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

NucPred

Fetching Q8VHY0 from www.uniprot.org...

The NucPred score for your sequence is 0.40 (see score help below)

   1  MLLGPGHPLSAPALALALTLALLVRSTAPASFFGENHLEVPVPSALTRVD    50
  51  LLLQFSTSQPEALLLLAAGQDDHLLLQLHSGCLQVRLALGQKELKLQTPA   100
 101  DTVLSDSAPHTVVLTVSDSWAVLSVDGVLNTSAPIPRASHLKATYGLFVG   150
 151  SSGSLDLPYLKGISRPLRGCLHSAILNGRNLLRPLTSDVHEGCAEEFSAG   200
 201  DEVGLGFSGPHSLAAFPAWSTREEGTLEFTLTTRSQQAPLAFQAGDKRGN   250
 251  FIYVDIFEGHLRAVVEKGQGTMLLRNSVPVADGQPHEVSVHIDVHRLEIS   300
 301  VDQYPTRTFNRGVLSYLEPRGSLLLGGLDTEASRHLQEHRLGLAPGAANI   350
 351  SLVGCIEDFSVNGRRQGLRDAWLTRDMSAGCRPEEDEYEEEVYGPYETFS   400
 401  TLAPEAWPAMELPEPCIPEPGLPAVFANFTQLLTISPLVVAEGGTAWLEW   450
 451  RHVQPTLDLTEAELRKSQVLFSVSQSARHGDLELDILGAQTRKMFTLLDV   500
 501  VNRKARFVHDGSEDTSDQLMLEVSVTARAPVPSCLRRGQIYILPIQVNPV   550
 551  NDPPRIIFPHGSLMVILEHTQKPLGPEIFQAYDPDSACEGLTFQLLGVSS   600
 601  GVPVEHRDQPGEPATEFSCRELEVGDIVYVHRGGPAQDLTFRVSDGMQAS   650
 651  APATLKVVAVRPAIQILHNTGLHLAQGSAAAILPANLSVETNAVGQDVSV   700
 701  LFRVTGTLQFGELQKQGAGGVEGTEWWDTLAFHQRDVEQGRVRYLSTDPQ   750
 751  HHTQDTVEDLILEVQVGQETLSNLSFPVTIQRATVWMLRLEPLHTQNPHQ   800
 801  ETLTPAHLEASLEEEEEEGSPQPHTFHYELVQAPRRGNLLLQGTRLSDGE   850
 851  SFSQSDLQAGRVTYRATMRTSEAADDSFRFRVTSPPHFSPLYTFPIHIGG   900
 901  DPNAPVLTNVLLMVPEGGEGVLSADHLFVKSLNSASYLYEVMEQPHHGKL   950
 951  AWRDPKGKSTPVTSFTNEDLLHGRLVYQHDDSETIEDDIPFVATRQGEGS  1000
1001  GDMAWEEVRGVFRVAIQPVNDHAPVQTISRVFHVARGGQRLLTTDDVAFS  1050
1051  DADSGFSDAQLVLTRKDLLFGSIVAMEEPTRPIYRFTQEDLRKKQVLFVH  1100
1101  SGADHGWLQLQVSDGQHQATAMLEVQASEPYLHVANSSSLVVPQGGQGTI  1150
1151  DTAVLQLDTNLDIRSGNEVHYHVTAGPQWGQLLRDGQSVTSFSQRDLLDG  1200
1201  AILYSHNGSLSPQDTLAFSVAAGPVHTNTFLQVTIALEGPLAPLQLVQHK  1250
1251  KIYVFQGEAAEIRRDQLEVVQEAVLPADIMFSLRSPPNAGYLVMVSHGAS  1300
1301  AEEPPSLDPVQSFSQEAVNSGRVLYLHSRPGAWSDSFSLDVASGLGDPLE  1350
1351  GISVELEVLPTVIPLDVQNFSVPEGGTRTLAPPLVQITGPYFPTLPGLVL  1400
1401  QVLEPPQHGALQKEDHSQDGSLSTFSWREVEEQLIRYVHDGSETQTDAFV  1450
1451  LLANASEMDRQSQPVAFTITILPVNDQPPVLTTNTGLQIWEGAIVPIPPE  1500
1501  ALRGTDNDSGPEDLVYTIEQPSNGRIALRVAPDTEVHRFTQAQLDSGLVL  1550
1551  FSHRGALEGGFHFDLSDGAHTSPGHFFRVVAQKQALLSLEGTRKLTVCPE  1600
1601  SVQPLSSQSLSASSSTGADPRHLLYRVVRGPQLGRLLHAQQGSAEEVLVN  1650
1651  FTQAEVNAGNILYEHEMSSEPFWEAHDTIGLLLSSPPARDLAATLAVMVS  1700
1701  FDAACPQRPSRLWKNKGLWVPEGQRAKITVAALDAANLLASVPASQRSRH  1750
1751  DVLFQVTQFPTRGQLLVSEEPLHARRPYFLQSELAAGQLVYAHGGGGTQQ  1800
1801  DGFRFRAHLQGPTGTSVAGPQTSEAFVITVRDVNERPPQPQASIPLRVTR  1850
1851  GSRAPVSRAQLSVVDPDSAPGEIEYEVQRAPHNGFLSLAGDNTGPVTHFT  1900
1901  QADVDAGRLAFVANGSSVAGVFQLSMSDGASPPIPMSLAVDVLPSTIEVQ  1950
1951  LRAPLEVPQALGRTSLSRQQLQVISDREEPDVAYRLTQGPLYGQLLVGGQ  2000
2001  PASAFSQLQVDQGDVVFVFTNFSSSQDHFKVVALARGVNASATVNVTVQA  2050
2051  LLHVWAGGPWPQGTTLRLDPTVLDASELANRTGSMPHFRLLAGPRYGRVV  2100
2101  RVSQGRTESRSNQLVEHFTQRDLEEGQLGLEVGKPEGRSTGPAGDRLTLE  2150
2151  LWAKGVPPAVALLDFATEPYHAAKSYSVALLSVPEAVRTETEKPGRSVPT  2200
2201  GQPGQAASSPVPTAAKGGFLGFLEANMFSIIIPVCLILLLLALILPLLFY  2250
2251  LRKRNKTGKHDVQVLTAKPRNGLAGDTETFRKVEPGQAIPLITVPGQGPP  2300
2301  PGGQPDPELLQFCRTPNPALRNGQYWV                         2327

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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