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

NucPred

Fetching Q9N3X8 from www.uniprot.org...

The NucPred score for your sequence is 0.74 (see score help below)

   1  MRNRLLLIFYTTTVLWTIGYTQLVLGKPPIFQDGGSVEQKVAVEGEIIRL    50
  51  KCDDAELAEQYEWRIGDASGELIATSKFCEVQASRVNDEKKYRCVARNTV   100
 101  GAAISPPSMVRSKYLDDFDASDESVQYEVTTGVGRYFVLRRPTLLASRNL   150
 151  DISYSWIKDDSHQVTPDATHFVTSDGNLVVTGVKRDDFGAYKLMASSDDL   200
 201  KEIVSKEYNVRDNGLSPSLQNTLSIVYFPTDRTIIESTLPHDEIFDCVTS   250
 251  FGSKDDVRIRWFLNGQQISGSEVGMTTTLNNRRLIISNPSSFTRGEHKLE   300
 301  CRADAAMGRTSDQKSAYMTFISRPILKDLPNEIQKTVGSSLSLKCSVKKK   350
 351  SSMDIKWYKNGLMMTTQRGKLTIDRIKQDDFGLYQCEATNAAGADLASVW   400
 401  VKEGEANETVATEMSEDGMSLEEEISMETPPPRKLKFFDNSKSQEQLFPF   450
 451  TSELEPSQKLIKTPKDLTVASGTDRIMMECAATGSPPPNIIWLLNGHEIQ   500
 501  TDNVKYDLTNDGLAIHDIRKSDEGEYTCEISGSNVKATANVQVNGDSLIE   550
 551  YGPADQKSLIGTNVEFSCEVAKEYVRKASVEWYLNDVLLPVNGNSGLRIS   600
 601  RNRKGSLIIRQVGPDNTGEYRCRVTVDGREENASAMLQIIEKPAMPERVR   650
 651  AELHNETMPAKVRVRWNEGFDGNEPIIKHAIEMRTMGPTGLWSDWTTAID   700
 701  NIPKEEGKPCCWTDIEDLRPSSTAEFRVVASNKHGPGKPSLPSYSVTMPQ   750
 751  QPPSAAPRNVAASARSPHSVMVQWQQPKEELDSGDVLGYVVRYRLAGYSS   800
 801  LTWNEKNLTTKDARNTLVDELITWREYEIQVAAYNKRGLGVFSESIEVTT   850
 851  SEGRPTQAPKNVRVKVLNSTAVAIEFTAPEQQRIPGVNLGYKVQFWKGEP   900
 901  EKGELYKQVILDPDRRQLTTVVNELEKFGHYNLTTLCFTTPGDGPRSNVV   950
 951  KVVTEEDTPESVDELSIAEVMYNGAVITWNSPLKQNGIVTKYTIRHWAAS  1000
1001  SPDVKTKHEVDGSTTNFTIDGLQPSTRYGVDVMASTRKGDGPVEETKFES  1050
1051  GVPPELPGRPSMLSIGDISATTVQLHFTPGFDGHTAIRQWVVEGKMADSS  1100
1101  VFAHVFNVSAPKARSITVTGLRPFTQYQLRLIAENVKGRGAPSEPSRSFE  1150
1151  TLQTNPDTPSQRLFAEPVSATSISVSWTPLLATHWNGQPKGYLIVYREID  1200
1201  DENWKEVRTPALRSSEHTVTDLRPFTSYEVNVFSENGFGRSLPTDSVKAR  1250
1251  TYESVPSGSPRNIVVTAEGSKAAIIKWNPVAELSTNGDVIGYKLRVVPER  1300
1301  ESLMADETKVIDIPGQSTLMAKVSDLRPFTSYHVYMSAYTIVGNGPENST  1350
1351  PISFETMEDVPAPPESFQCSYISEQEVRMKWLPPGSPNGKITNYIISYWK  1400
1401  SHEPRSMAIDAPLLGNLLMFAAMSLNPNTQYTFAIKARNSKGESEEAVAE  1450
1451  VMTSSVRLPVRNAPAPVRDTLSQHQATEIIIRWDESLPRKLTEDAESPVR  1500
1501  AVQVSYQKTNEDEWITLEKKFEYSKRRSVIKHLSPNSMFRFRIRFIGDFL  1550
1551  ESSWSPESEWMRTLPSAPFAQPISLKATPYERNSVQLEWVVPHKSTWNSD  1600
1601  AIGYRIHYREYPSNETWQMEEIAIRDEHEDKEEKILAKLDSFKHYILRMR  1650
1651  IFNSEGEGPFSAPVFAYVGYSIPKRNLNNIITEPLSSSSIRVKWDAWPKE  1700
1701  DSETITSFKVRYVPVASVLSSVSSEEEIMIVDTNECTLNDLRKFTEYQIS  1750
1751  VSPYNRAGEGKMSQVRDKTLEDKPGPVGILRFSDVLMDSVKVSWDEPSQP  1800
1801  NGNVIGYIVNYKGYRMQEEFKNEDQQRTSRNYFDTHGLAEGVTYFFSVWA  1850
1851  ETSAGKGEQRSANVTIGPSKDGPPPPSKPQITSGQSYVTLNWNDVADSDE  1900
1901  IVGHLLQAKRVSVAEEAPANGYVSQRPRRNEIKGAKSAAQTAAATSTRPT  1950
1951  HPIGEWITLRPTEGRSEKEQVSYRELQPSSYYAFRVFTRNVRGIGMASVE  2000
2001  TEQLFVPESIPDDPFYTTWWFMALVAMGAFVLIVIIIAILCVTGSSAKYR  2050
2051  REKRSRSIDSLQLADGNFASFQLKGTSAANMTRSRELPTRPGTTQSWVSD  2100
2101  QSREPPAYGSVLGGSRNSGGVMNMYGLATDVIPPLPNSGPPHTSVEAMQK  2150
2151  LSALVGRDIRSQNTAYVTPSARGGSDNGRNEYMPTRSDLYATRSEYGRVE  2200
2201  YRGHIPSSSGGSGAGSQPQGSPLQQPEVYDSFDEEEDVVDDDTVIRGDRT  2250
2251  MTDGVDDIARHYGSTDQYRDTWRKVRDTDMVRAPILTGHPSSAAGRSSTT  2300
2301  DSTSEGPWANIPATPNLTTGFSSFV                           2325

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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