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

NucPred

Fetching Q9NY46 from www.uniprot.org...

The NucPred score for your sequence is 0.56 (see score help below)

   1  MAQALLVPPGPESFRLFTRESLAAIEKRAAEEKAKKPKKEQDNDDENKPK    50
  51  PNSDLEAGKNLPFIYGDIPPEMVSEPLEDLDPYYINKKTFIVMNKGKAIF   100
 101  RFSATSALYILTPLNPVRKIAIKILVHSLFSMLIMCTILTNCVFMTLSNP   150
 151  PDWTKNVEYTFTGIYTFESLIKILARGFCLEDFTFLRDPWNWLDFSVIVM   200
 201  AYVTEFVSLGNVSALRTFRVLRALKTISVIPGLKTIVGALIQSVKKLSDV   250
 251  MILTVFCLSVFALIGLQLFMGNLRNKCLQWPPSDSAFETNTTSYFNGTMD   300
 301  SNGTFVNVTMSTFNWKDYIGDDSHFYVLDGQKDPLLCGNGSDAGQCPEGY   350
 351  ICVKAGRNPNYGYTSFDTFSWAFLSLFRLMTQDYWENLYQLTLRAAGKTY   400
 401  MIFFVLVIFLGSFYLVNLILAVVAMAYEEQNQATLEEAEQKEAEFQQMLE   450
 451  QLKKQQEEAQAVAAASAASRDFSGIGGLGELLESSSEASKLSSKSAKEWR   500
 501  NRRKKRRQREHLEGNNKGERDSFPKSESEDSVKRSSFLFSMDGNRLTSDK   550
 551  KFCSPHQSLLSIRGSLFSPRRNSKTSIFSFRGRAKDVGSENDFADDEHST   600
 601  FEDSESRRDSLFVPHRHGERRNSNVSQASMSSRMVPGLPANGKMHSTVDC   650
 651  NGVVSLVGGPSALTSPTGQLPPEGTTTETEVRKRRLSSYQISMEMLEDSS   700
 701  GRQRAVSIASILTNTMEELEESRQKCPPCWYRFANVFLIWDCCDAWLKVK   750
 751  HLVNLIVMDPFVDLAITICIVLNTLFMAMEHYPMTEQFSSVLTVGNLVFT   800
 801  GIFTAEMVLKIIAMDPYYYFQEGWNIFDGIIVSLSLMELGLSNVEGLSVL   850
 851  RSFRLLRVFKLAKSWPTLNMLIKIIGNSVGALGNLTLVLAIIVFIFAVVG   900
 901  MQLFGKSYKECVCKINDDCTLPRWHMNDFFHSFLIVFRVLCGEWIETMWD   950
 951  CMEVAGQTMCLIVFMLVMVIGNLVVLNLFLALLLSSFSSDNLAATDDDNE  1000
1001  MNNLQIAVGRMQKGIDYVKNKMRECFQKAFFRKPKVIEIHEGNKIDSCMS  1050
1051  NNTGIEISKELNYLRDGNGTTSGVGTGSSVEKYVIDENDYMSFINNPSLT  1100
1101  VTVPIAVGESDFENLNTEEFSSESELEESKEKLNATSSSEGSTVDVVLPR  1150
1151  EGEQAETEPEEDLKPEACFTEGCIKKFPFCQVSTEEGKGKIWWNLRKTCY  1200
1201  SIVEHNWFETFIVFMILLSSGALAFEDIYIEQRKTIKTMLEYADKVFTYI  1250
1251  FILEMLLKWVAYGFQTYFTNAWCWLDFLIVDVSLVSLVANALGYSELGAI  1300
1301  KSLRTLRALRPLRALSRFEGMRVVVNALVGAIPSIMNVLLVCLIFWLIFS  1350
1351  IMGVNLFAGKFYHCVNMTTGNMFDISDVNNLSDCQALGKQARWKNVKVNF  1400
1401  DNVGAGYLALLQVATFKGWMDIMYAAVDSRDVKLQPVYEENLYMYLYFVI  1450
1451  FIIFGSFFTLNLFIGVIIDNFNQQKKKFGGQDIFMTEEQKKYYNAMKKLG  1500
1501  SKKPQKPIPRPANKFQGMVFDFVTRQVFDISIMILICLNMVTMMVETDDQ  1550
1551  GKYMTLVLSRINLVFIVLFTGEFVLKLVSLRHYYFTIGWNIFDFVVVILS  1600
1601  IVGMFLAEMIEKYFVSPTLFRVIRLARIGRILRLIKGAKGIRTLLFALMM  1650
1651  SLPALFNIGLLLFLVMFIYAIFGMSNFAYVKKEAGIDDMFNFETFGNSMI  1700
1701  CLFQITTSAGWDGLLAPILNSAPPDCDPDTIHPGSSVKGDCGNPSVGIFF  1750
1751  FVSYIIISFLVVVNMYIAVILENFSVATEESAEPLSEDDFEMFYEVWEKF  1800
1801  DPDATQFIEFSKLSDFAAALDPPLLIAKPNKVQLIAMDLPMVSGDRIHCL  1850
1851  DILFAFTKRVLGESGEMDALRIQMEDRFMASNPSKVSYEPITTTLKRKQE  1900
1901  EVSAAIIQRNFRCYLLKQRLKNISSNYNKEAIKGRIDLPIKQDMIIDKLN  1950
1951  GNSTPEKTDGSSSTTSPPSYDSVTKPDKEKFEKDKPEKESKGKEVRENQK  2000

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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