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

NucPred

Fetching O14228 from www.uniprot.org...

The NucPred score for your sequence is 0.25 (see score help below)

   1  MLVYYGGSALSVQSKKKILELTVSGVSDLNAVYFYLIYTKSNSSLNCESL    50
  51  RPILSDLQESEFKPDGTTMVYVFPRPGTISPWSSKATNIANVCGYKDVIR   100
 101  IERGIAYSVVFKDDISEEMLKSALNHLYDRMTEALRFKLPEEDEVFDKHE   150
 151  PAPLVRIELNCGQGGDKQAATERLNHANKKFGLALAPDEIDYLVECYTSE   200
 201  PSLKSREPTDVELFMFGQVNSEHCRHKIFNADWTIDGEKKDYSLFKMIRN   250
 251  THLKNPQYTISAYSDNAAVFEGNSGTLFAPVNGIWSMKDEPVEFLGKVET   300
 301  HNHPTAVSPFPGAATGSGGEIRDEGAVGQGSLSKAGLAGYSVSDLNIPGY   350
 351  KQPWELDVGKPYHIATSLDIMLEAPIGSSAFNNEFGRPCINGYFRTFCME   400
 401  VPRGDGTLEIRGYHKPIMAAGGIGRIRKQHAFKKSIAPGSPIIVLGGPAL   450
 451  LVGLGGGAASSMNAGEGSEELDFASVQRGNPEMQRRAQMVIDACTTMDEN   500
 501  IIQSIHDVGAGGVSNALPELVHDAGLGARFELRDIPCIEPSMSPMQIWCC   550
 551  ESQERYVLSVKSEDLDTFKSICERERCPYGVVGYSTVEQRLILTDRLYNT   600
 601  TPIDLPMEVLFGKPPKMSRVAETQTIPLSKFDSSLKSYLAPSSDPILDAV   650
 651  ERVLRMPAVASKSFLITIGDRSVTGLIARDQMVGPWQVPVADVGVTVTSY   700
 701  GKGINTGEALAMGEKPISALVSAAASARMAVAECIMNLVAASIPALDRIR   750
 751  LSANWMAAPSHPGEGAKLYEAVQAIGLELCPSLGISIPVGKDSMSMSMKW   800
 801  NEDGREKSVTAPLSLIITGFSPVDDLYSIWTPQLRKVEDIGSTSLIFIDL   850
 851  ANGKQRLGGSILAQSYKQLGDEVPDLDNLDTFKNFINVITQLHKTNYIQA   900
 901  YHDKSDGGLFVTLSEMAFAGHVGIECELDSLSSDNIAALFNEELGAVIQV   950
 951  CDRDIAKVLELFAANGLSTCVHRIGKVLSGQAQTISFSRSGKIIFKSTRS  1000
1001  KLHGIWHETSYKMQEIRDNPECARQEMENIADNNDPGLGYHLTFDPNVSV  1050
1051  TADLALTSRPKVAILREQGVNGYLEMAYAFYASGFTAVDVHMTDILSGRV  1100
1101  HLDDFVGIAACGGFSYGDVLGSGNGWATSILLHEDARNEFYRFFNERKDT  1150
1151  FGLGICNGCQLFSRLKSLIPGAKSWPMFTFNESAQYEGRAVMLKIDETSG  1200
1201  SKSIFTESMAGSSLPVVVAHGEGRAVFDSESDYEQFKKEGLDLIYYVNNY  1250
1251  NERTSRYPFNPNGSRDAIAGVRSPCGRFLAMMPHPERVVLKVANSYYPHS  1300
1301  KASEWGVHGPWIRLFQSARKWVG                             1323

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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