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

NucPred

Fetching Q00657 from www.uniprot.org...

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

   1  MLLSPGHPLSAPALALILTLALLVRSTAPASFFGENHLEVPVPSALTRVD    50
  51  LLLQFSTSQPEALLLLAAGQTDHLLLQLQSGHLQVRLALGQNELSLQTPA   100
 101  DTVLSDSTTHTVVLTVSNSWAVLSVDGVLNTSAPIPKASHLKVPYGLFVG   150
 151  SSGSLDLPYLKGISRPLRGCLHSAILNGRNLLRPLTPDVHEGCAEEFSAG   200
 201  DEVGLGFSGPHSLAAFPAWSTREEGTLEFTLTTRSQQAPLAFQAGDKRGN   250
 251  FIYVDIFEGHLRAVVEKGQGTMLLRNSVPVADGQPHEVSVHIDVHRLEIS   300
 301  VDQYPTRTFNRGVLSYLEPRGSLLLGGLDTEASRHLQEHRLGLTPGAANI   350
 351  SLVGCIEDFSVNGRRLGLRDAWLTRDMAAGCRPEEDEYEEEVYGPFEAFS   400
 401  TLAPEAWPVMDLPEPCVPEPGLPAVFANFTQLLTISPLVVAEGGTAWLEW   450
 451  RHVQPTLDLTEAELRKSQVLFSVSQGARHGELELDIPGAQTRKMFTLLDV   500
 501  VNRKARFVHDGSEDTSDQLMLEVSVTSRAPVPSCLRRGQIYILPIQVNPV   550
 551  NDPPRIVFPHGSLMVILEHTQKPLGPEIFQAYDPDSACEGLTIQLLGVSA   600
 601  SVPVEHRDQPGEPVTEFSCRDLEAGNIVYVHRGGPAQDLTFRVSDGMQAS   650
 651  GPATLKVVAVRPAIQILHNTGLRLAQGSAAAILPANLSVETNAVGQDVSV   700
 701  LFRVTGTLQFGELQKQGAGGVEGTEWWDTLAFHQRDVEQGRVRYLSTDPQ   750
 751  HHTQDTVEDLTLEVQVGQETLSNLSFPVTIQRATVWMLQLEPLHTQNPHQ   800
 801  ETLTSAHLEASLEEEGEGGPYPHIFHYELVQAPRRGNLLLQGTRLSDGQS   850
 851  FSQSDLQAGRVTYRATTRTSEAAEDSFRFRVTSPPHFSPLYTFPIHIGGD   900
 901  PNAPVLTNVLLMVPEGGEGVLSADHLFVKSLNSASYLYEVMEQPHHGSLA   950
 951  WRDPKGRATPVTSFTNEDLLHGRLVYQHDDSETIEDDIPFVATRQGEGSG  1000
1001  DMAWEEVRGVFRVAIQPVNDHAPVQTISRVFHVARGGQRLLTTDDVAFSD  1050
1051  ADSGFSDAQLVLTRKDLLFGSIVAMEEPTRPIYRFTQEDLRKKQVLFVHS  1100
1101  GADHGWLQLQVSDGQHQATAMLEVQASEPYLHVANSSSLVVPQGGQGTID  1150
1151  TAVLHLDTNLDIRSGNEVHYHVTAGPHWGQLLRDGQSVTSFSQRDLLDGA  1200
1201  ILYSHNGSLSPQDTLALSVAAGPVHTSTVLQVTIALEGPLAPLQLVQHKR  1250
1251  IYVFQGEAAEIRRDQLEVVQEAVLPADIMFSLRSPPNAGYLVMVSHGASA  1300
1301  DGPPSLDPVQRFSQEAINSGRVLYLHSRPGAWSDSFSLDVASGLGDPLEG  1350
1351  ISVELEVLPTVIPLDVQNFSVPEGGTRTLAPPLIQITGPYLGTLPGLVLQ  1400
1401  VLEPPQHGALQKEDRPQDGTLSTFSWREVEEQLIRYVHDGSETQTDGFIL  1450
1451  LANASEMDRQSQPMAFTITILPVNDQPPVITTNTGLQIWEGAIVPIPPEA  1500
1501  LRGIDSDSGPEDLVYTIEQPSNGRIALRVAPDAEAHRFTQAQLDSGLVLF  1550
1551  SHRGALEGGFHFDLSDGVHTSPGHFFRVVAQKQVLLSLEGSRKLTVCPES  1600
1601  VQPLSSQSLSASSSTGSDPRHLLYQVVRGPQLGRLLHAQQGSAEEALVNF  1650
1651  TQAEVNAGNILYEHEISSEPFWEAHDTIGLLLSSSPARDLAATLAVTVSF  1700
1701  DAACPQRPSRLWRNKGLWVPEGQRAKITVAALDAANLLASVPASQRGRHD  1750
1751  VLFQITQFPTRGQLLVSEEPLHARRPHFLQSELTAGQLVYAHGGGGTQQD  1800
1801  GFRFRAHLQGPTGASVAGPQTSEAFVITVRDVNERPPQPQASIPLRITRG  1850
1851  SRAPVSRAQLSVVDPDSAPGEIEYEVQRAPHNGFLSLAGDNTGPVTHFTQ  1900
1901  ADVDAGRLAFVANGSSVAGVFQLSMSDGASPPIPMSLAVDVLPSTIEVQL  1950
1951  RAPLEVPQALGRSSLSRQQLQVISDREEPDVAYRLTQGPLYGQVLVGGQP  2000
2001  ASAFSQLQVDQGDVVFAFTNFSSSQDHFKVLALARGVNASATVNVTVQAL  2050
2051  LHVWAGGPWPQGTTLRLDPTVLDASELANRTGSMPRFRLLEGPRYGRVVR  2100
2101  VSQGRAESRTNQLVEDFTQQDLEEGRLGLEVGRPEGRSTGPTGDRLTLEL  2150
2151  QATGVPPAVALLDFATEPYHAAKFYKVTLLSVPEAARTETEKTGKSTPTG  2200
2201  QPGQAASSPMPTVAKSGFLGFLEANMFSVIIPVCLVLLLLALILPLLFYL  2250
2251  RKRNKTGKHDVQVLTAKPRNGLAGDTETFRKVEPGQAIPLTTVPGQGPPP  2300
2301  GGQPDPELLQFCRTPNPALRNGQYWV                          2326

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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