred score for your sequence is 0.86 (see score help below)

   1  MGTSSEVSLAHHRDIFHYYVSLKTFFEVTGENRDRSNSTRAQKARAKLLK    50
  51  LSSSQFYELSTDVSDELQRRIGEDANQPDYLLPKANFHMKRNQARQKLAN   100
 101  LSQTRFNDLLDDILFEIKRRGFDKDLDAPRPPLPQPMKQEVSKDSDDTAR   150
 151  TSTNSSSVTQVAPNVSVQPSLVIPKMASIDWSSEEEEEEQVKEKPNEPEG   200
 201  KQTSMDEKKEAKPALNPIVTDSDLPDSQVLARDITSMARTPTTTHKNYWD   250
 251  VNDSPIIKVDKDIDNEKGPEQLKSPEVQRAENNNPNSEMEDKVKELTDLN   300
 301  SDLHLQIEDLNAKLASLTSEKEKEKKEEKEEKEKEKNLKINYTIDESFQK   350
 351  ELLSLNSQIGELSIENENLKQKISEFELHQKKNDNHNDLKITDGFISKYS   400
 401  SADGLIPAQYILNANNLIIQFTTRLSAVPIGDSTAISHQIGEELFQILSQ   450
 451  LSNLISQLLLSADLLQYKDQVILLKASLSHAITSIRYFSVYGPVLIPKIT   500
 501  VQAAVSEVCFAMCNLIDSAKIKSDSNGESTTSNEGNRQVLEYSSPTATTP   550
 551  MTPTFPSTSGINMKKGFINPRKPASFLNDVEEEESPVKPLKITQKAINSP   600
 601  IIRPSSSNGVPTTSRKPSGTGLFSLMIDSSIAKNSSHKEDNDKYVSPIKA   650
 651  VTSASNSASSNISEIPKLTLPPQAKIGTVIPPSENQVPNIKIENTEEDNK   700
 701  RSDITNEISVKPTSSIADKLKQFEQSSEKKSSPKENPIAKEEMDSKPKLS   750
 751  NKFITSMNDVSTDDSSSDGNENDDADDDDDFTYMALKQTMKREGSKIEKN   800
 801  NDSKLPANIVELDLHESPESVKIESPESIKEITSSEMSSEMPSSSLPKRL   850
 851  VEDVEPSEMPEKGASVESVRKKNFQEPLGNVESPDMTQKVKSLGMTGKAV   900
 901  GPESDSRVESPGMTGQIKSLNMAGKVVGPEADSRVESPGMKEQIKSLGMT   950
 951  GKITAQESIKSPEAARKLASSGEVDKIESPRMVRESESLEAVGNTIPSNM  1000
1001  TVKMESPNLKGNTVSEPQEIRRDIASSEPIENVDPPKVLKKIVFPKAVNR  1050
1051  TGSPKSVEKTPSSATLKKSGLPEPNSQIVSPELAKNSPLAPIKKNVELRE  1100
1101  TNKPHTETITSVEPTNKDANTSWRDADLNRTIKREEEDEDFDRVNHNIQI  1150
1151  TGAYTKTGKIDYHKIPVDRKAKSEAEVHTSEEDIDESNNVNGKRADAQIH  1200
1201  ITERKHAFVNPTENSQVKKTSHSPFLNSKPVQYENSESNGGINNHIKIKN  1250
1251  TGETTAHDEKHYSDDDDSSYQFVPMKHEEQEQEQNRSEEEESEDDDEEEE  1300
1301  DSDFDVDTFDIENPDNTLSELLLYLEHQTMDVISTIQSLLTSIKKPQVTK  1350
1351  GNLRGESNAINQVIGQMVDATSISMEQSRNANLKKHGDWVVQSLRDCSRR  1400
1401  MTILCQLTGDGILAKEKSDQDYADKNFKQRLAGIAFDVAKCTKELVKTVE  1450
1451  EASLKDEINYLNSKLK                                    1466

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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