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

NucPred

Fetching Q71F56 from www.uniprot.org...

The NucPred score for your sequence is 0.85 (see score help below)

   1  MTAAANWVANGASLEDCHSNLFSLAELTGIKWRRYNFGGHGDCGPIISAP    50
  51  AQDDPILLSFIRCLQANLLCVWRRDVKPDCKELWIFWWGDEPNLVGVIHH   100
 101  ELQVVEEGLWENGLSYECRTLLFKAIHNLLERCLMDKNFVRIGKWFVRPY   150
 151  EKDEKPVNKSEHLSCAFTFFLHGESNVCTSVEIAQHQPIYLINEEHIHMA   200
 201  QSSPAPFQVLVSPYGLNGTLTGQAYKMSDPATRKLIEEWQYFYPMVLKKK   250
 251  EESKEEDELGYDDDFPVAVEVIVGGVRMVYPSAFVLISQNDIPVPQSVAS   300
 301  AGGHIAVGQQGLGSVKDPSNCGMPLTPPTSPEQAILGESGGMQSAASHLV   350
 351  SQDGGMITMHSPKRSGKIPPKLHNHMVHRVWKECILNRTQSKRSQMSTPT   400
 401  LEEEPASNPATWDFVDPTQRVSCSCSRHKLLKRCAVGPNRPPTVSQPGFS   450
 451  AGPSSSSSLPPPASSKHKTAERQEKGDKLQKRPLIPFHHRPSVAEELCME   500
 501  QDTPGQKLGLAGIDSSLEVSSSRKYDKQMAVPSRNTSKQMNLNPMDSPHS   550
 551  PISPLPPTLSPQPRGQETESLDPPSVPVNPALYGNGLELQQLSTLDDRTV   600
 601  LVGQRLPLMAEVSETALYCGIRPSNPESSEKWWHSYRLPPSDDAEFRPPE   650
 651  LQGERCDAKMEVNSESTALQRLLAQPNKRFKIWQDKQPQLQPLHFLDPLP   700
 701  LSQQPGDSLGEVNDPYTFEDGDIKYIFTANKKCKQGTEKDSLKKNKSEDG   750
 751  FGTKDVTTPGHSTPVPDGKNAMSIFSSATKTDVRQDNAAGRAGSSSLTQV   800
 801  TDLAPSLHDLDNIFDNSDDDELGAVSPALRSSKMPAVGTEDRPLGKDGRA   850
 851  AVPYPPTVADLQRMFPTPPSLEQHPAFSPVMNYKDGISSETVTALGMMES   900
 901  PMVSMVSTQLTEFKMEVEDGLGSPKPEEIKDFSYVHKVPSFQPFVGSSMF   950
 951  APLKMLPSHCLLPLKIPDACLFRPSWAIPPKIEQLPMPPAATFIRDGYNN  1000
1001  VPSVGSLADPDYLNTPQMNTPVTLNSAAPASNSGAGVLPSPATPRFSVPT  1050
1051  PRTPRTPRTPRGGGTASGQGSVKYDSTDQGSPASTPSTTRPLNSVEPATM  1100
1101  QPIPEAHSLYVTLILSDSVMNIFKDRNFDSCCICACNMNIKGADVGLYIP  1150
1151  DSSNEDQYRCTCGFSAIMNRKLGYNSGLFLEDELDIFGKNSDIGQAAERR  1200
1201  LMMCQSTFLPQVEGTKKPQEPPISLLLLLQNQHTQPFASLNFLDYISSNN  1250
1251  RQTLPCVSWSYDRVQADNNDYWTECFNALEQGRQYVDNPTGGKVDEALVR  1300
1301  SATVHSWPHSNVLDISMLSSQDVVRMLLSLQPFLQDAIQKKRTGRTWENI  1350
1351  QHVQGPLTWQQFHKMAGRGTYGSEESPEPLPIPTLLVGYDKDFLTISPFS  1400
1401  LPFWERLLLDPYGGHRDVAYIVVCPENEALLEGAKTFFRDLSAVYEMCRL  1450
1451  GQHKPICKVLRDGIMRVGKTVAQKLTDELVSEWFNQPWSGEENDNHSRLK  1500
1501  LYAQVCRHHLAPYLATLQLDSSLLIPPKYQTPPAAAQGQATPGNAGPLAP  1550
1551  NGSAAPPAGSAFNPTSNSSSTNPAASSSASGSSVPPVSSSASAPGISQIS  1600
1601  TTSSSGFSGSVGGQNPSTGGISADRTQGNIGCGGDTDPGQSSSQPSQDGQ  1650
1651  ESVTERERIGIPTEPDSADSHAHPPAVVIYMVDPFTYAAEEDSTSGNFWL  1700
1701  LSLMRCYTEMLDNLPEHMRNSFILQIVPCQYMLQTMKDEQVFYIQYLKSM  1750
1751  AFSVYCQCRRPLPTQIHIKSLTGFGPAASIEMTLKNPERPSPIQLYSPPF  1800
1801  ILAPIKDKQTELGETFGEASQKYNVLFVGYCLSHDQRWLLASCTDLHGEL  1850
1851  LETCVVNIALPNRSRRSKVSARKIGLQKLWEWCIGIVQMTSLPWRVVIGR  1900
1901  LGRLGHGELKDWSILLGECSLQTISKKLKDVCRMCGISAADSPSILSACL  1950
1951  VAMEPQGSFVVMPDAVTMGSVFGRSTALNMQSSQLNTPQDASCTHILVFP  2000
2001  TSSTIQVAPANYPNEDGFSPNNDDMFVDLPFPDDMDNDIGILMTGNLHSS  2050
2051  PNSSPVPSPGSPSGIGVGSHFQHSRSQGERLLSREAPEELKQQPLALGYF  2100
2101  VSTAKAENLPQWFWSSCPQAQNQCPLFLKASLHHHISVAQTDELLPARNS  2150
2151  QRVPHPLDSKTTSDVLRFVLEQYNALSWLTCNPATQDRTSCLPVHFVVLT  2200
2201  QLYNAIMNIL                                          2210

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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