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

NucPred

Fetching Q6JPI3 from www.uniprot.org...

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

   1  MTAAANWVANGASLEDCHSNLFSLAELTGIKWRRYNFGGHGDCGPIISAP    50
  51  AQDDPILLSFIRCLQANLLCVWRRDVKPDCKELWIFWWGDEPNLVGVIHH   100
 101  ELQVVEEGLWENGLSYECRTLLFKAIHNLLERCLMDKNFVRIGKWFVRPY   150
 151  DKDEKPVNKSEHLSCAFTFFLHGESNVCTSVEIAQHQPIYLINEEHLHMA   200
 201  QSSPAPFQVLVSPYGLNGTLTGHAYKMSDPAARKLIEEWHCFYPMVLRKR   250
 251  EEPREEAELGYDDDFPVAVEVIVGGVRMVYPSAFVLVSQNDIPVPQSGHG   300
 301  TVAQQGLGSVKDPSNCGMPLTPPTSPEQVVIGESGGVQSAASHLGSQDGG   350
 351  MSTMHSPKRSRKTPPKLHSHMVRRVWRECILSRAQSKRSQMSTPTREEEA   400
 401  AHSPAAWDFVDPTQRVSCSCSRHKLLKRCAVGPSRPPAISQPGFSAGLPS   450
 451  SSSLPPPASSKHKTTERQEKGDKLQKRPLVPFHHRPSVAEELCVEQDAPG   500
 501  QKLGLAGIDASLEVSNTRKYDKQMAVPSRNTSKQMNLNPMDSPHSPISPL   550
 551  PPTLSPQPRGQEAESLDPPSVPVNPALYGNGLDLQQLSTIEDRTVLVGQR   600
 601  LPLMAEASETALYSGLRPSYTESSDRWWQSFRLPSSEDAEFRPPELQGER   650
 651  FDTALDLNPESTALQRLLAQPNKRFKIWQDEQPQVQPLPFLDPSPLSQQP   700
 701  GDTLGEVNDPYTFEDGDIKYIFTANKKCKQGTEKDSLKKNKSEDGFGTKD   750
 751  VTTPGHSTPVPDGKNAMSIFSSATKTDVRQDSAAGRAGSGSLTQVTDLAP   800
 801  SLHDLDNIFDNSDDDELGAVSPALRSSKMPTVGTEERPPGKDGRAAGPYP   850
 851  PTVADLQRMFPTPPSLEQHPAFSPVMNYKDGVSSETVTALGMMESPVVSM   900
 901  VPTHLTEFRMEVEDGLGSPKPEEIKDFSYVHKVPQFQPFVGSSMFAPLKT   950
 951  LPSHCLLPLKTPDACLFRPSWAVPPKMEQLPMPPAASSIRDGYNNVPSVG  1000
1001  SLADPDYVNTPQMNTPVTLNSAAPASNSGAGVLPSPATPRFSVPTPRTPR  1050
1051  TPRTPRGGGTASGQGSVKYDSTDQGSPASTPSTTRPLNSVEPATMQPIPE  1100
1101  AHSLYVTLILSDSVMNVFKDRNFDSCCICACNMNIKGADVGLYIPDSSKE  1150
1151  DQYRCTCGFSAIVNRKLGYNSGLFLEDELDIFGKNSDIGQAAERRLMMCQ  1200
1201  SSGQSTLLPQVEGARKAPEPPVSLLLLLQNQHTQPFASLSFLDYISSANR  1250
1251  HALPCVSWTYDRVQADNNDYWTECFNALEQGRQYVDNPTGGKVDEALVRS  1300
1301  ATVHCWPHSNVLDTSMLSSQDVVRMLLSLQPFLQDAIQKKRTGRTWENIQ  1350
1351  HVQGPLTWQQFHKMAGRGTYGSEESPEPLPIPTLLVGYDKEFLTISPFSL  1400
1401  PFWERLLLEPYGGHRDVAYIVVCPENEALLEGAKTFFRDLSAVYEMCRLG  1450
1451  QHKPICKVLRDGIMRVGKTVAQKLTEELVSEWFNQPWSSEESDNHSRLKL  1500
1501  YAQVCRHHLAPYLATLQLDSGLLMPPKHQSPPAEAQGQATPGNAGSLPSN  1550
1551  SGSGAPPAGSAFNPTSSSSANPTTSSSSASSGPPGSSAASAPGITQMNTT  1600
1601  SSSGFGGGVGGQNPSAGGSSTDRTPGNVACGDTEPGQSCTQSSQDGQDSV  1650
1651  TERERIGIPTEPDSADSHAYPPAVVIYMVDPFTYTAEEDSSSGNFWLLSL  1700
1701  MRCYTEMLDHLPEHMRSSFILQIVPCQYMLQTMKDEHVFYIQYLKSMAFS  1750
1751  VYCQCRRPLPTQIHIKSLTGFGPAASIEMTLKNPERPSPIQLYSPPFILA  1800
1801  PIKDKQTEPGETFGEASQKYNVLFVGYCLSHDQRWLLASCTDLHGELLET  1850
1851  CVVNIALPSRSRKSKVSARKVGLQKLWEWCLGIVQMTSLPWRVVIGRLGR  1900
1901  LGHGELKDWSILLGECSLQTISKQLKDVCRMCGISAADSPSILSACLVAM  1950
1951  EPQGSFVVMPDAVTMGSVFGRSTALNMQSSQLNTPQDASCTHILVFPTSS  2000
2001  TIQVAPANYPNEDGFSPNNDDMFVDLPFPDDMDNDIGILMTGNLHSSPNS  2050
2051  SPVPSPGSPSGIGVGSHFQHSRSQGERLLSREAPEELKQQPLALGYFVST  2100
2101  AKAENLPQWFWSSCPQARNQCPLFLKASLHHHISVAQTDELLPARTSQRA  2150
2151  PHPLDSKTTSDVLRFVLEQYNALSWLTCNPATQDRTSCLPVHFVVLTQLY  2200
2201  NAIMNML                                             2207

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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