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

NucPred

Fetching O17582 from www.uniprot.org...

The NucPred score for your sequence is 0.97 (see score help below)

   1  MSSEPTSSIESDNLRRSKRKKFKLDFVAAAHGNNQKKSRKDPHGQGDDDD    50
  51  DTFDDDLNHFEPLSVLTEQDVSMEMFEDDEEDTVSRRRTRRSTAHFQDYQ   100
 101  EPDRWIENSGPHACHKCPSRYESKSSLANHTKMHLGEKRKFACELCDFSA   150
 151  STLKSLTHHNNIHQNFGVLSQQTSPVIPVASSADSTLNSSINSTGCQINA   200
 201  PPAPKLDEEAPIAVESVVVHHEDVAEFDTTPPPILEREDDGPPVLIREAP   250
 251  VRKSNRPMKPTQKAQKMTKQRERKSKTVESPKGSLPSSSASSVTPPPVRK   300
 301  DVEKPKIFVKTTKKNLKKTMKITKVRQRCPHCPFTTSTVTRLNRHSGGHK   350
 351  LKEGYICPSENCNFMCRKAGFLQKHYILHKGTLPWPPEYVKKGGAKMKRT   400
 401  FPESEEKKIEVTEKVQKMKKMHKRRANTVQVVAKAQLKSYIKVEVDDVIF   450
 451  KKCNIGECEFLTQTLTQLIVHKVKTHDTKTAFPQHRFLCLTCGHRAKSYA   500
 501  ALRTHKLIEHTSTHKRFHRTYYLKECVGDKFFVKYNLSKVQEEVKEEPKE   550
 551  ADGDESGDESFDSMCPASDVHPETLAAIEMKDVFFCCNMCPYKAPTMNRC   600
 601  QRHYDKHFKNDEFKCQYCSWSSRSKEVIVNHEKLHPTVVVANTNEAPVVK   650
 651  NEIEAKVEVLSKTVSSPVECTEESSLSKSIQLWCQREKLRHPELDEQFTR   700
 701  KMIDGVKGFQCTDCPYTSKYRGDMRSHKKRHDIEQLYRCVQCTYTTNRPV   750
 751  SLKDHLKQHAIVNMSIADIKSRRVVVNQGVKIGMRRGVGKDKIYCCDKCP   800
 801  YVTLALGCLWRHHRNHRDTAKINICSNCSYSSIDQRKMEEHTIIHLGLGL   850
 851  NEAVPFVKRVDQKGRPVSSLTDLNSEKMNERKSTKRKMLDKVEKMEVGED   900
 901  EEDDEESVDKGTDDGDYKQRPEKKRKQSSEEPASDPELFGSSSQPTRQLS   950
 951  ERATRNRINYSLLSKNGSGKPTPSTSSANLEKLAGSSGGASSESPEPDES  1000
1001  VEVSHWKIRTFLRSEYGVKESLKCPDCPYKSSEPDVLEKHRYYHMTKTTP  1050
1051  RPYACSDCTFNTYTPTALLQHLKLHSEGVYFDPMVKKHMKHRKGDSIPPG  1100
1101  VKGYYCKNCSFKTSIHRNFIEHSAYHRQQLINRINITLKRQPPRIEYQRP  1150
1151  KLKHQFVAKNAKYCKKCTFKCVSQSNFIEHLDRHGWNQLYKCYSCDYSDN  1200
1201  TKSVVDFHQLNHHIVKDQTLHSICQSAKFRLENGVIQIPEFQTEKSKPTP  1250
1251  DEFVSKTRGLLKCPSCEYFCHVSSELAFHMSVHHLTEPNARETISYLHMG  1300
1301  LVPPKATVTTV                                         1311

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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