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

NucPred

Fetching Q5BHE2 from www.uniprot.org...

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

   1  MKGEITLDGAIALLSSDKTKDRTDGLADLKHILQKNKRNSNLQSMSDKAC    50
  51  HKIFESLFRLVSTEKTFYNRANSKGASSSKAAATRLSACASVVRTAVETF   100
 101  LRNLRIKSVRAILDHITNVLVSPDSSLFELLSVDYTKCLSTILHYPPHVE   150
 151  HLGVEEWESVLKFCLKVVNVRNDHNSQQSTWSPHSSVMDDYIGASGGRST   200
 201  PSRMTPSLAVREKPKGPTGVVEEALSCIKILSGVPNAPLQDNAESILLGL   250
 251  ASYVGSPSLSGSGHQTAFSAINAVAMGIIFDNSELVRVTLLDLVPVIRQH   300
 301  WTTKLMGLKDELLVTTMLIVTFLIDEIRRKPDEALIAVIDGLIHTLQREY   350
 351  FRRSEKDILQVDELVFDTNSIGQHEKFRLWPRLESPRSEHNWTVVWIMAR   400
 401  LLELSEELTTRLSTHCPPEAETPSKRQRISSKIDDVFRDSTASFGIRRVC   450
 451  ALQLIPFLLNHYACIDSKVSLLERLIPNINDDNATISSWTMIAIACIAAS   500
 501  PQADKPPLKRYWQQAWDLTSRASTSQLTSRAACYLQNSILQYSLLDYAAV   550
 551  AETINSMLSFVRLNGPSTVSDASLELWASVIRMTAQINPGSVSNASVQIC   600
 601  ELVDIYDIWDAETTVSIQKSSQSDPNDLGILDLLQAKSESFLHTWQSLSE   650
 651  DKSRHVTPDIVQILTSFCITVALYTSCLPEQPGPRLQTLLSNSRPTAIHR   700
 701  ALYGLLTPLSEVLESQRQSHKQRLYALNDDTMDLDDPFGPSTDQVEEASN   750
 751  ILCTNRSDLPLFQDSASFHRYMTILISIYNRMYSQQSEPQQHVTRALEDY   800
 801  LNDLDEVDLLAAHDLLPYVYQSCARTDRQTQLVLLENLGEKCLQTYELER   850
 851  CENSHLLCIQMMCSLAMSWTRGTQDSLSDSAADIYTWFTTIFLKKGRASS   900
 901  SVLIAFAKLLGVILSLNPAYSSDQSSPSPKTTLFKIISDGEVLVKFNAGS   950
 951  LVPQLFGQFLLEDHDNVFNDVLECLPRDPTWEEGIAVRLFLLAQLASKWH  1000
1001  TLLRRSIYHIFETPAQVHHSLWYAEKCLRSVSDALGLQDAKEIFRLFSSQ  1050
1051  ILYTWTETQSIKSMPFSIFGYANLNDMICDAQDEIVGQIMMRASESDAAE  1100
1101  LSEILGRPFVGLLTDSFYKAEAYTIAHDISTPPREGSQPKGVENRLKKIL  1150
1151  GAEVFVTLIEAQFPQIVATFFGSLDFFQQVEKAFSKRESFQEALVTLKRI  1200
1201  TEKGAARTVLPPNQQPSFRARYLLDELEFLCKRSGYELETIWTPTLASYV  1250
1251  CRTLLESIHPALGSLHACSVLRKIKILICVAGPVMLSDYPFEMIIHGLQP  1300
1301  FLVDISCSEDAVAIFWYLLEAGKTYLCEQPGLMAGIAVSTSLSLGRFLAS  1350
1351  PPVNSRQESQLQAVVGNLRTFCRWFDGYLRSYTSPALDDESSRSFRRFTC  1400
1401  SLQTIVEQESSGSGANETDLLLEVLKDRESKSGLLSKPISDRVISLLCST  1450
1451  SKAALGYHLTTIERDEDAILNAVTVCQTLRDFNPGTEYRSWAARVIGRAF  1500
1501  AATGKISDALLREQDLTLFRSSSTQSGTDILCRSKANILEVLGSKLLNSR  1550
1551  QTGPIERTLQLIISNLANFPDFEPCVSAISPSVMKALTWSPYQCPGISLN  1600
1601  ALEAKELENVHGWDLSLSPSYWARNVGLFLSKAAAEDPVIGSLSNILYLI  1650
1651  PDLAVQLLPYILHDALLAEIRGKVAEVRDSISQIFNETLRAGAENSIPHA  1700
1701  RLIIKCVLYLRNQPKPGEETIVDRDDWLDINYAVASSAASRCRLPKTALM  1750
1751  FLETHVSRCTASSRRSSVAKYDLPAGLLHDIFKNIDDPDFFYGVQQTSSL  1800
1801  DSVIETLEHESSGFKNLLFQSAQYDSEIQMTGSGNAYGVLKALNSTNLQG  1850
1851  IANSMIGALGNSSDTAVPLGSMLKAATNLRQWEIPISPLNTSPPATIFRA  1900
1901  FQALNTPGPLVDMRASIGESYRSNLNLINSDRRSATSLRTAMRTLGILTE  1950
1951  IEEVLGSGSAAEIDQKWEEISARTSWLKNTDVQEVGEILSSHETLFSSIK  2000
2001  QKDYLRSAFNLSDIDAQLLEVKVIRQSLHIARNHGIAQASLRSAVYLSKL  2050
2051  ANHSVSLGLNIEGVAKFDLANVLWDQGEMAPSIQILQQLKDRNDLHKQAI  2100
2101  PISRAELLVTLSQGHHIAEARLEKPEAIIQNYLTPAVKELKGRSEGEDAG  2150
2151  RVYHGFAIFCDQQLQNPDGLEDFARIEQLRNRKEKEVVALDAMLKTAEGK  2200
2201  ERDNLKFHRTKTKQWFDLDDREYQRLKRSREAFLQQCLENYLICLRESEA  2250
2251  YNNDVLRFCALWLAQSHSDIANSAVSKYIAGVPSRKFAPLMNQLTSRLLD  2300
2301  VSDDFQALLSELIYRICSDHPFHGMYQIFASSKSKGGRDQSALSRNRAAA  2350
2351  KLADIMRNDRHIGPLWVAVHNTNINYVRFAVERLDDKAKSGAKIRLNKLA  2400
2401  PGIRLEQDAVNQRLPPPTMKIDIRVDCDYSDVPKLAKYLPDFTVASGVSA  2450
2451  PKIVTAIASNGVRYKQLFKGGNDDLRQDAIMEQVFEQVSSLLKDHQATRQ  2500
2501  RNLGIRAYKVLPLTSNAGIIEFVPNTIPLNDFLMPAHQRYYPRDMKPSAC  2550
2551  RKHIADVQTRSFEQRVRTYRQVIEKFHPVMRYFFMEKFNNPDDWFGRRLS  2600
2601  YTQSTAAISILGHVLGLGDRHGHNILLDERTGEVVHIDLGVAFEQGRVLP  2650
2651  VPEVVPFRLTRDLVDGMGITKTEGVFRRCCEFTLEALRQESYSIMTILDV  2700
2701  LRYDPLYSWTVSPLRMKKMQEQDTSDGPPVLPGSTTDQQRPTNEPSEADR  2750
2751  ALTVVAKKLSKTLSVTATVNELIQQATDEKNLAVLYCGWAAYA         2793

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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