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

NucPred

Fetching Q15643 from www.uniprot.org...

The NucPred score for your sequence is 0.97 (see score help below)

   1  MSSWLGGLGSGLGQSLGQVGGSLASLTGQISNFTKDMLMEGTEEVEAELP    50
  51  DSRTKEIEAIHAILRSENERLKKLCTDLEEKHEASEIQIKQQSTSYRNQL   100
 101  QQKEVEISHLKARQIALQDQLLKLQSAAQSVPSGAGVPATTASSSFAYGI   150
 151  SHHPSAFHDDDMDFGDIISSQQEINRLSNEVSRLESEVGHWRHIAQTSKA   200
 201  QGTDNSDQSEICKLQNIIKELKQNRSQEIDDHQHEMSVLQNAHQQKLTEI   250
 251  SRRHREELSDYEERIEELENLLQQGGSGVIETDLSKIYEMQKTIQVLQIE   300
 301  KVESTKKMEQLEDKIKDINKKLSSAENDRDILRREQEQLNVEKRQIMEEC   350
 351  ENLKLECSKLQPSAVKQSDTMTEKERILAQSASVEEVFRLQQALSDAENE   400
 401  IMRLSSLNQDNSLAEDNLKLKMRIEVLEKEKSLLSQEKEELQMSLLKLNN   450
 451  EYEVIKSTATRDISLDSELHDLRLNLEAKEQELNQSISEKETLIAEIEEL   500
 501  DRQNQEATKHMILIKDQLSKQQNEGDSIISKLKQDLNDEKKRVHQLEDDK   550
 551  MDITKELDVQKEKLIQSEVALNDLHLTKQKLEDKVENLVDQLNKSQESNV   600
 601  SIQKENLELKEHIRQNEEELSRIRNELMQSLNQDSNSNFKDTLLKEREAE   650
 651  VRNLKQNLSELEQLNENLKKVAFDVKMENEKLVLACEDVRHQLEECLAGN   700
 701  NQLSLEKNTIVETLKMEKGEIEAELCWAKKRLLEEANKYEKTIEELSNAR   750
 751  NLNTSALQLEHEHLIKLNQKKDMEIAELKKNIEQMDTDHKETKDVLSSSL   800
 801  EEQKQLTQLINKKEIFIEKLKERSSKLQEELDKYSQALRKNEILRQTIEE   850
 851  KDRSLGSMKEENNHLQEELERLREEQSRTAPVADPKTLDSVTELASEVSQ   900
 901  LNTIKEHLEEEIKHHQKIIEDQNQSKMQLLQSLQEQKKEMDEFRYQHEQM   950
 951  NATHTQLFLEKDEEIKSLQKTIEQIKTQLHEERQDIQTDNSDIFQETKVQ  1000
1001  SLNIENGSEKHDLSKAETERLVKGIKERELEIKLLNEKNISLTKQIDQLS  1050
1051  KDEVGKLTQIIQQKDLEIQALHARISSTSHTQDVVYLQQQLQAYAMEREK  1100
1101  VFAVLNEKTRENSHLKTEYHKMMDIVAAKEAALIKLQDENKKLSTRFESS  1150
1151  GQDMFRETIQNLSRIIREKDIEIDALSQKCQTLLAVLQTSSTGNEAGGVN  1200
1201  SNQFEELLQERDKLKQQVKKMEEWKQQVMTTVQNMQHESAQLQEELHQLQ  1250
1251  AQVLVDSDNNSKLQVDYTGLIQSYEQNETKLKNFGQELAQVQHSIGQLCN  1300
1301  TKDLLLGKLDIISPQLSSASLLTPQSAECLRASKSEVLSESSELLQQELE  1350
1351  ELRKSLQEKDATIRTLQENNHRLSDSIAATSELERKEHEQTDSEIKQLKE  1400
1401  KQDVLQKLLKEKDLLIKAKSDQLLSSNENFTNKVNENELLRQAVTNLKER  1450
1451  ILILEMDIGKLKGENEKIVETYRGKETEYQALQETNMKFSMMLREKEFEC  1500
1501  HSMKEKALAFEQLLKEKEQGKTGELNQLLNAVKSMQEKTVVFQQERDQVM  1550
1551  LALKQKQMENTALQNEVQRLRDKEFRSNQELERLRNHLLESEDSYTREAL  1600
1601  AAEDREAKLRKKVTVLEEKLVSSSNAMENASHQASVQVESLQEQLNVVSK  1650
1651  QRDETALQLSVSQEQVKQYALSLANLQMVLEHFQQEEKAMYSAELEKQKQ  1700
1701  LIAEWKKNAENLEGKVISLQECLDEANAALDSASRLTEQLDVKEEQIEEL  1750
1751  KRQNELRQEMLDDVQKKLMSLANSSEGKVDKVLMRNLFIGHFHTPKNQRH  1800
1801  EVLRLMGSILGVRREEMEQLFHDDQGGVTRWMTGWLGGGSKSVPNTPLRP  1850
1851  NQQSVVNSSFSELFVKFLETESHPSIPPPKLSVHDMKPLDSPGRRKRDTN  1900
1901  APESFKDTAESRSGRRTDVNPFLAPRSAAVPLINPAGLGPGGPGHLLLKP  1950
1951  ISDVLPTFTPLPALPDNSAGVVLKDLLKQ                       1979

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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