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

NucPred

Fetching O74475 from www.uniprot.org...

The NucPred score for your sequence is 0.75 (see score help below)

   1  MSGNNENVSGITGHDAVSDDQYAYDSEVYDDQNAYQRQPADAYSNEEFLD    50
  51  QADYDSMYGEGYNGYDYPTGVTESYGDEYTPVDTASSGINQYSTEKGKFT   100
 101  RPSDEYESEYSDYNAQPSDANNFYNLRGDGRYNAYDPSSDSLANVYNSVP   150
 151  YGSSPYDFSNSSFVGNSGSGTPLDGDSGSFYADSANLTNREPYPAWTPEN   200
 201  ELPLTKEEIEDIFIDLTNKLGFQRDSMRNMYDFFMCLLDSRASRMTPDQA   250
 251  LLTLHADYIGSDIANYKKWYFASQMDREDAVGLANVGIYGGKVTSIKEKG   300
 301  KFFSRNKKAPKVVKPPRKSRFKRKKKKEQPEEAEDEYIDVNTDDSLESAE   350
 351  YRWRSHMRSMTQFERAQQIALWLLLWGEANNVRFMPEVIAFLFKCAYDYI   400
 401  ISPEAQNVTEPVPEGYYLDNIVSPLYQYMHDQQFEIINGKYVRRERPHDQ   450
 451  LIGYDDINQLFWHAEGIARLIFEDGTRLIDIPASERFHRLPEVQWNRAFY   500
 501  KTYYESRSWFHLITNFNRIWVIHFGMFWYFTAFNSPTLYTKPFHQRDGPK   550
 551  PTGASQWAAVACTSVVSCIIMAAASLCEYLFVPRRFPGSKPIWKRLCIIV   600
 601  LIAIINLIPIVYIFGFSSKHQQRSGRRIAVGVVAFLMSIATYVYFSLVPL   650
 651  QSTFGKLSVKDSRKYLANKYFTSNFAPLKFDNQALSVIIWVCVFTCKFAE   700
 701  SYFFLTLSIRDPIIVLSTMRPYLCSIYWAGSRLCFVQPRIILGIMYFTDL   750
 751  ILFFLDTYLWYIIFNTIFSVLRSFVLGISILTPWRNIFSRMPQRIYGKIL   800
 801  ATNDMEIKYKPKILISQIWNAIVISMYREHLLSIDHVQRLLYHQVPAEEG   850
 851  RRTLRTPTFFVSQDDNIVHTTFFPANSEAERRLSFFAQSLATPIPEPVPV   900
 901  DNMPTFTVLIPHYAEKILLSLREIIREEDQLSRVTLLEYLKQLHPVEWDC   950
 951  FVKDTKILVEENAPYENDSVSEKEGTYKSKVDDLPFYCIGFKSAMPEYTL  1000
1001  RTRIWASLRSQTLYRTISGFMNYSRAIKLLYRVENPEIVQMFGGNTDRLE  1050
1051  RELDRMARRKFKLVVSMQRYAKFTKEEYENAEFLLRAYPDLQIAYLDEDP  1100
1101  PEEEGAEPQLFAALIDGHSEIMENERRRPKYRIRLSGNPILGDGKSDNQN  1150
1151  MSLPFYRGEYIQLIDANQDNYLEECLKIRSVLAEFEEMETDNVNPYSESA  1200
1201  RERNKHPVAILGAREYIFSENIGILGDVAAGKEQTFGTLFSRTLAQIGGK  1250
1251  LHYGHPDFLNGIFMTTRGGVSKAQKGLHVNEDIYAGMNAMLRGGRIKHCE  1300
1301  YFQCGKGRDLGFGSILNFNTKVGTGMGEQMLSREYYYLGTQLQLDRFLSF  1350
1351  YFAHPGFHLNNMFIMLSVQLFMVVLINLGAIYHVVTVCYYNGNQKLSYDT  1400
1401  SIVPRGCYQLGPVLSWLKRCVISIFIVFWISFIPLTVHELIERGVWRATK  1450
1451  RFFKQIGSFSPLFEVFTCQVYSQAITSDLAYGGARYIGTGRGFATARLPF  1500
1501  SILYSRFAVPSIYIGARFLMMLLFGTMTVWVAHLIYWWVSIMALCVAPFL  1550
1551  FNPHQFDWNDFFVDYREFIRWLSRGNSRSHANSWIGYCRLTRTRITGYKR  1600
1601  RVLGQPSDKISMDTPRAKFTNVFFSDVLIPALLAAGAIIPYFFINSQPGN  1650
1651  PMFITDPNNPSPYVHDTKTGTNPILRLVIISLIPIAAGFGMSGFFGGMAC  1700
1701  CLGPAFGLCCKKFPSIFAAIAHTIQIFIFIAIFEVCWFLDGWSLPKTVLA  1750
1751  FCAVTAIHRFIFKILTLLCLSREVKQDSANISWWSGKWYGKGYGYHAFTL  1800
1801  PAREFVCKAIELNLFATDFFLGHLLLFFMLPVICIPYIDRWHSVLLFWLR  1850
1851  PSRQIRPPIFSTKQNRLRKRIVRRYSALYFSILVIFLILIIVPLAAGAEI  1900
1901  RQGLTASEAVAKGAVGWNQTNSSIGSGIIQPRDTNYTANYSFWYDRYHFE  1950
1951  FNTTY                                               1955

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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