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

NucPred

Fetching P43071 from www.uniprot.org...

The NucPred score for your sequence is 0.42 (see score help below)

   1  MSDSKMSSQDESKLEKAISQDSSSENHSINEYHGFDAHTSENIQNLARTF    50
  51  THDSFKDDSSAGLLKYLTHMSEVPGVNPYEHEEINNDQLNPDSENFNAKF   100
 101  WVKNLRKLFESDPEYYKPSKLGIGYRNLRAYGVANDSDYQPTVTNALWKL   150
 151  ATEGFRHFQKDDDSRYFDILKSMDAIMRPGELTVVLGRPGAGCSTLLKTI   200
 201  AVNTYGFHIGKESQITYDGLSPHDIERHYRGDVIYSAETDVHFPHLSVGD   250
 251  TLEFAARLRTPQNRGEGIDRETYAKHMASVYMATYGLSHTRNTNVGNDFV   300
 301  RGVSGGERKRVSIAEASLSGANIQCWDNATRGLDSATALEFIRALKTSAV   350
 351  ILDTTPLIAIYQCSQDAYDLFDKVVVLYEGYQIFFGKATKAKEYFEKMGW   400
 401  KCPQRQTTADFLTSLTNPAEREPLPGYEDKVPRTAQEFETYWKNSPEYAE   450
 451  LTKEIDEYFVECERSNTRETYRESHVAKQSNNTRPASPYTVSFFMQVRYG   500
 501  VARNFLRMKGDPSIPIFSVFGQLVMGLILSSVFYNLSQTTGSFYYRGAAM   550
 551  FFAVLFNAFSSLLEIMSLFEARPIVEKHKKYALYRPSADALASIISELPV   600
 601  KLAMSMSFNFVFYFMVNFRRNPGRFFFYWLMCIWCTFVMSHLFRSIGAVS   650
 651  TSISGAMTPATVLLLAMVIYTGFVIPTPSMLGWSRWINYINPVGYVFESL   700
 701  MVNEFHGREFQCAQYVPSGPGYENISRSNQVCTAVGSVPGNEMVSGTNYL   750
 751  AGAYQYYNSHKWRNLGITIGFAVFFLAIYIALTEFNKGAMQKGEIVLFLK   800
 801  GSLKKHKRKTAASNKGDIEAGPVAGKLDYQDEAEAVNNEKFTEKGSTGSV   850
 851  DFPENREIFFWRDLTYQVKIKKEDRVILDHVDGWVKPGQITALMGASGAG   900
 901  KTTLLNCLSERVTTGIITDGERLVNGHALDSSFQRSIGYVQQQDVHLPTS   950
 951  TVREALQFSAYLRQSNKISKKEKDDYVDYVIDLLEMTDYADALVGVAGEG  1000
1001  LNVEQRKRLTIGVELVAKPKLLLFLDEPTSGLDSQTAWSICKLMRKLADH  1050
1051  GQAILCTIHQPSALIMAEFDRLLFLQKGGRTAYFGELGENCQTMINYFEK  1100
1101  YGADPCPKEANPAEWMLQVVGAAPGSHAKQDYFEVWRNSSEYQAVREEIN  1150
1151  RMEAELSKLPRDNDPEALLKYAAPLWKQYLLVSWRTIVQDWRSPGYIYSK  1200
1201  IFLVVSAALFNGFSFFKAKNNMQGLQNQMFSVFMFFIPFNTLVQQMLPYF  1250
1251  VKQRDVYEVREAPSRTFSWFAFIAGQITSEIPYQVAVGTIAFFCWYYPLG  1300
1301  LYNNATPTDSVNPRGVLMWMLVTAFYVYTATMGQLCMSFSELADNAANLA  1350
1351  TLLFTMCLNFCGVLAGPDVLPGFWIFMYRCNPFTYLVQAMLSTGLANTFV  1400
1401  KCAEREYVSVKPPNGESCSTYLDPYIKFAGGYFETRNDGSCAFCQMSSTN  1450
1451  TFLKSVNSLYSERWRNFGIFIAFIAINIILTVIFYWLARVPKGNREKKNK  1500
1501  K                                                   1501

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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