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

NucPred

Fetching Q62261 from www.uniprot.org...

The NucPred score for your sequence is 0.94 (see score help below)

   1  MTTTVATDYDNIEIQQQYSDVNNRWDVDDWDNENSSARLFERSRIKALAD    50
  51  EREAVQKKTFTKWVNSHLARVSCRITDLYTDLRDGRMLIKLLEVLSGERL   100
 101  PKPTKGRMRIHCLENVDKALQFLKEQRVHLENMGSHDIVDGNHRLTLGLI   150
 151  WTIILRFQIQDISVETEDNKEKKSAKDALLLWCQMKTAGYPNVNIHNFTT   200
 201  SWRDGMAFNALIHKHRPDLIDFDKLKKSNAHYNLQNAFNLAEQHLGLTKL   250
 251  LDPEDISVDHPDEKSIITYVVTYYHYFSKMKALAVEGKRIGKVLDNAIET   300
 301  EKMIEKYESLASDLLEWIEQTIIILNNRKFANSLVGVQQQLQAFNTYRTV   350
 351  EKPPKFTEKGNLEVLLFTIQSKMRANNQKVYMPREGKLISDINKAWERLE   400
 401  KAEHERELALRNELIRQEKLEQLARRFDRKAAMRETWLSENQRLVSQDNF   450
 451  GFDLPAVEAATKKHEAIETDIAAYEERVQAVVAVARELEAENYHDIKRIT   500
 501  ARKDNVIRLWEYLLELLRARRQRLEMNLGLQKIFQEMLYIMDWMDEMKVL   550
 551  LLSQDYGKHLLGVEDLLQKHALVEADIAIQAERVRGVNASAQKFATDGEG   600
 601  YKPCDPQVIRDRVAHMEFCYQELCQLAAERRARLEESRRLWKFFWEMAEE   650
 651  EGWIREKEKILSSDDYGKDLTSVMRLLSKHRAFEDEMSGRSGHFEQAIKE   700
 701  GEDMIAEEHFGSEKIRERIIYIREQWANLEQLSAIRKKRLEEASLLHQFQ   750
 751  ADADDIDAWMLDILKIVSSNDVGHDEYSTQSLVKKHKDVAEEITNYRPTI   800
 801  DTLHEQASALPQAHAESPDVKGRLAGIEERCKEMAELTRLRKQALQDTLA   850
 851  LYKMFSEADACELWIDEKEQWLNNMQIPEKLEDLEVIQHRFESLEPEMNN   900
 901  QASRVAVVNQIARQLMHNGHPSEKEIRAQQDKLNTRWSQFRELVDRKKDA   950
 951  LLSALSIQNYHLECNETKSWIREKTKVIESTQDLGNDLAGVMALQRKLTG  1000
1001  MERDLVAIEAKLSDLQKEAEKLESEHPDQAQAILSRLAEISDVWEEMKTT  1050
1051  LKNREASLGEASKLQQFLRDLDDFQSWLSRTQTAIASEDMPNTLTEAEKL  1100
1101  LTQHENIKNEIDNYEEDYQKMRDMGEMVTQGQTDAQYMFLRQRLQALDTG  1150
1151  WNELHKMWENRQNLLSQSHAYQQFLRDTKQAEAFLNNQEYVLAHTEMPTT  1200
1201  LEGAEAAIKKQEDFMTTMDANEEKINAVVETGRRLVSDGNINSDRIQEKV  1250
1251  DSIDDRHRKNREAASELLMRLKDNRDLQKFLQDCQELSLWINEKMLTAQD  1300
1301  MSYDEARNLHSKWLKHQAFMAELASNKEWLDKIEKEGMQLISEKPETEAV  1350
1351  VKEKLTGLHKMWEVLESTTQTKAQRLFDANKAELFTQSCADLDKWLHGLE  1400
1401  SQIQSDDYGKDLTSVNILLKKQQMLENQMEVRKKEIEELQSQAQALSQEG  1450
1451  KSTDEVDSKRLTVQTKFMELLEPLSERKHNLLASKEIHQFNRDVEDEILW  1500
1501  VGERMPLATSTDHGHNLQTVQLLIKKNQTLQKEIQGHQPRIDDIFERSQN  1550
1551  IITDSSSLNAEAIRQRLADLKQLWGLLIEETEKRHRRLEEAHKAQQYYFD  1600
1601  AAEAEAWMSEQELYMMSEEKAKDEQSAVSMLKKHQILEQAVEDYAETVHQ  1650
1651  LSKTSRALVADSHPESERISMRQSKVDKLYAGLKDLAEERRGKLDERHRL  1700
1701  FQLNREVDDLEQWIAEREVVAGSHELGQDYEHVTMLQERFREFARDTGNI  1750
1751  GQERVDTVNNMADELINSGHSDAATIAEWKDGLNEAWADLLELIDTRTQI  1800
1801  LAASYELHKFYHDAKEIFGRIQDKHKKLPEELGRDQNTVETLQRMHTTFE  1850
1851  HDIQALGTQVRQLQEDAARLQAAYAGDKADDIQKRENEVLEAWKSLLDAC  1900
1901  EGRRVRLVDTGDKFRFFSMVRDLMLWMEDVIRQIEAQEKPRDVSSVELLM  1950
1951  NNHQGIKAEIDARNDSFTACIELGKSLLARKHYASEEIKEKLLQLTEKRK  2000
2001  EMIDKWEDRWEWLRLILEVHQFSRDASVAEAWLLGQEPYLSSREIGQSVD  2050
2051  EVEKLIKRHEAFEKSAATWDERFSALERLTTLELLEVRRQQEEEERKRRP  2100
2101  PSPDPNTKVSEEAESQQWDTSKGDQVSQNGLPAEQGSPRMAGTMETSEMV  2150
2151  NGAAEQRTSSKESSPVPSPTLDRKAKSALPAQSAATLPARTLETPAAQME  2200
2201  GFLNRKHEWEAHNKKASSRSWHNVYCVINNQEMGFYKDAKSAASGIPYHS  2250
2251  EVPVSLKEAICEVALDYKKKKHVFKLRLSDGNEYLFQAKDDEEMNTWIQA  2300
2301  ISSAISSDKHDTSASTQSTPASSRAQTLPTSVVTITSESSPGKREKDKEK  2350
2351  DKEKRFSLFGKKK                                       2363

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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